Running examples in ‘cgdsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgdsr-getProfileData
> ### Title: Retrieves genomic profile data for genes and genetic profiles.
> ### Aliases: cgdsr-getProfileData getProfileData getProfileData.CGDS
> 
> ### ** Examples
> 
> # Create CGDS object
> mycgds = CGDS("http://www.cbioportal.org/")
> 
> # Get list of cancer studies at server
> getCancerStudies(mycgds)
                      cancer_study_id
1                       paac_jhu_2014
2                 mel_tsam_liang_2017
3                     all_stjude_2015
4                     all_stjude_2016
5                       aml_ohsu_2018
6                           laml_tcga
7                       laml_tcga_pub
8        laml_tcga_pan_can_atlas_2018
9                      mnm_washu_2016
10                      acyc_fmi_2014
11                      acyc_jhu_2016
12                      acyc_mda_2015
13                      acyc_mgh_2016
14                    acyc_mskcc_2013
15                   acyc_sanger_2013
16                           acc_2019
17                    acbc_mskcc_2015
18                           acc_tcga
19        acc_tcga_pan_can_atlas_2018
20                      sarc_tcga_pub
21                     ampca_bcm_2016
22                       odg_msk_2017
23                     bcc_unige_2016
24                 blca_msk_tcga_2020
25              blca_mskcc_solit_2014
26              blca_mskcc_solit_2012
27       blca_plasmacytoid_mskcc_2016
28                 blca_tcga_pub_2017
29                           blca_bgi
30            blca_dfarber_mskcc_2014
31                          blca_tcga
32                      blca_tcga_pub
33       blca_tcga_pan_can_atlas_2018
34                           lgg_tcga
35        lgg_tcga_pan_can_atlas_2018
36         gbm_mayo_pdx_sarkaria_2019
37                      brca_metabric
38                    breast_msk_2018
39              breast_alpelisib_2020
40                    brca_mskcc_2019
41                      brca_smc_2018
42          brca_bccrc_xenograft_2014
43                  bfn_duke_nus_2015
44                         brca_bccrc
45                         brca_broad
46                        brca_sanger
47                  brca_tcga_pub2015
48                          brca_tcga
49                      brca_tcga_pub
50       brca_tcga_pan_can_atlas_2018
51                    ccle_broad_2019
52                cellline_ccle_broad
53                        msk_ch_2020
54       cesc_tcga_pan_can_atlas_2018
55                          cesc_tcga
56                  pan_origimed_2020
57                     chol_icgc_2017
58                      chol_msk_2018
59                     chol_nccs_2013
60                      chol_nus_2012
61                          chol_tcga
62       chol_tcga_pan_can_atlas_2018
63                    lcll_broad_2013
64                     cll_broad_2015
65                     cll_iuopa_2015
66                   cllsll_icgc_2011
67                    ccrcc_dfci_2019
68                  coad_caseccc_2015
69                    coad_cptac_2019
70                 coadread_dfci_2016
71                 coadread_genentech
72                      coadread_tcga
73                  coadread_tcga_pub
74   coadread_tcga_pan_can_atlas_2018
75                     coadread_mskcc
76                crc_apc_impact_2020
77                   hccihch_pku_2019
78                  cscc_dfarber_2015
79                 cscc_hgsc_bcm_2014
80                     cscc_ucsf_2021
81                 ctcl_columbia_2015
82                      pact_jhu_2011
83                    desm_broad_2015
84                    dlbcl_dfci_2018
85                    dlbc_broad_2012
86                    dlbcl_duke_2017
87       dlbc_tcga_pan_can_atlas_2018
88                     nhl_bcgsc_2013
89                      ucec_msk_2018
90                         esca_broad
91       esca_tcga_pan_can_atlas_2018
92                  egc_trap_msk_2020
93                          esca_tcga
94                      stes_tcga_pub
95                          escc_icgc
96                     escc_ucla_2014
97                     egc_mskcc_2020
98                    es_iocurie_2014
99                       gbc_msk_2018
100                 gbc_shanghai_2014
101                   egc_tmucih_2015
102                  stad_oncosg_2018
103                      gct_msk_2016
104                      gct_msk_2020
105                 gbm_columbia_2019
106                  gbm_tcga_pub2013
107                      gbm_tcga_pub
108                          gbm_tcga
109       gbm_tcga_pan_can_atlas_2018
110                   glioma_msk_2018
111                 glioma_mskcc_2019
112                        hnsc_broad
113                          hnsc_jhu
114                         hnsc_tcga
115                     hnsc_tcga_pub
116      hnsc_tcga_pan_can_atlas_2018
117               liad_inserm_fr_2014
118                hcc_mskimpact_2018
119                hcc_inserm_fr_2015
120                    hgsoc_msk_2021
121       histiocytosis_cobi_msk_2019
122                   all_stjude_2013
123               panet_shanghai_2013
124                     chol_jhu_2013
125                   ihch_mskcc_2020
126                     ihch_msk_2021
127                   ihch_ismms_2015
128                    ihch_smmu_2014
129                 brca_jup_msk_2020
130                     kich_tcga_pub
131                         kich_tcga
132      kich_tcga_pan_can_atlas_2018
133                          kirc_bgi
134                    ccrcc_irc_2014
135                         kirc_tcga
136                     kirc_tcga_pub
137      kirc_tcga_pan_can_atlas_2018
138                         kirp_tcga
139      kirp_tcga_pan_can_atlas_2018
140             hcc_msk_venturaa_2018
141                      lihc_amc_prv
142                        lihc_riken
143                         lihc_tcga
144      lihc_tcga_pan_can_atlas_2018
145                     lgg_ucsf_2014
146                        luad_broad
147                   luad_mskcc_2020
148               luad_mskimpact_2021
149                   luad_mskcc_2015
150               luad_msk_npjpo_2021
151                  luad_oncosg_2020
152                         luad_tcga
153                     luad_tcga_pub
154      luad_tcga_pan_can_atlas_2018
155                          luad_tsp
156                     lung_smc_2016
157                         lusc_tcga
158                     lusc_tcga_pub
159      lusc_tcga_pan_can_atlas_2018
160                         dlbc_tcga
161        lymphoma_cellline_msk_2020
162                   msk_impact_2017
163                   msk_access_2021
164                  mixed_allen_2018
165                       mpnst_mskcc
166                  mcl_idibips_2013
167                    mbn_mdacc_2013
168                    mbl_broad_2012
169                     mbl_dkfz_2017
170                          mbl_icgc
171                          mbl_pcgp
172                 mbl_sickkids_2016
173                skcm_broad_dfarber
174                mel_mskimpact_2020
175                   skcm_mskcc_2014
176                skcm_tcga_pub_2015
177                   lgggbm_tcga_pub
178                         meso_tcga
179      meso_tcga_pan_can_atlas_2018
180                      mbc_msk_2021
181                     brca_igr_2015
182              breast_ink4_msk_2021
183                      crc_msk_2017
184                      egc_msk_2017
185                     mel_dfci_2019
186                    skcm_dfci_2015
187        skcm_vanderbilt_mskcc_2015
188                     mel_ucla_2016
189                         prad_mich
190                    prad_su2c_2019
191                    prad_su2c_2015
192 metastatic_solid_tumors_mich_2017
193             prad_mcspc_mskcc_2020
194                    cfdna_msk_2019
195              mixed_cfdna_msk_2020
196                          mm_broad
197                    mds_tokyo_2011
198                    mds_mskcc_2020
199                     mpn_cimr_2013
200                    cellline_nci60
201                   npc_nusingapore
202                      nbl_amc_2012
203                    nbl_broad_2013
204                 nbl_ucologne_2015
205                     nepc_wcm_2016
206                    nhl_bcgsc_2011
207                     lung_msk_2017
208                  nsclc_mskcc_2018
209                nsclc_pd1_msk_2018
210                nsclc_tracerx_2017
211                  nsclc_unito_2016
212                  nsclc_mskcc_2015
213                   blca_nmibc_2017
214              hnsc_mdanderson_2013
215                           ov_tcga
216                       ov_tcga_pub
217        ov_tcga_pan_can_atlas_2018
218             nsclc_tcga_broad_2016
219                         paad_icgc
220                 paad_qcmg_uq_2016
221                         paad_tcga
222      paad_tcga_pan_can_atlas_2018
223                    paad_utsw_2015
224                    panet_jhu_2011
225                 panet_arcnet_2017
226                     thca_tcga_pub
227        all_phase2_target_2018_pub
228               aml_target_2018_pub
229             es_dfarber_broad_2014
230               nbl_target_2018_pub
231               pediatric_dkfz_2017
232                 mixed_pipseq_2017
233                         pptc_2019
234                rt_target_2018_pub
235                wt_target_2018_pub
236                     pcpg_tcga_pub
237                         pcpg_tcga
238      pcpg_tcga_pan_can_atlas_2018
239         past_dkfz_heidelberg_2013
240                   plmeso_nyu_2015
241                thyroid_mskcc_2016
242                   pcnsl_mayo_2015
243                   prad_broad_2013
244                        prad_broad
245                    prad_cpcg_2017
246                        prad_fhcrc
247             prad_cdk12_mskcc_2020
248                        prad_mskcc
249                   prad_mskcc_2014
250                        prad_p1000
251                 prad_eururol_2017
252                     prad_tcga_pub
253                         prad_tcga
254      prad_tcga_pan_can_atlas_2018
255  prad_mskcc_cheny1_organoids_2014
256                prostate_dkfz_2018
257                     prad_msk_2019
258                   prad_mskcc_2017
259               mixed_msk_tcga_2021
260            prad_msk_stopsack_2021
261                   rectal_msk_2019
262                    hnc_mskcc_2016
263                 ccrcc_utokyo_2013
264             nccrcc_genentech_2014
265                    rbl_mskcc_2020
266                rbl_cfdna_msk_2020
267                    mrt_bcgsc_2016
268                      rms_nih_2014
269                       summit_2018
270                        sarc_mskcc
271                         sarc_tcga
272      sarc_tcga_pan_can_atlas_2018
273                        skcm_broad
274                         skcm_tcga
275      skcm_tcga_pan_can_atlas_2018
276                         skcm_yale
277        skcm_broad_brafresist_2012
278                        scco_mskcc
279                        sclc_clcgp
280                          sclc_jhu
281                sclc_ucologne_2015
282      sclc_cancercell_gardner_2017
283                      vsc_cuk_2018
284             stad_pfizer_uhongkong
285                         stad_tcga
286                     stad_tcga_pub
287      stad_tcga_pan_can_atlas_2018
288                       stad_utokyo
289                    stad_uhongkong
290                    tmb_mskcc_2018
291                         tgct_tcga
292      tgct_tcga_pan_can_atlas_2018
293                 angs_painter_2020
294         angs_project_painter_2018
295        brca_mbcproject_wagle_2017
296              prad_mpcproject_2018
297                 lung_pdx_msk_2021
298                      lung_msk_pdx
299                      tet_nci_2014
300                         thym_tcga
301      thym_tcga_pan_can_atlas_2018
302                         thca_tcga
303      thca_tcga_pan_can_atlas_2018
304                     ntrk_msk_2019
305                   urcc_mskcc_2016
306                   utuc_mskcc_2015
307    utuc_cornell_baylor_mdacc_2019
308                   utuc_igbmc_2021
309                     utuc_msk_2019
310                 utuc_pdx_msk_2019
311                 blca_cornell_2016
312                      ucs_jhu_2014
313                          ucs_tcga
314       ucs_tcga_pan_can_atlas_2018
315                     uccc_nih_2017
316                         ucec_tcga
317                     ucec_tcga_pub
318      ucec_tcga_pan_can_atlas_2018
319                    usarc_msk_2020
320                      um_qimr_2016
321                          uvm_tcga
322       uvm_tcga_pan_can_atlas_2018
                                                                                                 name
1                                          Acinar Cell Carcinoma of the Pancreas (JHU, J Pathol 2014)
2                                                              Acral Melanoma (TGEN, Genome Res 2017)
3                                              Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
4                                              Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2016)
5                                                          Acute Myeloid Leukemia (OHSU, Nature 2018)
6                                                      Acute Myeloid Leukemia (TCGA, Firehose Legacy)
7                                                            Acute Myeloid Leukemia (TCGA, NEJM 2013)
8                                                      Acute Myeloid Leukemia (TCGA, PanCancer Atlas)
9                                   Acute myeloid leukemia or myelodysplastic syndromes (WashU, 2016)
10                                              Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
11                                               Adenoid Cystic Carcinoma (JHU, Cancer Prev Res 2016)
12                                               Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
13                                                       Adenoid Cystic Carcinoma (MGH, Nat Gen 2016)
14                                                   Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
15                                                    Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
16                                              Adenoid Cystic Carcinoma Project (J Clin Invest 2019)
17                                     Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
18                                                   Adrenocortical Carcinoma (TCGA, Firehose Legacy)
19                                                   Adrenocortical Carcinoma (TCGA, PanCancer Atlas)
20                                                       Adult Soft Tissue Sarcomas (TCGA, Cell 2017)
21                                Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016)
22             Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytoma (MSKCC, Neuro Oncol 2017)
23                                                       Basal Cell Carcinoma (UNIGE, Nat Genet 2016)
24                                                                    Bladder Cancer (MSK/TCGA, 2020)
25                                                              Bladder Cancer (MSKCC, Eur Urol 2014)
26                                                           Bladder Cancer (MSKCC, J Clin Onco 2013)
27                                                             Bladder Cancer (MSKCC, Nat Genet 2016)
28                                                                   Bladder Cancer (TCGA, Cell 2017)
29                                                 Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
30                                      Bladder Urothelial Carcinoma (DFCI/MSKCC, Cancer Discov 2014)
31                                               Bladder Urothelial Carcinoma (TCGA, Firehose Legacy)
32                                                   Bladder Urothelial Carcinoma (TCGA, Nature 2014)
33                                               Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)
34                                                   Brain Lower Grade Glioma (TCGA, Firehose Legacy)
35                                                   Brain Lower Grade Glioma (TCGA, PanCancer Atlas)
36                                                               Brain Tumor PDXs (Mayo Clinic, 2019)
37                                            Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
38                                                              Breast Cancer (MSK, Cancer Cell 2018)
39                                                            Breast Cancer (MSK, Nature Cancer 2020)
40                                                      Breast Cancer (MSKCC, NPJ Breast Cancer 2019)
41                                                                           Breast Cancer (SMC 2018)
42                                           Breast Cancer Xenografts (British Columbia, Nature 2015)
43                                           Breast Fibroepithelial Tumors (Duke-NUS, Nat Genet 2015)
44                                          Breast Invasive Carcinoma (British Columbia, Nature 2012)
45                                                     Breast Invasive Carcinoma (Broad, Nature 2012)
46                                                    Breast Invasive Carcinoma (Sanger, Nature 2012)
47                                                        Breast Invasive Carcinoma (TCGA, Cell 2015)
48                                                  Breast Invasive Carcinoma (TCGA, Firehose Legacy)
49                                                      Breast Invasive Carcinoma (TCGA, Nature 2012)
50                                                  Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
51                                                        Cancer Cell Line Encyclopedia (Broad, 2019)
52                                        Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
53                                      Cancer Therapy and Clonal Hematopoiesis (MSK, Nat Genet 2020)
54                                           Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
55           Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Firehose Legacy)
56                                                                    China Pan-cancer (OrigiMed2020)
57                                                      Cholangiocarcinoma (ICGC, Cancer Discov 2017)
58                                                     Cholangiocarcinoma (MSK, Clin Cancer Res 2018)
59                           Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
60                              Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
61                                                         Cholangiocarcinoma (TCGA, Firehose Legacy)
62                                                         Cholangiocarcinoma (TCGA, PanCancer Atlas)
63                                                    Chronic Lymphocytic Leukemia (Broad, Cell 2013)
64                                                  Chronic Lymphocytic Leukemia (Broad, Nature 2015)
65                                                  Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
66                                          Chronic lymphocytic leukemia (ICGC, Nature Genetics 2011)
67                                               Clear Cell Renal Cell Carcinoma (DFCI, Science 2019)
68                                                          Colon Adenocarcinoma (CaseCCC, PNAS 2015)
69                                                      Colon Cancer (CPTAC-2 Prospective, Cell 2019)
70                                                Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
71                                                 Colorectal Adenocarcinoma (Genentech, Nature 2012)
72                                                  Colorectal Adenocarcinoma (TCGA, Firehose Legacy)
73                                                      Colorectal Adenocarcinoma (TCGA, Nature 2012)
74                                                  Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)
75                                       Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
76                                                     Colorectal Cancer (MSK, Gastroenterology 2020)
77  Combined Hepatocellular and Intrahepatic Cholangiocarcinoma (Peking University, Cancer Cell 2019)
78                                     Cutaneous Squamous Cell Carcinoma (DFCI, Clin Cancer Res 2015)
79                              Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014)
80                                       Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021)
81                                             Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
82                                            Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011)
83                                            Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
84                                                 Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018)
85                                                   Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
86                                                    Diffuse Large B-Cell Lymphoma (Duke, Cell 2017)
87                                              Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)
88                                                  Diffuse Large B-cell Lymphoma (BCGSC, Blood 2013)
89                                                                     Endometrial Cancer (MSK, 2018)
90                                                   Esophageal Adenocarcinoma (DFCI, Nat Genet 2013)
91                                                  Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)
92                                            Esophageal Cancer-TRAP Project (MSK, Lancet Oncol 2020)
93                                                       Esophageal Carcinoma (TCGA, Firehose Legacy)
94                                                           Esophageal Carcinoma (TCGA, Nature 2017)
95                                             Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
96                                          Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
97                                                              Esophageal/Stomach Cancer (MSK, 2020)
98                                                 Ewing Sarcoma (Institut Curie, Cancer Discov 2014)
99                                                              Gallbladder Cancer (MSK, Cancer 2018)
100                                                  Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
101                                                        Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
102                                                                     Gastric Cancer (OncoSG, 2018)
103                                                       Germ Cell Tumors (MSKCC, J Clin Oncol 2016)
104                                                 Germ Cell Tumors and Shared Leukemias (MSK, 2020)
105                                                            Glioblastoma (Columbia, Nat Med. 2019)
106                                                                    Glioblastoma (TCGA, Cell 2013)
107                                                                  Glioblastoma (TCGA, Nature 2008)
108                                                   Glioblastoma Multiforme (TCGA, Firehose Legacy)
109                                                   Glioblastoma Multiforme (TCGA, PanCancer Atlas)
110                                                                         Glioma (MSK, Nature 2019)
111                                                              Glioma (MSKCC, Clin Cancer Res 2019)
112                                       Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
113                               Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
114                                     Head and Neck Squamous Cell Carcinoma (TCGA, Firehose Legacy)
115                                         Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
116                                     Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
117                                                 Hepatocellular Adenoma (INSERM, Cancer Cell 2014)
118                                              Hepatocellular Carcinoma (MSK, Clin Cancer Res 2018)
119                                                Hepatocellular Carcinomas (INSERM, Nat Genet 2015)
120                                                      High-Grade Serous Ovarian Cancer (MSK, 2021)
121                                                      Histiocytosis Cobimetinib (MSK, Nature 2019)
122                                     Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
123                                                            Insulinoma (Shanghai, Nat Commun 2013)
124                                             Intrahepatic Cholangiocarcinoma (JHU, Nat Genet 2013)
125                                                       Intrahepatic Cholangiocarcinoma (MSK, 2020)
126                                            Intrahepatic Cholangiocarcinoma (MSK, Hepatology 2021)
127                                                Intrahepatic Cholangiocarcinoma (Mount Sinai 2015)
128                                       Intrahepatic Cholangiocarcinoma (Shanghai, Nat Commun 2014)
129                                             Juvenile Papillomatosis and Breast Cancer (MSK, 2020)
130                                                       Kidney Chromophobe (TCGA, Cancer Cell 2014)
131                                                        Kidney Chromophobe (TCGA, Firehose Legacy)
132                                                        Kidney Chromophobe (TCGA, PanCancer Atlas)
133                                           Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
134                                           Kidney Renal Clear Cell Carcinoma (IRC, Nat Genet 2014)
135                                         Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)
136                                             Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
137                                         Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)
138                                     Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy)
139                                     Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)
140                                  Liver Hepatocellular Adenoma and Carcinomas (MSK, PLOS One 2018)
141                                             Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
142                                            Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
143                                            Liver Hepatocellular Carcinoma (TCGA, Firehose Legacy)
144                                            Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)
145                                                            Low-Grade Gliomas (UCSF, Science 2014)
146                                                            Lung Adenocarcinoma (Broad, Cell 2012)
147                                                                 Lung Adenocarcinoma (MSKCC, 2020)
148                                                                 Lung Adenocarcinoma (MSKCC, 2021)
149                                                         Lung Adenocarcinoma (MSKCC, Science 2015)
150                                            Lung Adenocarcinoma (NPJ Precision Oncology, MSK 2021)
151                                                      Lung Adenocarcinoma (OncoSG, Nat Genet 2020)
152                                                       Lung Adenocarcinoma (TCGA, Firehose Legacy)
153                                                           Lung Adenocarcinoma (TCGA, Nature 2014)
154                                                       Lung Adenocarcinoma (TCGA, PanCancer Atlas)
155                                                            Lung Adenocarcinoma (TSP, Nature 2008)
156                                                           Lung Cancer (SMC, Cancer Research 2016)
157                                              Lung Squamous Cell Carcinoma (TCGA, Firehose Legacy)
158                                                  Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
159                                              Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
160                           Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Firehose Legacy)
161                                                                 Lymphoma Cell Lines (MSKCC, 2020)
162                                       MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
163                                                MSK-IMPACT and MSK-ACCESS Mixed Cohort (MSK, 2021)
164                                        MSS Mixed Solid Tumors (Broad/Dana-Farber, Nat Genet 2018)
165                                   Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
166                                                         Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
167                                            Mature B-cell malignancies (MD Anderson Cancer Center)
168                                                              Medulloblastoma (Broad, Nature 2012)
169                                                               Medulloblastoma (DKFZ, Nature 2017)
170                                                               Medulloblastoma (ICGC, Nature 2012)
171                                                               Medulloblastoma (PCGP, Nature 2012)
172                                                           Medulloblastoma (Sickkids, Nature 2016)
173                                                         Melanoma (Broad/Dana Farber, Nature 2012)
174                                                                            Melanoma (MSKCC, 2018)
175                                                                       Melanoma (MSKCC, NEJM 2014)
176                                                                       Melanomas (TCGA, Cell 2015)
177                                                    Merged Cohort of LGG and GBM (TCGA, Cell 2016)
178                                                              Mesothelioma (TCGA, Firehose Legacy)
179                                                              Mesothelioma (TCGA, PanCancer Atlas)
180                                                             Metaplastic Breast Cancer (MSK, 2021)
181                                                  Metastatic Breast Cancer (INSERM, PLoS Med 2016)
182                                             Metastatic Breast Cancer (MSK, Cancer Discovery 2021)
183                                            Metastatic Colorectal Cancer (MSKCC, Cancer Cell 2018)
184                                  Metastatic Esophagogastric Cancer (MSKCC, Cancer Discovery 2017)
185                                                  Metastatic Melanoma (DFCI, Nature Medicine 2019)
186                                                          Metastatic Melanoma (DFCI, Science 2015)
187                                                Metastatic Melanoma (MSKCC, JCO Precis Oncol 2017)
188                                                             Metastatic Melanoma (UCLA, Cell 2016)
189                                            Metastatic Prostate Adenocarcinoma (MCTP, Nature 2012)
190                               Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019)
191                                       Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015)
192                                                     Metastatic Solid Cancers (UMich, Nature 2017)
193                       Metastatic castration-sensitive prostate cancer (MSK, Clin Cancer Res 2020)
194                                                           Mixed cfDNA (MSK, Nature Medicine 2019)
195                                                                         Mixed cfDNA (MSKCC, 2020)
196                                                        Multiple Myeloma (Broad, Cancer Cell 2014)
197                                                              Myelodysplasia (UTokyo, Nature 2011)
198                                                                     Myelodysplastic (MSKCC, 2020)
199                                                    Myeloproliferative Neoplasms (CIMR, NEJM 2013)
200                                                          NCI-60 Cell Lines (NCI, Cancer Res 2012)
201                                              Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
202                                                        Neuroblastoma (AMC Amsterdam, Nature 2012)
203                                                             Neuroblastoma (Broad, Nat Genet 2013)
204                                                                Neuroblastoma (Broad, Nature 2015)
205                                    Neuroendocrine Prostate Cancer (Multi-Institute, Nat Med 2016)
206                                                         Non-Hodgkin Lymphoma (BCGSC, Nature 2011)
207                                                 Non-Small Cell Cancer (MSKCC, Cancer Discov 2017)
208                                                Non-Small Cell Lung Cancer (MSK, Cancer Cell 2018)
209                                             Non-Small Cell Lung Cancer (MSKCC, J Clin Oncol 2018)
210                                          Non-Small Cell Lung Cancer (TRACERx, NEJM & Nature 2017)
211                                Non-Small Cell Lung Cancer (University of Turin, Lung Cancer 2017)
212                                                    Non-small cell lung cancer (MSK, Science 2015)
213                                             Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017)
214                                    Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
215                                         Ovarian Serous Cystadenocarcinoma (TCGA, Firehose Legacy)
216                                             Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
217                                         Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)
218                                                            Pan-Lung Cancer (TCGA, Nat Genet 2016)
219                                                     Pancreatic Adenocarcinoma (ICGC, Nature 2012)
220                                                     Pancreatic Adenocarcinoma (QCMG, Nature 2016)
221                                                 Pancreatic Adenocarcinoma (TCGA, Firehose Legacy)
222                                                 Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)
223                                                         Pancreatic Cancer (UTSW, Nat Commun 2015)
224                         Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
225                                   Pancreatic Neuroendocrine Tumors (Multi-Institute, Nature 2017)
226                                                     Papillary Thyroid Carcinoma (TCGA, Cell 2014)
227                                       Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018)
228                                                   Pediatric Acute Myeloid Leukemia (TARGET, 2018)
229                                                Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
230                                                            Pediatric Neuroblastoma (TARGET, 2018)
231                                                          Pediatric Pan-Cancer (DKFZ, Nature 2017)
232                                                Pediatric Pan-cancer (Columbia U, Genome Med 2016)
233                                   Pediatric Preclinical Testing Consortium  (CHOP, Cell Rep 2019)
234                                                           Pediatric Rhabdoid Tumor (TARGET, 2018)
235                                                             Pediatric Wilms' Tumor (TARGET, 2018)
236                                              Pheochromocytoma and Paraganglioma (TCGA, Cell 2017)
237                                        Pheochromocytoma and Paraganglioma (TCGA, Firehose Legacy)
238                                        Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)
239                                                Pilocytic Astrocytoma (ICGC, Nature Genetics 2013)
240                                                       Pleural Mesothelioma (NYU, Cancer Res 2015)
241                            Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
242                       Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
243                                                Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
244                                           Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
245                                                   Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
246                                       Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
247                                                      Prostate Adenocarcinoma (MSK, Eur Urol 2020)
248                                                 Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
249                                                        Prostate Adenocarcinoma (MSKCC, PNAS 2014)
250                                        Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018)
251                                                     Prostate Adenocarcinoma (SMMU, Eur Urol 2017)
252                                                         Prostate Adenocarcinoma (TCGA, Cell 2015)
253                                                   Prostate Adenocarcinoma (TCGA, Firehose Legacy)
254                                                   Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
255                                              Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
256                                                          Prostate Cancer (DKFZ, Cancer Cell 2018)
257                                                            Prostate Cancer (MSK, Cell Metab 2020)
258                                                    Prostate Cancer (MSKCC, JCO Precis Oncol 2017)
259                                                  RAD51B Associated Mixed Cancers (Mandelker 2021)
260                                                   Race Differences in Prostate Cancer (MSK, 2021)
261                                                          Rectal Cancer (MSK,Nature Medicine 2019)
262                              Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016)
263                                               Renal Clear Cell Carcinoma (UTokyo, Nat Genet 2013)
264                                        Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
265                                                                Retinoblastoma (MSK, Cancers 2021)
266                                                                 Retinoblastoma cfDNA (MSKCC 2020)
267                                                         Rhabdoid Cancer (BCGSC, Cancer Cell 2016)
268                                                        Rhabdomyosarcoma (NIH, Cancer Discov 2014)
269                                    SUMMIT - Neratinib Basket Study (Multi-Institute, Nature 2018)
270                                                             Sarcoma (MSKCC/Broad, Nat Genet 2010)
271                                                                   Sarcoma (TCGA, Firehose Legacy)
272                                                                   Sarcoma (TCGA, PanCancer Atlas)
273                                                        Skin Cutaneous Melanoma (Broad, Cell 2012)
274                                                   Skin Cutaneous Melanoma (TCGA, Firehose Legacy)
275                                                   Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)
276                                                    Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
277                                                Skin Cutaneous Melanoma(Broad, Cancer Discov 2014)
278                                         Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
279                                                    Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
280                                            Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
281                                                   Small Cell Lung Cancer (U Cologne, Nature 2015)
282                                        Small-Cell Lung Cancer (Multi-Institute, Cancer Cell 2017)
283                                      Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)
284                                           Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
285                                                    Stomach Adenocarcinoma (TCGA, Firehose Legacy)
286                                                        Stomach Adenocarcinoma (TCGA, Nature 2014)
287                                                    Stomach Adenocarcinoma (TCGA, PanCancer Atlas)
288                                                  Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
289                                                      Stomach Adenocarcinoma (UHK, Nat Genet 2011)
290                                                     TMB and Immunotherapy (MSKCC, Nat Genet 2019)
291                                               Testicular Germ Cell Cancer (TCGA, Firehose Legacy)
292                                               Testicular Germ Cell Tumors (TCGA, PanCancer Atlas)
293                                                 The Angiosarcoma Project (Provisional, July 2020)
294                                    The Angiosarcoma Project - Count Me In (Nature Medicine, 2020)
295                                 The Metastatic Breast Cancer Project (Provisional, February 2020)
296                               The Metastatic Prostate Cancer Project (Provisional, November 2019)
297                                                                       Thoracic Cancer (MSK, 2021)
298                                                                   Thoracic PDX (MSK, Provisional)
299                                                    Thymic Epithelial Tumors (NCI, Nat Genet 2014)
300                                                                   Thymoma (TCGA, Firehose Legacy)
301                                                                   Thymoma (TCGA, PanCancer Atlas)
302                                                         Thyroid Carcinoma (TCGA, Firehose Legacy)
303                                                         Thyroid Carcinoma (TCGA, PanCancer Atlas)
304                                               Tumors with TRK fusions (MSK, Clin Cancer Res 2020)
305                                              Unclassified Renal Cell Carcinoma (MSK, Nature 2016)
306                                                Upper Tract Urothelial Cancer (MSK, Eur Urol 2015)
307                          Upper Tract Urothelial Carcinoma (Cornell/Baylor/MDACC, Nat Commun 2019)
308                                     Upper Tract Urothelial Carcinoma (IGBMC, Genome Biology 2021)
309                                           Upper Tract Urothelial Carcinoma (MSK, Nat Commun 2020)
310                                       Upper Tract Urothelial Carcinoma PDX (MSK, Nat Commun 2020)
311                                               Urothelial Carcinoma (Cornell/Trento, Nat Gen 2016)
312                                           Uterine Carcinosarcoma (Johns Hopkins, Nat Commun 2014)
313                                                    Uterine Carcinosarcoma (TCGA, Firehose Legacy)
314                                                    Uterine Carcinosarcoma (TCGA, PanCancer Atlas)
315                                                   Uterine Clear Cell Carcinoma (NIH, Cancer 2017)
316                                      Uterine Corpus Endometrial Carcinoma (TCGA, Firehose Legacy)
317                                          Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
318                                      Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
319                                           Uterine Sarcoma/Mesenchymal (MSK, Clin Cancer Res 2020)
320                                                            Uveal Melanoma (QIMR, Oncotarget 2016)
321                                                            Uveal Melanoma (TCGA, Firehose Legacy)
322                                                            Uveal Melanoma (TCGA, PanCancer Atlas)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            description
1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation and their matched normals.
2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals).
3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive profiling of infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL)
4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-genome and/or whole-exome sequencing of ERG-altered B-ALL tumor/normal pairs.
5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome sequencing of 672 acute myeloid leukemia samples (with 454 matched normals) from the Beat AML program.
6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Acute Myeloid Leukemia. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LAML/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-genome or whole-exome sequencing analysis of 200 adult de novo AML tumor/normal pairs. TCGA Acute Myeloid Leukemia Project; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LAML&diseaseName=Acute%20Myeloid%20Leukemia">NCI</A>.
8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Acute Myeloid Leukemia TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Enhanced exome or targeted sequencing of 116 acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS) patients' tumor/normal pairs .
10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted Sequencing of 28 metastatic Adenoid Cystic Carcinoma samples.
11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-genome or whole-exome sequencing of 25 adenoid cystic carcinoma tumor/normal pairs.
12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients).
13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-genome/exome sequencing of 10 ACC PDX models.
14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome or whole-genome sequencing analysis of 60 ACC tumor/normal pairs
15                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 24 ACCs.
16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Multi-Institute Cohort of 1045 Adenoid Cystic Carcinoma patients.
17                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole exome sequencing of 12 breast AdCCs.
18                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Adrenocortical Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/ACC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
19                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Adrenocortical Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
20                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 206 Adult Soft Tissue Sarcoma tumor/normal pairs.
21                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Exome sequencing analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44) or the duodenum (n = 18) and 98 for which the epithelium of origin could not be clearly defined morphologically (AMPCA).
22                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               IMPACT sequencing of 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.
23                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 126 basal cell carcinoma tumor/normal pairs; targeted sequencing of 163 sporadic samples (40 tumor/normal pairs) and 4 Gorlin symdrome basal cell carcinomas.
24                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome or targeted sequencing of 476 muscle-invasive bladder tumor/normal pairs via TCGA or MSK-IMPACT sequencing.
25                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014).
26                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive profiling of 97 high-grade bladder tumors, including targeted sequencing of 15 cancer genes
27                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome and targeted sequencing of 34 plasmacytoid-variant (signet ring cell) tumors of the bladder
28                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 412 muscle-invasive bladder tumors and matched normal samples.
29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome and whole-genome sequencing of 99 bladder cancer tumor/normal pairs. Generated by BGI.
30                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of tumor/normal samples from 50 patients treated with cisplatin-based chemotherapy for muscle invasive urothelial carcinoma.
31                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   TCGA Bladder Urothelial Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BLCA/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-exome sequencing of 131 high-grade muscle-invasive urothelial bladder carcinomas
33                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Bladder Urothelial Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
34                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Brain Lower Grade Glioma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LGG/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
35                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Brain Lower Grade Glioma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
36                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  WES on a total of 83 PDXs and 55 PDXs have the matched germline (blood) samples sequenced. A total of 66 PDXs have RNASeq available
37                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Targeted sequencing of 2509 primary breast tumors with 548 matched normals.
38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Targeted Sequencing of tumor/normal sample pairs from 1918 Breast cancers.
39                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Targeted sequencing of pre- and post-treatment tumor/cfDNA samples from 51 Breast Cancer patients to understand the mechanisms of resistance to Alepelisib.
40                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted Sequencing of buparlisib + letrozole and alpelisib + letrozole-treated metastatic ER+ unmatched breast tumors.
41                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-exome sequencing of 187 primary tumors from a Korean breast cancer cohort (SMC).
42                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome/targeted sequencing to evaluate the clonal dynamics in 116 breast cancer patient xenografts.
43                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 22 phyllodes tumors
44                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole genome/exome sequencing analysis of 65 breast cancer samples
45                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 103 breast cancer tumor/normal sample pairs. Generated by the Broad Institute.
46                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole exome sequencing from 100 breast cancer tumor/normal sample pairs. Generated by the Sanger Institute.
47                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-exome sequencing of 817 Breast Invasive Carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma Project.
48                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Breast Invasive Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
49                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing (510 samples with matched normals), genomic DNA copy number arrays, DNA methylation, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays analysis on 825 primary breast cancer samples. <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/brca_2012/">Raw data via the TCGA Data Portal</a>.
50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Breast Invasive Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
51                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, updated 2019. Data downloaded from the <a href="https://portals.broadinstitute.org/ccle/data">Broad CCLE Portal</a>. For more info about the proteomics data, see the <a href="https://github.com/cbioportal/datahub/blob/master/public/ccle_broad_2019/README.md">README</a>.
52                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted sequencing of 1020 samples from Cancer Cell Line Encyclopedia from the Broad Institute and Novartis.
53                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Clonal hematopoiesis mutations identified in blood samples from 24,146 patients whose tumor-blood pairs were analyzed using MSK-IMPACT.
54                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cervical Squamous Cell Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
55                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/CESC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
56                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Landscape of genomic alterations in 10,194 solid tumors from the Chinese population
57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-exome sequencing and Targeted/Exome sequencing of 489 Cholangiocarcinoma samples from 10 countries.
58                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing (MSK-IMPACT) of 195 tumor samples (194 with matched normals) from 192 cholangiocarcinoma patients.
59                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome sequencing of 15 cholangiocarcinoma cases.
60                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
61                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Cholangiocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/CHOL/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
62                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Cholangiocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 160 CLL tumor/normal pairs.
64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 537 chronic lymphocytic leukemia tumor/normal pairs.
65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Mutation data from whole-genome or whole-exome sequencing of 428 CLL, 54 MBL, and 24 SLL tumor/normal pairs.
66                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome sequencing of 105 Chronic Lymphocytic Leukemia samples.
67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 35 tumor/normal pairs.
68                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of tumor/normal pairs from 29 African American Colon Cancers.
69                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Proteogenomic analysis of prospectively collected 110 colon adenocarcinoma tumor normal pairs. Data generated by CPTAC.
70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations.
71                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-genome sequencing of 74 paired colon tumor-normal samples.
72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCGA Colorectal Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COADREAD/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
73                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole exome sequencing in 224 of the 276 colorectal carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Colorectal Cancer project.
74                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Colorectal Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
75                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Targeted sequencing of primary, metastatic, and normal tissues from 69 colorectal adenocarcinoma patients.
76                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted sequencing of 471 unresectable colorectal tumor/normal pairs via MSK-IMPACT.
77                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-exome sequencing of 121 combined hepatocellular and intrahepatic cholangiocarcinoma (cHCC-ICC) patients with matched normal pairs (whole-genome sequenced samples are not included here).
78                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Targeted sequencing of 29 metastatic cutaneous squamous cell carcinoma samples.
79                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of tumor/normal pairs from 39 aggressive cutaneous squamous cell carcinoma cases.
80                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Catalogue of driver genes in cutaneous squamous cell carcinoma. Meta-analysis of 105 normal/tumor pairs.
81                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-Exome Sequencing (WXS) of tumor-normal sample pairs from 25 patients with Sezary Syndrome and 17 patients with other Cutaneous T Cell Lymphoma (CTCLs).
82                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing of major neoplastic cyst types of the pancreas: 8 serous cystadenomas (SCAs), 8 intraductal papillary mucinous neoplasms (IPMNs), 8 mucinous cystic neoplasms (MCNs), and 8 solid pseudopapillary neoplasms (SPNs).
83                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Exome/Whole Genome sequencing of 20 desmoplastic melanoma tumor/normal pairs.
84                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of tumor/matching normal sample pairs from 135 DLBCL patients.
85                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 58 primary DLBCL samples and their matched normals.
86                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 1,001 Diffuse Large B Cell Lymphoma (DLBCL) tumors (N = 1001) and paired-normal tissue (N = 400).
87                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Diffuse Large B-Cell Lymphoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
88                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome sequencing of 40 DLBCL tumor/normal pairs and 13 cell lines.
89                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MSK-IMPACT sequencing of 197 advanced-staged endometrial cancer tumor samples with matched normals, from 189 patients treated at MSK.
90                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 149 tumor/normal pairs and whole-genome sequencing of 16 pairs from 149 esophageal adenocarcinoma patients.
91                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Esophageal Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
92                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Targeted and WES recapture sequencing of tumor/normal samples from 37 Esophageal Cancer patients.
93                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Esophageal Carcinoma . Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/ESCA/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
94                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole exome sequencing of 559 esophageal and gastric carcinoma tumors with matched normals.
95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-genome or whole-exome sequencing of 88 esophageal squamous cell carcinoma tumor/normal pairs.
96                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
97                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 487 Esophageal/stomach cancer tumor-normal pairs via MSK-IMPACT.
98                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-genome sequencing of 112 Ewing sarcoma samples and matched germ line DNA.
99                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted Sequencing of 103 samples with matched normals from 101 Gallbladder cancer patients.
100                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing of 32 gallbladder carcinoma tumor/normal pairs.
101                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 78 Gastric Adenocarcinomas and their matched normal samples.
102                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome sequencing of 147 gastric cancer tumors with matched normals. Courtesy of <a href="https://src.gisapps.org/OncoSG/">OncoSG</a>.
103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome and Targeted sequencing of 19 samples and Targeted sequencing of 161 samples from 180 Germ Cell Tumor patients.
104                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted and WES sequencing of germ cell tumor and shared leukemia samples.
105                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of 32 out of 42 glioblastomas patients with matched normals.
106                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome and/or whole-genome sequencing of 257 of the 543 glioblastoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Glioblastoma Project.
107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing in 91 of the 206 primary glioblastoma tumors (143 with matched normals) from the Cancer Genome Atlas (TCGA) Glioblastoma Project.
108                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Glioblastoma Multiforme. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/GBM/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
109                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Glioblastoma Multiforme TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
110                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Targeted Sequencing of CSF samples (91 samples with 86 matched normals) from 42 glioma patients.
111                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing on MSK-IMPACT and FMI Panels of 1004 samples (837 with matched normals) from 923 glioma patients.
112                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 74 head and neck squamous cell carcinoma tumor/normal pairs.
113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome sequencing of 32 head and neck squamous cell carcinoma tumor/normal sample pairs.
114                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TCGA Head and Neck Squamous Cell Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/HNSC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
115                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing and/or whole-genome sequencing of 279 head and neck squamous cell carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma Project.
116                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Head and Neck Squamous Cell Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
117                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 46 liver tumor/normal pairs.
118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MSK-IMPACT sequencing of 127 Hepatocellular Carcinoma tumor samples with matched normals.
119                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of 243 liver tumors and matched normals.
120                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted Sequencing of 45 Serous Ovarian Cancer tumor/normal pairs from 45 patients.
121                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted and whole exome sequencing of 52 histiocytosis tumor/normal pairs.
122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole genome or exome sequencing of 44 (20 whole genome, 20 exome) ALL tumor/normal pairs.
123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 10 benign insulinoma tumor/normal pairs.
124                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome sequencing of tumor/normal pairs from 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
125                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Targeted sequencing of IMPACT and CMO samples
126                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing of 412 intrahepatic cholangiocarcinoma tumor/normal sample pairs.
127                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome sequencing of 8 tumor-normal paired iCCA samples by Liver Cancer Program at the Icahn School of Medicine at Mount Sinai, in collaboration with Barcelona-ClÃ­nic Liver Cancer Group.
128                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 103 tumor/normal sample pairs in 103 intrahepatic cholangiocarcinoma patients.
129                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma.
130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 66 chromophobe renal cell carcinoma (ChRCCs) tumor/normal pairs.
131                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Kidney Chromophobe. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KICH/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
132                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Kidney Chromophobe TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 10 ccRCC tumor/normal pairs and targeted sequencing of 88 clear cell carcinoma tumor/normal pairs. Generated by BGI-Shenzhen.
134                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
135                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Kidney Renal Clear Cell Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
136                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-exome sequencing in 417 of 446 clear cell renal cell carcinoma tumor/normal pairs.
137                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Kidney Renal Clear Cell Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TCGA Kidney Renal Papillary Cell Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRP/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
139                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Kidney Renal Papillary Cell Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
140                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Targeted sequencing of tumor/normal pairs of 9 LIAD and 10 HCC patients via MSK-IMPACT platform.
141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 231 hepatocellular carcinomas and matched normal tissue pairs.
142                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-genome sequencing of 27 hepatocellular carcinoma tumor/norma pairs from RIKEN.
143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCGA Liver Hepatocellular Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LIHC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Liver Hepatocellular Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 23 grade II glioma tumor/normal pairs.
146                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome and/or whole-genome sequencing of 183 lung adenocarcinomas and matched normal tissue pairs.
147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Targeted sequencing of 604 lung adenocarcinoma tumor/normal pairs via MSK-IMPACT.
148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 186 matched normal samples from 186 lung adenocarcinoma patient via MSK-IMPACT.
149                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing of 34 non small cell lung cancer tumor/normal pairs.
150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 426 matched normal samples from 426 lung adenocarcinoma patients.
151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome and transcriptome sequencing of 305 east asian lung adenocarcinomas with matched normals. Courtesy of <a href="https://src.gisapps.org/OncoSG/">OncoSG</a>. Lung Cancer Consortium Singapore (LCCS).
152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Lung Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUAD/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 230 lung adenocarcinoma tumor/normal pairs. <a href="https://tcga-data.nci.nih.gov/docs/publications/luad_2014/">Raw data via the TCGA Data Portal</a>.
154                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Lung Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
155                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted sequencing of 163 lung adenocarcinoma tumor/normal pairs. Generated by WashU/Broad.
156                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome and whole transcriptome sequencing of primary and multiple metastatic lymph node samples from 6 lung cancer patients with their matched normals.
157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCGA Lung Squamous Cell Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUSC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
158                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole exome sequencing of 178 lung squamous cell carcinoma tumor/normal pairs. <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Lung Squamous Cell Carcinoma project.
159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Lung Squamous Cell Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
160                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/DLBC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
161                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 34 lymphoma cell lines using HemePACT_v3
162                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
163                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 1446 Tumor and cfDNA samples (1440 with matched normals) from MSK-IMPACT and MSK-ACCESS.
164                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing of tumor/normal pairs and corresponding clinical outcomes from patients treated with immune checkpoint inhibitors across multiple cancer types including melanoma, non-small cell lung cancer, head and neck cancer, and bladder cancer.
165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 15 malignant peripheral nerve sheath tumor/normal pairs.
166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of 29 primary mantle cell lymphomas and their matched normals.
167                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        We performed targeted deep sequencing of 380 recurrently mutated genes across a cohort of 755 mature B-cell malignancies to define conserved and disease-specific patterns of genomic alterations.<a href="https://www.biorxiv.org/content/10.1101/674259v1.full">PubMed</a>
168                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 92 primary medulloblastoma tumor/normal pairs.
169                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole genome or whole exome sequencing of 491 previously untreated Medulloblastoma tumor/normal pairs.
170                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive profiling of 125 matched tumor and germline medulloblastoma samples
171                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole genome sequencing of 37 medulloblastoma tumors and their matched normals from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University.
172                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-genome sequencing of 46 recurrent medulloblastoma samples.
173                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole Genome Sequencing of 25  metastatic melanoma samples with matched normals
174                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MSK-IMPACT sequencing of 720 Melanoma tumor samples with matched normals.
175                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome sequencing of 64 pretreated (ipilimumab or tremelimumab) melanoma tumor-normal pairs.
176                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome sequencing of 333 primary and/or metastatic melanomas.
177                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing of 1,122 LGG and GBM tumor/normal pairs.
178                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCGA Mesothelioma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/MESO/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Mesothelioma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
180                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted or whole-exome sequencing of 19 Metaplastic Breast Cancer tumor/normal pairs.
181                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 216 tumor/normal (blood) pairs from metastatic breast cancer patients who underwent a biopsy in the context of the SAFIR01/SAFIR02 (Unicancer, France), SHIVA (Institut Curie, France) or MOSCATO (Gustave Roussy, France) prospective trials.
182                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted Sequencing of 1365 metastatic Breast Cancer tumor/normal pairs via MSK-IMPACT to understand the role of INK4 on CDK4/6 resistance.
183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing of 1134 metastatic colorectal tumor/normal pairs.
184                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 341 samples from 305 metastatic esophagogastric cancer patients
185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing of 144 pre-treatment samples from 144 patients with metastatic melanoma treated with anti-PD1 ICB.
186                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-exome sequencing of 110 metastatic melanoma tumor-normal pairs.
187                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of pre-treatment 66 Melanoma tumor samples. <a href="https://ascopubs.org/doi/full/10.1200/PO.16.00054">PubMed</a>
188                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of 38 pretreated (pembrolizumab, nivolumab) melanoma tumor-normal pairs.
189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Exome sequencing of 61 prostate cancer tumor/normal pairs (50 metastatic CRPCs and 11 high-grade localized prostate cancers). Generated by Arul Chinnaiyan's and Scott Tomlins' labs at the University of Michigan.
190                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole exome sequencing of 444 castrate resistant prostate cancer tumor/normal pairs. SU2C-PCF Dream Team: Precision Therapy for Advanced Prostate Cancer.
191                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 150 metastatic prostate cancer tumor/normal pairs by the SU2C/PCF Dream Team.
192                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome and -transcriptome sequencing of 500 adult patients with metastatic solid tumor/primary normal pairs of diverse lineage and biopsy site.
193                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MSK-IMPACT sequencing of 424 matched tumor-normal samples from patients with metastatic castration-sensitive prostate cancer. Germline alterations are not shown here.
194                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 248 samples from 124 patients' cfDNA/WBC and tumor/normal pairs.
195                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     IMPACT sequencing of 229 cell-free DNA (cfDNA) and associated tumor samples with matched normal
196                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome or whole-genome sequencing of 203 multiple myeloma paired tumor/normal sample pairs.
197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing of 29 myelodysplasia tumor/normal pairs.
198                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms
199                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing of paired tumor/normal pairs from 151 cases of Myeloproliferative Neoplasms.
200                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-exome sequencing of 67 samples by NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
201                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole exome sequencing of 56 NPC tumor/normal pairs.
202                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole genome sequencing of 87 primary neuroblastoma tumors and their matched normals.
203                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole Genome and Whole Exome sequencing of 240 high-risk neuroblastoma tumor/normal pairs.
204                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-genome sequencing of 56 neuroblastoma tumor/normal pairs.
205                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 114 metastatic tumor/normal pairs to understand genomic overlap between castration resistant adenocarcinoma (CRPC-Adeno) and neuroendocrine histologies (CRPC-NE).
206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole genome or whole exome sequencing of 14 NHL tumors and their matched normals.
207                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 860 patients with metastatic lung adenocarcinoma
208                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-exome sequencing of 75 tumor/normal NSCLC pairs treated with PD-1 plus CTLA-4 blockade..
209                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 IMPACT sequencing of 240 NSCLC tumor/normal pairs treated at MSKCC with anti-PD-(L)1 based therapy.
210                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 327 primary tumors with matched germline samples, and phylogenetic ctDNA sequencing of 96 pre- and 24 postoperative samples from 100 NSCLC TRACERx patients.
211                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted next-generation sequencing of 41 NSCLC samples.
212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of tumor-normal tissue pairs from 16 non-small cell lung cancer samples.
213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       IMPACT sequencing of 105 High Risk Nonmuscle Invasive Bladder Cancer samples.
214                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 40 oral squamous cell carcinoma tumor/normal sample pairs.
215                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Ovarian Serous Cystadenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/OV/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
216                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 489 high-grade serous ovarian adenocarcinoma tumor/normal pairs. <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Serous Ovarian Cancer project. 489 cases. <br><a href="https://tcga-data.nci.nih.gov/docs/publications/ov_2011/">Raw data via the TCGA Data Portal</a>.
217                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Ovarian Serous Cystadenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
218                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-exome sequencing of 660 lung ADC and 484 lung SqCC tumor/normal pairs.
219                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 99 pancreatic samples and their matched normals.
220                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-genome and deep-exome sequencing analysis of 456 pancreatic ductal adenocarcinomas
221                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Pancreatic Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PAAD/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
222                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pancreatic Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
223                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
224                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients.
225                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome sequencing of 98 pancreatic neuroendocrine tumours (PanNETs) and matched normal DNA pairs.
226                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome and whole genome sequencing of 496 papillary thyroid carcinoma tumor/normal pairs
227 Whole genome or whole exome sequencing on 298 Pediatric Acute Lymphoid Leukemia - Phase II samples. Comprehensive profiling of ALL Phase 2 samples. <p>TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see <a href="https://ocg.cancer.gov/programs/target/using-target-data">Using TARGET Data</a> section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the <a href="https://ocg.cancer.gov/programs/target/target-publication-guidelines">TARGET Publication Guidelines</a>.</p
228                                   Whole genome or whole exome sequencing on 333 TARGET-AML samples. Comprehensive profiling of TARGET-AML samples. <p>TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see <a href="https://ocg.cancer.gov/programs/target/using-target-data">Using TARGET Data</a> section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the <a href="https://ocg.cancer.gov/programs/target/target-publication-guidelines">TARGET Publication Guidelines</a>.</p>
229                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
230                                           Whole genome or whole exome sequencing on 1089 NBL samples. Comprehensive profiling of 1089 NBL samples. <p>TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see <a href="https://ocg.cancer.gov/programs/target/using-target-data">Using TARGET Data</a> section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the <a href="https://ocg.cancer.gov/programs/target/target-publication-guidelines">TARGET Publication Guidelines</a>.</p>
231                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-genome/exome sequencing of 961 Pediatric Cancer samples. Data generated from Pfister Lab & DKFZ/German Cancer Consortium.
232                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 103 samples (88 with matched normals) from 88 high-risk pediatric cancer patients.
233                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 261 patient derived xenografts (PDXs) samples from high-risk childhood cancers (with no matched normals). Website: <a href='http://www.ncipptc.org/'>PPTC</a>
234                               Whole-genome sequencing 72 patients with Rhabdoid Tumor. Comprehensive profiling of 72 patients with Rhabdoid Tumor. <p>TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see <a href="https://ocg.cancer.gov/programs/target/using-target-data">Using TARGET Data</a> section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the <a href="https://ocg.cancer.gov/programs/target/target-publication-guidelines">TARGET Publication Guidelines</a>.</p>
235                                           Whole-exome sequencing of 657 Wilms' tumor samples. Comprehensive profiling of 657 Wilms' Tumor samples. <p>TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see <a href="https://ocg.cancer.gov/programs/target/using-target-data">Using TARGET Data</a> section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the <a href="https://ocg.cancer.gov/programs/target/target-publication-guidelines">TARGET Publication Guidelines</a>.</p>
236                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of 178 Pheochromocytoma or Paraganglioma tumor/normal pairs.
237                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Pheochromocytoma and Paraganglioma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PCPG/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
238                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pheochromocytoma and Paraganglioma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
239                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-genome sequencing of 96 pilocytic astrocytoma tumor/normal pairs. Conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
240                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) tumor/normal pairs.
241                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 341 cancer genes from 117 patient-derived PDTCs and ATCs
242                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome sequencing of 19 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
243                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome sequencing of 57 prostate tumor and matches normal tissues.
244                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing of 112 prostate adenocarcinomas and matched normal samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
245                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-genome/exome sequencing of 477 prostate samples from CPC-GENE and public data sets, including TCGA-PRAD.
246                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling of 176 tumors from 63 patients with disseminated prostate cancer with matched normals.
247                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 1465 prostate adenocarcinoma tumor/normal pairs via MSK-IMPACT.
248                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of 218 prostate tumors (181 primaries, 37 metastases) and 14 prostate cancer cell lines and xenografts. MSKCC Prostate Oncogenome Project.<br><a href="http://cbio.mskcc.org/cancergenomics/prostate/data/">Normalized flat data files</a>. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21032">Raw data via GEO (GSE21032)</a>.
249                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Genome-wide copy number profiling in 104 primary prostate cancer tumor/normal pairs. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54691">Raw data via GEO (GSE54691)</a>.
250                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome Sequencing of 1013 prostate cancer samples and their matched normals.
251                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome and transcriptome sequencing of 65 Prostate Adenocarcinoma  tumor/normal pairs.
252                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome and/or whole genome sequencing of 333 primary prostate adenocarcinoma tumor/normal pairs; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/prad_2015/">NCI</A>.
253                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Prostate Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PRAD/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
254                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Prostate Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
255                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Exome sequencing of 12 advanced prostate cancer samples and matched organoids
256                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole genome and transcriptome sequencing of tumor/normal pairs from 292 prostate cancer patients.
257                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     MSK-IMPACT Sequencing of 18 prostate cancer tumor/normal pairs.
258                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        IMPACT sequencing of 504 prostate cancer tumor/normal pairs.
259                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Germline RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in homologous recombination-deficient tumors
260                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 2,069 prostate cancers from different races via MSK-IMPACT.
261                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 MSK-IMPACT targeted sequencing of matched rectal cancer tumor and tumoroid samples.
262                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
263                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome and/or whole genome sequencing of 106 clear cell renal cell carcinoma tumor/normal pairs.
264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Exome sequencing of 139 samples with matched normals and RNA-sequencing of 7 samples (5 samples with matched normals) from 145 Renal Non-Clear Cell Carcinoma (nccRCC) patients.
265                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted sequencing of 83 Retinoblastoma tumor-normal pairs via MSK-IMPACT. Genomic data provided is limited to somatic alterations.
266                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Cell-free DNA profiling in 14 retinoblastoma patients with advanced intraocular disease: An MSKCC experience
267                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-genome sequencing of tumor-normal sample pairs from 40 patients with Malignant Rhabdoid Cancer.
268                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-genome or whole-exome sequencing of 43 rhabdomyosarcoma tumor/normal pairs.
269                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             MSK-IMPACT sequencing of 86 patients with HER2- and HER3-mutant cancers
270                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Sanger-sequenced 226 protein-coding genes (3,849 exons and adjacent intronic) on 207 samples (with 205 matched normals) encompassing 7 major sarcoma subtypes.
271                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Sarcoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/SARC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
272                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Sarcoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
273                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 121 melanoma samples with matched normals.
274                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Skin Cutaneous Melanoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/SKCM/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
275                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Skin Cutaneous Melanoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
276                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Exome sequencing of 147 melanoma samples with 99 matched normals.
277                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome Sequencing of tumors (with matched normals) from 45 patients with BRAFV600-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy.
278                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 12 SCCO paired tumor and normal samples.
279                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive whole exam profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
280                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole exome-sequencing of 80 human SCLCs, including 36 primary SCLC human tumor and adjacent normal sample pairs and 17 paired SCLC cell lines and their patient-matched lymphoblastoid lines, as well as 4 primary SCLC tumors and 23 SCLC cell lines without matched normal controls.
281                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome sequencing of 120 small cell lung cancer(SCLC) tumour samples and matched normal material.
282                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole Exome Sequencing of 10 paired chemosensitive and chemoresistant SCLC PDX.
283                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of tumor/normal pairs from 15 vulvar squamous cell carcinomas.
284                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole genome sequencing of 100 gastric cancer tumor-normal pairs from the University of Hong Kong and Pfizer.
285                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Stomach Adenocarcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/STAD/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
286                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole-exome sequencing of 295 primary gastric adenocarcinomas tumors with matched normals. TCGA Stomach Adenocarcinoma Project; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
287                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Stomach Adenocarcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
288                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples (with matched normals) from the University of Tokyo.
289                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Exome sequencing of 22 gastric cancer samples with matched normals.
290                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Genomic and survival data from 1661 tumor-normal pairs from 1661 patients with various cancer types sequenced with the MSK-IMPACT assay.
291                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   TCGA Testicular Germ Cell Cancer. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/TGCT/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
292                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Testicular Germ Cell Tumors TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
293                                                                                                                                                                                                                                                                                          The Angiosarcoma Project (www.ascproject.org) is an ongoing patient-driven initiative. This provisional dataset is currently derived from 83 samples, including tumor specimens (FFPE and cfDNA) from 62 angiosarcoma patients subjected to WES (along with matched germline WES). This study includes genomic data, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). As these data were generated in a research laboratory, not a clinical laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. For questions about these data, including how to cite, please visit www.ascproject.org/data-release or direct questions to data@ascproject.org.
294                                                                                                                                                                                                                                                                                                                                                                                                     The Angiosarcoma Project is an ongoing patient-driven initiative. This archived Angiosarcoma Project dataset was analyzed in the linked Nature Medicine 2020 manuscript, and is derived from 48 samples from 36 angiosarcoma patients. Angiosarcoma tumor specimens (FFPE) were subjected to whole-exome sequencing (along with matched germline whole-exome sequencing). In addition to genomic data, this study includes patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). All annotations have been de-identified. Questions about these data can be directed to data@ascproject.org.
295                                                                                  The Metastatic Breast Cancer Project (www.mbcproject.org) is an ongoing patient-driven initiative. This dataset release is derived from 237 samples, including both primary and/or metastatic tumor specimens (FFPE) from 180 patients who developed metastatic breast cancer. 237 samples have undergone whole-exome sequencing (along with matched germline whole-exome sequencing) and 146 of those samples have also undergone RNA-sequencing. This study includes genomic data, patient-reported data (prepended as PRD), medical record data (MedR), and pathology report data (PATH). All annotations have been de-identified. As these data were generated in a research laboratory, not a clinical laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. For questions about these data, including how to cite, please visit www.mbcproject.org/data-release or direct questions to data@mbcproject.org.
296                                                                                                                                                                                                                                                                                                                                                                                          The Metastatic Prostate Cancer Project is a patient-driven initiative. This study includes genomic data, cfDNA tumor fractions, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH).  As these data were generated in a research, not a clinical, laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. All annotations have been de-identified. More information is available at www.mpcproject.org. For questions about these data, including how to cite, please visit www.mpcproject.org/data-release or direct questions to data@mpcproject.org.
297                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of tumor and PDX thoracic samples.
298                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted sequencing of thoracic PDX lines to characterize genetic alterations in 138 tumor/normal pairs via MSK-IMPACT. Data generated in Charles Rudin Lab.
299                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 28 thymic epithelial tumors (TETs) with matched normals
300                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Thymoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THYM/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Thymoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
302                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Thyroid Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THCA/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
303                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Thyroid Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
304                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Tumors with TRK fusions based on MSK-IMPACT targeted sequencing.
305                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 62 high-grade primary Unclassified Renal Cell Carcinoma tumor samples with matched normals.
306                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Next-generation sequencing (MSK-IMPACT) on all protein-coding exons of 300 cancer associated genes of 85 Upper Tract Urothelial Carcinoma tumor samples and paired normals.
307                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing (37 samples) and RNA-seq analysis (32 samples) of 47 upper tract urothelial carcinoma patients.
308                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome sequencing of 30 upper-tract urothelial carcinoma patients and their matched normals.
309                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted Sequencing of 119 upper tract urothelial carcinoma tumor/normal pairs.
310                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MSK-IMPACT sequencing of 34 upper tract urothelial patients and the matching PDX or PDC generated from 17 patient tumors.
311                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole-exome sequencing of 72 tumor samples (with 32 matched normals) in Urothelial Carcinoma.
312                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing (WXS) of 22 uterine carcinosarcoma/uterine malignant mixed Mullerian (UCS) tumors with matched normals. <A HREF="http://www.nature.com/ncomms/2014/140919/ncomms6006/extref/ncomms6006-s1.pdf">
313                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TCGA Uterine Carcinosarcoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UCS/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
314                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Uterine Carcinosarcoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
315                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of paired tumor-normal DNAs from 16 cases of clear cell endometrial tumors.
316                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Uterine Corpus Endometrial Carcinoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UCEC/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
317                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 373 endometrial carcinoma tumors with matched normals. TCGA Uterine Corpus Endometrial Carcinoma project; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/">NCI</A>.
318                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Uterine Corpus Endometrial Carcinoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
319                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted Sequencing of 108 Uterine Sarcoma/Mesenchymal tumor/normal pairs from 107 patients.
320                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome or whole-exome sequencing of tumor/normal pairs from 28 uveal melanoma samples.
321                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Uveal Melanoma. Source data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UVM/20160128/">GDAC Firehose</A>. Previously known as TCGA Provisional.
322                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Uveal melanoma TCGA PanCancer data. The original data is <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
> 
> # Get available case lists (collection of samples) for a given cancer study  
> mycancerstudy = getCancerStudies(mycgds)[2,1]
> mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]
> 
> # Get available genetic profiles
> mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[1,1]
> 
> # Get data slices for a specified list of genes, genetic profile and case list
> getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get data slice for a single gene
> getProfileData(mycgds,'HMGA2',mygeneticprofile,mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get data slice for multiple genetic profiles and single gene
> getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get the same dataset from a vector of case IDs
> cases = unlist(strsplit(getCaseLists(mycgds,mycancerstudy)[1,'case_ids'],' '))
Error in strsplit(getCaseLists(mycgds, mycancerstudy)[1, "case_ids"],  : 
  non-character argument
Calls: unlist -> strsplit
Execution halted