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       histiocytosis_cobi_msk_2019
121                   all_stjude_2013
122               panet_shanghai_2013
123                     chol_jhu_2013
124                   ihch_mskcc_2020
125                     ihch_msk_2021
126                   ihch_ismms_2015
127                    ihch_smmu_2014
128                 brca_jup_msk_2020
129                     kich_tcga_pub
130                         kich_tcga
131      kich_tcga_pan_can_atlas_2018
132                          kirc_bgi
133                    ccrcc_irc_2014
134                         kirc_tcga
135                     kirc_tcga_pub
136      kirc_tcga_pan_can_atlas_2018
137                         kirp_tcga
138      kirp_tcga_pan_can_atlas_2018
139             hcc_msk_venturaa_2018
140                      lihc_amc_prv
141                        lihc_riken
142                         lihc_tcga
143      lihc_tcga_pan_can_atlas_2018
144                     lgg_ucsf_2014
145                        luad_broad
146                   luad_mskcc_2020
147               luad_mskimpact_2021
148                   luad_mskcc_2015
149               luad_msk_npjpo_2021
150                  luad_oncosg_2020
151                         luad_tcga
152                     luad_tcga_pub
153      luad_tcga_pan_can_atlas_2018
154                          luad_tsp
155                     lung_smc_2016
156                         lusc_tcga
157                     lusc_tcga_pub
158      lusc_tcga_pan_can_atlas_2018
159                         dlbc_tcga
160        lymphoma_cellline_msk_2020
161                   msk_impact_2017
162                   msk_access_2021
163                  mixed_allen_2018
164                       mpnst_mskcc
165                  mcl_idibips_2013
166                    mbn_mdacc_2013
167                    mbl_broad_2012
168                     mbl_dkfz_2017
169                          mbl_icgc
170                          mbl_pcgp
171                 mbl_sickkids_2016
172                skcm_broad_dfarber
173                mel_mskimpact_2020
174                   skcm_mskcc_2014
175                skcm_tcga_pub_2015
176                   lgggbm_tcga_pub
177                         meso_tcga
178      meso_tcga_pan_can_atlas_2018
179                      mbc_msk_2021
180                     brca_igr_2015
181              breast_ink4_msk_2021
182                      crc_msk_2017
183                      egc_msk_2017
184                     mel_dfci_2019
185                    skcm_dfci_2015
186        skcm_vanderbilt_mskcc_2015
187                     mel_ucla_2016
188                         prad_mich
189                    prad_su2c_2019
190                    prad_su2c_2015
191 metastatic_solid_tumors_mich_2017
192             prad_mcspc_mskcc_2020
193                    cfdna_msk_2019
194              mixed_cfdna_msk_2020
195                          mm_broad
196                    mds_tokyo_2011
197                    mds_mskcc_2020
198                     mpn_cimr_2013
199                    cellline_nci60
200                   npc_nusingapore
201                      nbl_amc_2012
202                    nbl_broad_2013
203                 nbl_ucologne_2015
204                     nepc_wcm_2016
205                    nhl_bcgsc_2011
206                     lung_msk_2017
207                  nsclc_mskcc_2018
208                nsclc_pd1_msk_2018
209                nsclc_tracerx_2017
210                  nsclc_unito_2016
211                  nsclc_mskcc_2015
212                   blca_nmibc_2017
213              hnsc_mdanderson_2013
214                           ov_tcga
215                       ov_tcga_pub
216        ov_tcga_pan_can_atlas_2018
217             nsclc_tcga_broad_2016
218                         paad_icgc
219                 paad_qcmg_uq_2016
220                         paad_tcga
221      paad_tcga_pan_can_atlas_2018
222                    paad_utsw_2015
223                    panet_jhu_2011
224                 panet_arcnet_2017
225                     thca_tcga_pub
226        all_phase2_target_2018_pub
227               aml_target_2018_pub
228             es_dfarber_broad_2014
229               nbl_target_2018_pub
230               pediatric_dkfz_2017
231                 mixed_pipseq_2017
232                         pptc_2019
233                rt_target_2018_pub
234                wt_target_2018_pub
235                     pcpg_tcga_pub
236                         pcpg_tcga
237      pcpg_tcga_pan_can_atlas_2018
238         past_dkfz_heidelberg_2013
239                   plmeso_nyu_2015
240                thyroid_mskcc_2016
241                   pcnsl_mayo_2015
242                   prad_broad_2013
243                        prad_broad
244                    prad_cpcg_2017
245                        prad_fhcrc
246             prad_cdk12_mskcc_2020
247                        prad_mskcc
248                   prad_mskcc_2014
249                        prad_p1000
250                 prad_eururol_2017
251                     prad_tcga_pub
252                         prad_tcga
253      prad_tcga_pan_can_atlas_2018
254  prad_mskcc_cheny1_organoids_2014
255                prostate_dkfz_2018
256                     prad_msk_2019
257                   prad_mskcc_2017
258               mixed_msk_tcga_2021
259            prad_msk_stopsack_2021
260                   rectal_msk_2019
261                    hnc_mskcc_2016
262                 ccrcc_utokyo_2013
263             nccrcc_genentech_2014
264                    rbl_mskcc_2020
265                rbl_cfdna_msk_2020
266                    mrt_bcgsc_2016
267                      rms_nih_2014
268                       summit_2018
269                        sarc_mskcc
270                         sarc_tcga
271      sarc_tcga_pan_can_atlas_2018
272                        skcm_broad
273                         skcm_tcga
274      skcm_tcga_pan_can_atlas_2018
275                         skcm_yale
276        skcm_broad_brafresist_2012
277                        scco_mskcc
278                        sclc_clcgp
279                          sclc_jhu
280                sclc_ucologne_2015
281      sclc_cancercell_gardner_2017
282                      vsc_cuk_2018
283             stad_pfizer_uhongkong
284                         stad_tcga
285                     stad_tcga_pub
286      stad_tcga_pan_can_atlas_2018
287                       stad_utokyo
288                    stad_uhongkong
289                    tmb_mskcc_2018
290                         tgct_tcga
291      tgct_tcga_pan_can_atlas_2018
292                 angs_painter_2020
293         angs_project_painter_2018
294        brca_mbcproject_wagle_2017
295              prad_mpcproject_2018
296                 lung_pdx_msk_2021
297                      lung_msk_pdx
298                      tet_nci_2014
299                         thym_tcga
300      thym_tcga_pan_can_atlas_2018
301                         thca_tcga
302      thca_tcga_pan_can_atlas_2018
303                     ntrk_msk_2019
304                   urcc_mskcc_2016
305                   utuc_mskcc_2015
306    utuc_cornell_baylor_mdacc_2019
307                   utuc_igbmc_2021
308                     utuc_msk_2019
309                 utuc_pdx_msk_2019
310                 blca_cornell_2016
311                      ucs_jhu_2014
312                          ucs_tcga
313       ucs_tcga_pan_can_atlas_2018
314                     uccc_nih_2017
315                         ucec_tcga
316                     ucec_tcga_pub
317      ucec_tcga_pan_can_atlas_2018
318                    usarc_msk_2020
319                      um_qimr_2016
320                          uvm_tcga
321       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                                                      Histiocytosis Cobimetinib (MSK, Nature 2019)
121                                     Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
122                                                            Insulinoma (Shanghai, Nat Commun 2013)
123                                             Intrahepatic Cholangiocarcinoma (JHU, Nat Genet 2013)
124                                                       Intrahepatic Cholangiocarcinoma (MSK, 2020)
125                                            Intrahepatic Cholangiocarcinoma (MSK, Hepatology 2021)
126                                                Intrahepatic Cholangiocarcinoma (Mount Sinai 2015)
127                                       Intrahepatic Cholangiocarcinoma (Shanghai, Nat Commun 2014)
128                                             Juvenile Papillomatosis and Breast Cancer (MSK, 2020)
129                                                       Kidney Chromophobe (TCGA, Cancer Cell 2014)
130                                                        Kidney Chromophobe (TCGA, Firehose Legacy)
131                                                        Kidney Chromophobe (TCGA, PanCancer Atlas)
132                                           Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
133                                           Kidney Renal Clear Cell Carcinoma (IRC, Nat Genet 2014)
134                                         Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)
135                                             Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
136                                         Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)
137                                     Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy)
138                                     Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)
139                                  Liver Hepatocellular Adenoma and Carcinomas (MSK, PLOS One 2018)
140                                             Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
141                                            Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
142                                            Liver Hepatocellular Carcinoma (TCGA, Firehose Legacy)
143                                            Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)
144                                                            Low-Grade Gliomas (UCSF, Science 2014)
145                                                            Lung Adenocarcinoma (Broad, Cell 2012)
146                                                                 Lung Adenocarcinoma (MSKCC, 2020)
147                                                                 Lung Adenocarcinoma (MSKCC, 2021)
148                                                         Lung Adenocarcinoma (MSKCC, Science 2015)
149                                            Lung Adenocarcinoma (NPJ Precision Oncology, MSK 2021)
150                                                      Lung Adenocarcinoma (OncoSG, Nat Genet 2020)
151                                                       Lung Adenocarcinoma (TCGA, Firehose Legacy)
152                                                           Lung Adenocarcinoma (TCGA, Nature 2014)
153                                                       Lung Adenocarcinoma (TCGA, PanCancer Atlas)
154                                                            Lung Adenocarcinoma (TSP, Nature 2008)
155                                                           Lung Cancer (SMC, Cancer Research 2016)
156                                              Lung Squamous Cell Carcinoma (TCGA, Firehose Legacy)
157                                                  Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
158                                              Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
159                           Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Firehose Legacy)
160                                                                 Lymphoma Cell Lines (MSKCC, 2020)
161                                       MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
162                                                MSK-IMPACT and MSK-ACCESS Mixed Cohort (MSK, 2021)
163                                        MSS Mixed Solid Tumors (Broad/Dana-Farber, Nat Genet 2018)
164                                   Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
165                                                         Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
166                                            Mature B-cell malignancies (MD Anderson Cancer Center)
167                                                              Medulloblastoma (Broad, Nature 2012)
168                                                               Medulloblastoma (DKFZ, Nature 2017)
169                                                               Medulloblastoma (ICGC, Nature 2012)
170                                                               Medulloblastoma (PCGP, Nature 2012)
171                                                           Medulloblastoma (Sickkids, Nature 2016)
172                                                         Melanoma (Broad/Dana Farber, Nature 2012)
173                                                                            Melanoma (MSKCC, 2018)
174                                                                       Melanoma (MSKCC, NEJM 2014)
175                                                                       Melanomas (TCGA, Cell 2015)
176                                                    Merged Cohort of LGG and GBM (TCGA, Cell 2016)
177                                                              Mesothelioma (TCGA, Firehose Legacy)
178                                                              Mesothelioma (TCGA, PanCancer Atlas)
179                                                             Metaplastic Breast Cancer (MSK, 2021)
180                                                  Metastatic Breast Cancer (INSERM, PLoS Med 2016)
181                                             Metastatic Breast Cancer (MSK, Cancer Discovery 2021)
182                                            Metastatic Colorectal Cancer (MSKCC, Cancer Cell 2018)
183                                  Metastatic Esophagogastric Cancer (MSKCC, Cancer Discovery 2017)
184                                                  Metastatic Melanoma (DFCI, Nature Medicine 2019)
185                                                          Metastatic Melanoma (DFCI, Science 2015)
186                                                Metastatic Melanoma (MSKCC, JCO Precis Oncol 2017)
187                                                             Metastatic Melanoma (UCLA, Cell 2016)
188                                            Metastatic Prostate Adenocarcinoma (MCTP, Nature 2012)
189                               Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019)
190                                       Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015)
191                                                     Metastatic Solid Cancers (UMich, Nature 2017)
192                       Metastatic castration-sensitive prostate cancer (MSK, Clin Cancer Res 2020)
193                                                           Mixed cfDNA (MSK, Nature Medicine 2019)
194                                                                         Mixed cfDNA (MSKCC, 2020)
195                                                        Multiple Myeloma (Broad, Cancer Cell 2014)
196                                                              Myelodysplasia (UTokyo, Nature 2011)
197                                                                     Myelodysplastic (MSKCC, 2020)
198                                                    Myeloproliferative Neoplasms (CIMR, NEJM 2013)
199                                                          NCI-60 Cell Lines (NCI, Cancer Res 2012)
200                                              Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
201                                                        Neuroblastoma (AMC Amsterdam, Nature 2012)
202                                                             Neuroblastoma (Broad, Nat Genet 2013)
203                                                                Neuroblastoma (Broad, Nature 2015)
204                                    Neuroendocrine Prostate Cancer (Multi-Institute, Nat Med 2016)
205                                                         Non-Hodgkin Lymphoma (BCGSC, Nature 2011)
206                                                 Non-Small Cell Cancer (MSKCC, Cancer Discov 2017)
207                                                Non-Small Cell Lung Cancer (MSK, Cancer Cell 2018)
208                                             Non-Small Cell Lung Cancer (MSKCC, J Clin Oncol 2018)
209                                          Non-Small Cell Lung Cancer (TRACERx, NEJM & Nature 2017)
210                                Non-Small Cell Lung Cancer (University of Turin, Lung Cancer 2017)
211                                                    Non-small cell lung cancer (MSK, Science 2015)
212                                             Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017)
213                                    Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
214                                         Ovarian Serous Cystadenocarcinoma (TCGA, Firehose Legacy)
215                                             Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
216                                         Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)
217                                                            Pan-Lung Cancer (TCGA, Nat Genet 2016)
218                                                     Pancreatic Adenocarcinoma (ICGC, Nature 2012)
219                                                     Pancreatic Adenocarcinoma (QCMG, Nature 2016)
220                                                 Pancreatic Adenocarcinoma (TCGA, Firehose Legacy)
221                                                 Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)
222                                                         Pancreatic Cancer (UTSW, Nat Commun 2015)
223                         Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
224                                   Pancreatic Neuroendocrine Tumors (Multi-Institute, Nature 2017)
225                                                     Papillary Thyroid Carcinoma (TCGA, Cell 2014)
226                                       Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018)
227                                                   Pediatric Acute Myeloid Leukemia (TARGET, 2018)
228                                                Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
229                                                            Pediatric Neuroblastoma (TARGET, 2018)
230                                                          Pediatric Pan-Cancer (DKFZ, Nature 2017)
231                                                Pediatric Pan-cancer (Columbia U, Genome Med 2016)
232                                   Pediatric Preclinical Testing Consortium  (CHOP, Cell Rep 2019)
233                                                           Pediatric Rhabdoid Tumor (TARGET, 2018)
234                                                             Pediatric Wilms' Tumor (TARGET, 2018)
235                                              Pheochromocytoma and Paraganglioma (TCGA, Cell 2017)
236                                        Pheochromocytoma and Paraganglioma (TCGA, Firehose Legacy)
237                                        Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)
238                                                Pilocytic Astrocytoma (ICGC, Nature Genetics 2013)
239                                                       Pleural Mesothelioma (NYU, Cancer Res 2015)
240                            Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
241                       Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
242                                                Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
243                                           Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
244                                                   Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
245                                       Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
246                                                      Prostate Adenocarcinoma (MSK, Eur Urol 2020)
247                                                 Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
248                                                        Prostate Adenocarcinoma (MSKCC, PNAS 2014)
249                                        Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018)
250                                                     Prostate Adenocarcinoma (SMMU, Eur Urol 2017)
251                                                         Prostate Adenocarcinoma (TCGA, Cell 2015)
252                                                   Prostate Adenocarcinoma (TCGA, Firehose Legacy)
253                                                   Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
254                                              Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
255                                                          Prostate Cancer (DKFZ, Cancer Cell 2018)
256                                                            Prostate Cancer (MSK, Cell Metab 2020)
257                                                    Prostate Cancer (MSKCC, JCO Precis Oncol 2017)
258                                                  RAD51B Associated Mixed Cancers (Mandelker 2021)
259                                                   Race Differences in Prostate Cancer (MSK, 2021)
260                                                          Rectal Cancer (MSK,Nature Medicine 2019)
261                              Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016)
262                                               Renal Clear Cell Carcinoma (UTokyo, Nat Genet 2013)
263                                        Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
264                                                                Retinoblastoma (MSK, Cancers 2021)
265                                                                 Retinoblastoma cfDNA (MSKCC 2020)
266                                                         Rhabdoid Cancer (BCGSC, Cancer Cell 2016)
267                                                        Rhabdomyosarcoma (NIH, Cancer Discov 2014)
268                                    SUMMIT - Neratinib Basket Study (Multi-Institute, Nature 2018)
269                                                             Sarcoma (MSKCC/Broad, Nat Genet 2010)
270                                                                   Sarcoma (TCGA, Firehose Legacy)
271                                                                   Sarcoma (TCGA, PanCancer Atlas)
272                                                        Skin Cutaneous Melanoma (Broad, Cell 2012)
273                                                   Skin Cutaneous Melanoma (TCGA, Firehose Legacy)
274                                                   Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)
275                                                    Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
276                                                Skin Cutaneous Melanoma(Broad, Cancer Discov 2014)
277                                         Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
278                                                    Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
279                                            Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
280                                                   Small Cell Lung Cancer (U Cologne, Nature 2015)
281                                        Small-Cell Lung Cancer (Multi-Institute, Cancer Cell 2017)
282                                      Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)
283                                           Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
284                                                    Stomach Adenocarcinoma (TCGA, Firehose Legacy)
285                                                        Stomach Adenocarcinoma (TCGA, Nature 2014)
286                                                    Stomach Adenocarcinoma (TCGA, PanCancer Atlas)
287                                                  Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
288                                                      Stomach Adenocarcinoma (UHK, Nat Genet 2011)
289                                                     TMB and Immunotherapy (MSKCC, Nat Genet 2019)
290                                               Testicular Germ Cell Cancer (TCGA, Firehose Legacy)
291                                               Testicular Germ Cell Tumors (TCGA, PanCancer Atlas)
292                                                 The Angiosarcoma Project (Provisional, July 2020)
293                                    The Angiosarcoma Project - Count Me In (Nature Medicine, 2020)
294                                 The Metastatic Breast Cancer Project (Provisional, February 2020)
295                               The Metastatic Prostate Cancer Project (Provisional, November 2019)
296                                                                       Thoracic Cancer (MSK, 2021)
297                                                                   Thoracic PDX (MSK, Provisional)
298                                                    Thymic Epithelial Tumors (NCI, Nat Genet 2014)
299                                                                   Thymoma (TCGA, Firehose Legacy)
300                                                                   Thymoma (TCGA, PanCancer Atlas)
301                                                         Thyroid Carcinoma (TCGA, Firehose Legacy)
302                                                         Thyroid Carcinoma (TCGA, PanCancer Atlas)
303                                               Tumors with TRK fusions (MSK, Clin Cancer Res 2020)
304                                              Unclassified Renal Cell Carcinoma (MSK, Nature 2016)
305                                                Upper Tract Urothelial Cancer (MSK, Eur Urol 2015)
306                          Upper Tract Urothelial Carcinoma (Cornell/Baylor/MDACC, Nat Commun 2019)
307                                     Upper Tract Urothelial Carcinoma (IGBMC, Genome Biology 2021)
308                                           Upper Tract Urothelial Carcinoma (MSK, Nat Commun 2020)
309                                       Upper Tract Urothelial Carcinoma PDX (MSK, Nat Commun 2020)
310                                               Urothelial Carcinoma (Cornell/Trento, Nat Gen 2016)
311                                           Uterine Carcinosarcoma (Johns Hopkins, Nat Commun 2014)
312                                                    Uterine Carcinosarcoma (TCGA, Firehose Legacy)
313                                                    Uterine Carcinosarcoma (TCGA, PanCancer Atlas)
314                                                   Uterine Clear Cell Carcinoma (NIH, Cancer 2017)
315                                      Uterine Corpus Endometrial Carcinoma (TCGA, Firehose Legacy)
316                                          Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
317                                      Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
318                                           Uterine Sarcoma/Mesenchymal (MSK, Clin Cancer Res 2020)
319                                                            Uveal Melanoma (QIMR, Oncotarget 2016)
320                                                            Uveal Melanoma (TCGA, Firehose Legacy)
321                                                            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 and whole exome sequencing of 52 histiocytosis tumor/normal pairs.
121                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole genome or exome sequencing of 44 (20 whole genome, 20 exome) ALL tumor/normal pairs.
122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 10 benign insulinoma tumor/normal pairs.
123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome sequencing of tumor/normal pairs from 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
124                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Targeted sequencing of IMPACT and CMO samples
125                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing of 412 intrahepatic cholangiocarcinoma tumor/normal sample pairs.
126                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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.
127                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 103 tumor/normal sample pairs in 103 intrahepatic cholangiocarcinoma patients.
128                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma.
129                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 66 chromophobe renal cell carcinoma (ChRCCs) tumor/normal pairs.
130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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.
131                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
132                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 10 ccRCC tumor/normal pairs and targeted sequencing of 88 clear cell carcinoma tumor/normal pairs. Generated by BGI-Shenzhen.
133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
134                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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.
135                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-exome sequencing in 417 of 446 clear cell renal cell carcinoma tumor/normal pairs.
136                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
137                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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.
138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                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>.
139                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Targeted sequencing of tumor/normal pairs of 9 LIAD and 10 HCC patients via MSK-IMPACT platform.
140                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 231 hepatocellular carcinomas and matched normal tissue pairs.
141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-genome sequencing of 27 hepatocellular carcinoma tumor/norma pairs from RIKEN.
142                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                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.
143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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>.
144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 23 grade II glioma tumor/normal pairs.
145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome and/or whole-genome sequencing of 183 lung adenocarcinomas and matched normal tissue pairs.
146                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Targeted sequencing of 604 lung adenocarcinoma tumor/normal pairs via MSK-IMPACT.
147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 186 matched normal samples from 186 lung adenocarcinoma patient via MSK-IMPACT.
148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing of 34 non small cell lung cancer tumor/normal pairs.
149                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 426 matched normal samples from 426 lung adenocarcinoma patients.
150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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).
151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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.
152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  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>.
154                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted sequencing of 163 lung adenocarcinoma tumor/normal pairs. Generated by WashU/Broad.
155                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome and whole transcriptome sequencing of primary and multiple metastatic lymph node samples from 6 lung cancer patients with their matched normals.
156                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  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.
157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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.
158                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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>.
159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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.
160                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 34 lymphoma cell lines using HemePACT_v3
161                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
162                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 1446 Tumor and cfDNA samples (1440 with matched normals) from MSK-IMPACT and MSK-ACCESS.
163                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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.
164                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 15 malignant peripheral nerve sheath tumor/normal pairs.
165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of 29 primary mantle cell lymphomas and their matched normals.
166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>
167                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 92 primary medulloblastoma tumor/normal pairs.
168                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole genome or whole exome sequencing of 491 previously untreated Medulloblastoma tumor/normal pairs.
169                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive profiling of 125 matched tumor and germline medulloblastoma samples
170                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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.
171                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-genome sequencing of 46 recurrent medulloblastoma samples.
172                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole Genome Sequencing of 25  metastatic melanoma samples with matched normals
173                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MSK-IMPACT sequencing of 720 Melanoma tumor samples with matched normals.
174                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome sequencing of 64 pretreated (ipilimumab or tremelimumab) melanoma tumor-normal pairs.
175                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome sequencing of 333 primary and/or metastatic melanomas.
176                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing of 1,122 LGG and GBM tumor/normal pairs.
177                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  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.
178                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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>.
179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted or whole-exome sequencing of 19 Metaplastic Breast Cancer tumor/normal pairs.
180                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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.
181                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted Sequencing of 1365 metastatic Breast Cancer tumor/normal pairs via MSK-IMPACT to understand the role of INK4 on CDK4/6 resistance.
182                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Targeted sequencing of 1134 metastatic colorectal tumor/normal pairs.
183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 341 samples from 305 metastatic esophagogastric cancer patients
184                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing of 144 pre-treatment samples from 144 patients with metastatic melanoma treated with anti-PD1 ICB.
185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-exome sequencing of 110 metastatic melanoma tumor-normal pairs.
186                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of pre-treatment 66 Melanoma tumor samples. <a href="https://ascopubs.org/doi/full/10.1200/PO.16.00054">PubMed</a>
187                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of 38 pretreated (pembrolizumab, nivolumab) melanoma tumor-normal pairs.
188                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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.
189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole exome sequencing of 444 castrate resistant prostate cancer tumor/normal pairs. SU2C-PCF Dream Team: Precision Therapy for Advanced Prostate Cancer.
190                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of 150 metastatic prostate cancer tumor/normal pairs by the SU2C/PCF Dream Team.
191                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome and -transcriptome sequencing of 500 adult patients with metastatic solid tumor/primary normal pairs of diverse lineage and biopsy site.
192                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MSK-IMPACT sequencing of 424 matched tumor-normal samples from patients with metastatic castration-sensitive prostate cancer. Germline alterations are not shown here.
193                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 248 samples from 124 patients' cfDNA/WBC and tumor/normal pairs.
194                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     IMPACT sequencing of 229 cell-free DNA (cfDNA) and associated tumor samples with matched normal
195                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome or whole-genome sequencing of 203 multiple myeloma paired tumor/normal sample pairs.
196                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing of 29 myelodysplasia tumor/normal pairs.
197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms
198                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing of paired tumor/normal pairs from 151 cases of Myeloproliferative Neoplasms.
199                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
200                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole exome sequencing of 56 NPC tumor/normal pairs.
201                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole genome sequencing of 87 primary neuroblastoma tumors and their matched normals.
202                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole Genome and Whole Exome sequencing of 240 high-risk neuroblastoma tumor/normal pairs.
203                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-genome sequencing of 56 neuroblastoma tumor/normal pairs.
204                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 114 metastatic tumor/normal pairs to understand genomic overlap between castration resistant adenocarcinoma (CRPC-Adeno) and neuroendocrine histologies (CRPC-NE).
205                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole genome or whole exome sequencing of 14 NHL tumors and their matched normals.
206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 860 patients with metastatic lung adenocarcinoma
207                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-exome sequencing of 75 tumor/normal NSCLC pairs treated with PD-1 plus CTLA-4 blockade..
208                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 IMPACT sequencing of 240 NSCLC tumor/normal pairs treated at MSKCC with anti-PD-(L)1 based therapy.
209                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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.
210                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted next-generation sequencing of 41 NSCLC samples.
211                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of tumor-normal tissue pairs from 16 non-small cell lung cancer samples.
212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       IMPACT sequencing of 105 High Risk Nonmuscle Invasive Bladder Cancer samples.
213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 40 oral squamous cell carcinoma tumor/normal sample pairs.
214                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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.
215                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
216                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
217                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-exome sequencing of 660 lung ADC and 484 lung SqCC tumor/normal pairs.
218                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 99 pancreatic samples and their matched normals.
219                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole-genome and deep-exome sequencing analysis of 456 pancreatic ductal adenocarcinomas
220                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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.
221                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
222                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
223                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients.
224                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome sequencing of 98 pancreatic neuroendocrine tumours (PanNETs) and matched normal DNA pairs.
225                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome and whole genome sequencing of 496 papillary thyroid carcinoma tumor/normal pairs
226 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
227                                   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>
228                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
229                                           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>
230                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-genome/exome sequencing of 961 Pediatric Cancer samples. Data generated from Pfister Lab & DKFZ/German Cancer Consortium.
231                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 103 samples (88 with matched normals) from 88 high-risk pediatric cancer patients.
232                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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>
233                               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>
234                                           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>
235                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of 178 Pheochromocytoma or Paraganglioma tumor/normal pairs.
236                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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.
237                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
238                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-genome sequencing of 96 pilocytic astrocytoma tumor/normal pairs. Conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
239                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) tumor/normal pairs.
240                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 341 cancer genes from 117 patient-derived PDTCs and ATCs
241                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome sequencing of 19 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
242                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome sequencing of 57 prostate tumor and matches normal tissues.
243                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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.
244                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole-genome/exome sequencing of 477 prostate samples from CPC-GENE and public data sets, including TCGA-PRAD.
245                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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.
246                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 1465 prostate adenocarcinoma tumor/normal pairs via MSK-IMPACT.
247                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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>.
248                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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>.
249                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome Sequencing of 1013 prostate cancer samples and their matched normals.
250                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome and transcriptome sequencing of 65 Prostate Adenocarcinoma  tumor/normal pairs.
251                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
252                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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.
253                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
254                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Exome sequencing of 12 advanced prostate cancer samples and matched organoids
255                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole genome and transcriptome sequencing of tumor/normal pairs from 292 prostate cancer patients.
256                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     MSK-IMPACT Sequencing of 18 prostate cancer tumor/normal pairs.
257                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        IMPACT sequencing of 504 prostate cancer tumor/normal pairs.
258                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Germline RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in homologous recombination-deficient tumors
259                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 2,069 prostate cancers from different races via MSK-IMPACT.
260                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 MSK-IMPACT targeted sequencing of matched rectal cancer tumor and tumoroid samples.
261                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
262                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome and/or whole genome sequencing of 106 clear cell renal cell carcinoma tumor/normal pairs.
263                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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.
264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted sequencing of 83 Retinoblastoma tumor-normal pairs via MSK-IMPACT. Genomic data provided is limited to somatic alterations.
265                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Cell-free DNA profiling in 14 retinoblastoma patients with advanced intraocular disease: An MSKCC experience
266                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole-genome sequencing of tumor-normal sample pairs from 40 patients with Malignant Rhabdoid Cancer.
267                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-genome or whole-exome sequencing of 43 rhabdomyosarcoma tumor/normal pairs.
268                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             MSK-IMPACT sequencing of 86 patients with HER2- and HER3-mutant cancers
269                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Sanger-sequenced 226 protein-coding genes (3,849 exons and adjacent intronic) on 207 samples (with 205 matched normals) encompassing 7 major sarcoma subtypes.
270                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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.
271                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
272                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-exome sequencing of 121 melanoma samples with matched normals.
273                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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.
274                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
275                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Exome sequencing of 147 melanoma samples with 99 matched normals.
276                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome Sequencing of tumors (with matched normals) from 45 patients with BRAFV600-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy.
277                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted sequencing of 12 SCCO paired tumor and normal samples.
278                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive whole exam profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
279                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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.
280                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome sequencing of 120 small cell lung cancer(SCLC) tumour samples and matched normal material.
281                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole Exome Sequencing of 10 paired chemosensitive and chemoresistant SCLC PDX.
282                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of tumor/normal pairs from 15 vulvar squamous cell carcinomas.
283                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole genome sequencing of 100 gastric cancer tumor-normal pairs from the University of Hong Kong and Pfizer.
284                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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.
285                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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>.
286                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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>.
287                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples (with matched normals) from the University of Tokyo.
288                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Exome sequencing of 22 gastric cancer samples with matched normals.
289                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Genomic and survival data from 1661 tumor-normal pairs from 1661 patients with various cancer types sequenced with the MSK-IMPACT assay.
290                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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.
291                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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>.
292                                                                                                                                                                                                                                                                                          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.
293                                                                                                                                                                                                                                                                                                                                                                                                     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.
294                                                                                  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.
295                                                                                                                                                                                                                                                                                                                                                                                          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.
296                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of tumor and PDX thoracic samples.
297                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted sequencing of thoracic PDX lines to characterize genetic alterations in 138 tumor/normal pairs via MSK-IMPACT. Data generated in Charles Rudin Lab.
298                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 28 thymic epithelial tumors (TETs) with matched normals
299                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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.
300                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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.
302                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
303                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Tumors with TRK fusions based on MSK-IMPACT targeted sequencing.
304                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 62 high-grade primary Unclassified Renal Cell Carcinoma tumor samples with matched normals.
305                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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.
306                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing (37 samples) and RNA-seq analysis (32 samples) of 47 upper tract urothelial carcinoma patients.
307                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome sequencing of 30 upper-tract urothelial carcinoma patients and their matched normals.
308                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Targeted Sequencing of 119 upper tract urothelial carcinoma tumor/normal pairs.
309                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           MSK-IMPACT sequencing of 34 upper tract urothelial patients and the matching PDX or PDC generated from 17 patient tumors.
310                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole-exome sequencing of 72 tumor samples (with 32 matched normals) in Urothelial Carcinoma.
311                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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">
312                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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.
313                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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>.
314                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of paired tumor-normal DNAs from 16 cases of clear cell endometrial tumors.
315                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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.
316                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
317                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
318                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Targeted Sequencing of 108 Uterine Sarcoma/Mesenchymal tumor/normal pairs from 107 patients.
319                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome or whole-exome sequencing of tumor/normal pairs from 28 uveal melanoma samples.
320                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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.
321                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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