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

> ### 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                    all_stjude_2016
3                      laml_tcga_pub
4       laml_tcga_pan_can_atlas_2018
5                          laml_tcga
6                      acyc_fmi_2014
7                      acyc_mda_2015
8                    acyc_mskcc_2013
9                   acyc_sanger_2013
10                   acbc_mskcc_2015
11       acc_tcga_pan_can_atlas_2018
12                          acc_tcga
13                    ampca_bcm_2016
14             blca_mskcc_solit_2014
15             blca_mskcc_solit_2012
16                blca_tcga_pub_2017
17      blca_plasmacytoid_mskcc_2016
18                          blca_bgi
19           blca_dfarber_mskcc_2014
20                     blca_tcga_pub
21      blca_tcga_pan_can_atlas_2018
22                         blca_tcga
23       lgg_tcga_pan_can_atlas_2018
24                          lgg_tcga
25                     brca_metabric
26                   breast_msk_2018
27                 bfn_duke_nus_2015
28                        brca_bccrc
29                        brca_broad
30                       brca_sanger
31                 brca_tcga_pub2015
32                     brca_tcga_pub
33      brca_tcga_pan_can_atlas_2018
34                         brca_tcga
35         brca_bccrc_xenograft_2014
36               cellline_ccle_broad
37      cesc_tcga_pan_can_atlas_2018
38                         cesc_tcga
39                    chol_nccs_2013
40                     chol_nus_2012
41      chol_tcga_pan_can_atlas_2018
42                         chol_tcga
43                   lcll_broad_2013
44                    cll_iuopa_2015
45                  cllsll_icgc_2011
46                 ccrcc_utokyo_2013
47                coadread_dfci_2016
48                coadread_genentech
49                 coadread_tcga_pub
50  coadread_tcga_pan_can_atlas_2018
51                     coadread_tcga
52                    coadread_mskcc
53                cscc_hgsc_bcm_2014
54                ctcl_columbia_2015
55                 cscc_dfarber_2015
56                     pact_jhu_2011
57                   desm_broad_2015
58                   dlbcl_dfci_2018
59                   dlbc_broad_2012
60                   dlbcl_duke_2017
61      dlbc_tcga_pan_can_atlas_2018
62                    nhl_bcgsc_2013
63                     ucec_msk_2018
64                        esca_broad
65      esca_tcga_pan_can_atlas_2018
66                         esca_tcga
67                         escc_icgc
68                    escc_ucla_2014
69                   es_iocurie_2014
70                 gbc_shanghai_2014
71                   egc_tmucih_2015
72                  nsclc_unito_2016
73                    prad_cpcg_2017
74                      gct_msk_2016
75                  gbm_tcga_pub2013
76                      gbm_tcga_pub
77       gbm_tcga_pan_can_atlas_2018
78                          gbm_tcga
79                        hnsc_broad
80                          hnsc_jhu
81                     hnsc_tcga_pub
82      hnsc_tcga_pan_can_atlas_2018
83                         hnsc_tcga
84               liad_inserm_fr_2014
85                hcc_inserm_fr_2015
86                   all_stjude_2013
87                   all_stjude_2015
88               panet_shanghai_2013
89                     chol_jhu_2013
90                     kich_tcga_pub
91      kich_tcga_pan_can_atlas_2018
92                         kich_tcga
93                          kirc_bgi
94                     kirc_tcga_pub
95      kirc_tcga_pan_can_atlas_2018
96                         kirc_tcga
97      kirp_tcga_pan_can_atlas_2018
98                         kirp_tcga
99                      lihc_amc_prv
100                       lihc_riken
101     lihc_tcga_pan_can_atlas_2018
102                        lihc_tcga
103                    lgg_ucsf_2014
104                       luad_broad
105                  luad_mskcc_2015
106                    luad_tcga_pub
107     luad_tcga_pan_can_atlas_2018
108                        luad_tcga
109                         luad_tsp
110                    lusc_tcga_pub
111     lusc_tcga_pan_can_atlas_2018
112                        lusc_tcga
113                        dlbc_tcga
114                     lung_msk_pdx
115                  msk_impact_2017
116                    lung_msk_2017
117                  prad_mskcc_2017
118                 mixed_allen_2018
119                      mpnst_mskcc
120                  plmeso_nyu_2015
121                 mcl_idibips_2013
122                   mbl_broad_2012
123                         mbl_icgc
124                         mbl_pcgp
125                mbl_sickkids_2016
126               skcm_broad_dfarber
127                  lgggbm_tcga_pub
128     meso_tcga_pan_can_atlas_2018
129                        meso_tcga
130                     egc_msk_2017
131                        prad_mich
132                   prad_su2c_2015
133                         mm_broad
134                   ccrcc_irc_2014
135                    brca_igr_2015
136                   mds_tokyo_2011
137                   cellline_nci60
138                     odg_msk_2017
139                  npc_nusingapore
140                     nbl_amc_2012
141                   nbl_broad_2013
142                nbl_ucologne_2015
143                    nepc_wcm_2016
144       skcm_vanderbilt_mskcc_2015
145                   nhl_bcgsc_2011
146               nsclc_pd1_msk_2018
147                  blca_nmibc_2017
148             hnsc_mdanderson_2013
149                      ov_tcga_pub
150       ov_tcga_pan_can_atlas_2018
151                          ov_tcga
152              mel_tsam_liang_2017
153            nsclc_tcga_broad_2016
154                        paad_icgc
155                paad_qcmg_uq_2016
156     paad_tcga_pan_can_atlas_2018
157                        paad_tcga
158                   paad_utsw_2015
159                   panet_jhu_2011
160                    thca_tcga_pub
161       all_phase2_target_2018_pub
162              aml_target_2018_pub
163            es_dfarber_broad_2014
164                mixed_pipseq_2017
165              nbl_target_2018_pub
166              pediatric_dkfz_2017
167               rt_target_2018_pub
168               wt_target_2018_pub
169     pcpg_tcga_pan_can_atlas_2018
170                        pcpg_tcga
171               thyroid_mskcc_2016
172                  pcnsl_mayo_2015
173                  prad_broad_2013
174                       prad_broad
175                prad_eururol_2017
176                       prad_fhcrc
177                       prad_mskcc
178                       prad_p1000
179                    prad_tcga_pub
180     prad_tcga_pan_can_atlas_2018
181                        prad_tcga
182                  prad_mskcc_2014
183 prad_mskcc_cheny1_organoids_2014
184                   hnc_mskcc_2016
185            nccrcc_genentech_2014
186                   mrt_bcgsc_2016
187                     rms_nih_2014
188                      summit_2018
189                       sarc_mskcc
190     sarc_tcga_pan_can_atlas_2018
191                        sarc_tcga
192                       skcm_broad
193     skcm_tcga_pan_can_atlas_2018
194                        skcm_tcga
195                        skcm_yale
196       skcm_broad_brafresist_2012
197                       scco_mskcc
198                       sclc_clcgp
199                         sclc_jhu
200               sclc_ucologne_2015
201     sclc_cancercell_gardner_2017
202                     vsc_cuk_2018
203            stad_pfizer_uhongkong
204                    stad_tcga_pub
205     stad_tcga_pan_can_atlas_2018
206                        stad_tcga
207                      stad_utokyo
208                   stad_uhongkong
209                    stes_tcga_pub
210                  urcc_mskcc_2016
211                     crc_msk_2018
212                  utuc_mskcc_2013
213                        tgct_tcga
214     tgct_tcga_pan_can_atlas_2018
215        angs_project_painter_2018
216       brca_mbcproject_wagle_2017
217                     tet_nci_2014
218     thym_tcga_pan_can_atlas_2018
219                        thym_tcga
220     thca_tcga_pan_can_atlas_2018
221                        thca_tcga
222                blca_cornell_2016
223                     ucs_jhu_2014
224      ucs_tcga_pan_can_atlas_2018
225                         ucs_tcga
226                    uccc_nih_2017
227                    ucec_tcga_pub
228     ucec_tcga_pan_can_atlas_2018
229                        ucec_tcga
230                     um_qimr_2016
231      uvm_tcga_pan_can_atlas_2018
232                         uvm_tcga
233                panet_arcnet_2017
234                   skcm_ucla_2016
235        past_dkfz_heidelberg_2013
236            hcc_msk_venturaa_2018
                                                                                                                name
1                                               Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
2                                                             Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2016)
3                                                                           Acute Myeloid Leukemia (TCGA, NEJM 2013)
4                                                                     Acute Myeloid Leukemia (TCGA, PanCancer Atlas)
5                                                                         Acute Myeloid Leukemia (TCGA, Provisional)
6                                                              Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
7                                                               Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
8                                                                   Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
9                                                                    Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
10                                                    Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
11                                                                  Adrenocortical Carcinoma (TCGA, PanCancer Atlas)
12                                                                      Adrenocortical Carcinoma (TCGA, Provisional)
13                                               Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016)
14                                                                             Bladder Cancer (MSKCC, Eur Urol 2014)
15                                                                                  Bladder Cancer (MSKCC, JCO 2013)
16                                                                                  Bladder Cancer (TCGA, Cell 2017)
17                                                      Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016)
18                                                                Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
19                                            Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discov 2014)
20                                                                  Bladder Urothelial Carcinoma (TCGA, Nature 2014)
21                                                              Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)
22                                                                  Bladder Urothelial Carcinoma (TCGA, Provisional)
23                                                                  Brain Lower Grade Glioma (TCGA, PanCancer Atlas)
24                                                                      Brain Lower Grade Glioma (TCGA, Provisional)
25                                                           Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
26                                                                             Breast Cancer (MSK, Cancer Cell 2018)
27                                                          Breast Fibroepithelial Tumors (Duke-NUS, Nat Genet 2015)
28                                                         Breast Invasive Carcinoma (British Columbia, Nature 2012)
29                                                                    Breast Invasive Carcinoma (Broad, Nature 2012)
30                                                                   Breast Invasive Carcinoma (Sanger, Nature 2012)
31                                                                       Breast Invasive Carcinoma (TCGA, Cell 2015)
32                                                                     Breast Invasive Carcinoma (TCGA, Nature 2012)
33                                                                 Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
34                                                                     Breast Invasive Carcinoma (TCGA, Provisional)
35                                                  Breast cancer patient xenografts (British Columbia, Nature 2014)
36                                                       Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
37                                                          Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
38                              Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
39                                          Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
40                                             Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
41                                                                        Cholangiocarcinoma (TCGA, PanCancer Atlas)
42                                                                            Cholangiocarcinoma (TCGA, Provisional)
43                                                                   Chronic Lymphocytic Leukemia (Broad, Cell 2013)
44                                                                 Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
45                                                                     Chronic lymphocytic leukemia (ICGA, Nat 2011)
46                                                         Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
47                                                               Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
48                                                                Colorectal Adenocarcinoma (Genentech, Nature 2012)
49                                                                     Colorectal Adenocarcinoma (TCGA, Nature 2012)
50                                                                 Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)
51                                                                     Colorectal Adenocarcinoma (TCGA, Provisional)
52                                                      Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
53                                             Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014)
54                                                            Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
55                                                    Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
56                                                            Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011
57                                                           Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
58                                                                Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018)
59                                                                  Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
60                                                                   Diffuse Large B-Cell Lymphoma (Duke, Cell 2017)
61                                                             Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)
62                                                                 Diffuse Large B-cell Lymphoma (BCGSC, Blood 2013)
63                                                                                    Endometrial Cancer (MSK, 2018)
64                                                                 Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
65                                                                 Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)
66                                                                          Esophageal Carcinoma (TCGA, Provisional)
67                                                            Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
68                                                         Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
69                                                                Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
70                                                                  Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
71                                                                        Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
72                   Genetic Characterization of NSCLC young adult patients ( University of Turin, Lung Cancer 2016)
73                                              Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
74                                       Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016).
75                                                                                    Glioblastoma (TCGA, Cell 2013)
76                                                                                  Glioblastoma (TCGA, Nature 2008)
77                                                                   Glioblastoma Multiforme (TCGA, PanCancer Atlas)
78                                                                       Glioblastoma Multiforme (TCGA, Provisional)
79                                                       Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
80                                               Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
81                                                         Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
82                                                     Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
83                                                         Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
84                                                                 Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
85                                                                Hepatocellular Carcinomas (Inserm, Nat Genet 2015)
86                                                     Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
87                                      Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
88                                                                            Insulinoma (Shanghai, Nat Commun 2013)
89                                        Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
90                                                                       Kidney Chromophobe (TCGA, Cancer Cell 2014)
91                                                                        Kidney Chromophobe (TCGA, PanCancer Atlas)
92                                                                            Kidney Chromophobe (TCGA, Provisional)
93                                                           Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
94                                                             Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
95                                                         Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)
96                                                             Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
97                                                     Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)
98                                                         Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
99                                                             Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
100                                                           Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
101                                                           Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)
102                                                               Liver Hepatocellular Carcinoma (TCGA, Provisional)
103                                                                          Low-Grade Gliomas (UCSF, Science 2014).
104                                                                           Lung Adenocarcinoma (Broad, Cell 2012)
105                                                                                 Lung Adenocarcinoma (MSKCC 2015)
106                                                                          Lung Adenocarcinoma (TCGA, Nature 2014)
107                                                                      Lung Adenocarcinoma (TCGA, PanCancer Atlas)
108                                                                          Lung Adenocarcinoma (TCGA, Provisional)
109                                                                           Lung Adenocarcinoma (TSP, Nature 2008)
110                                                                 Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
111                                                             Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
112                                                                 Lung Squamous Cell Carcinoma (TCGA, Provisional)
113                                              Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
114                                                                              MSK Thoracic PDX (MSK, Provisional)
115                                                      MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
116                     MSK-IMPACT Clinical Sequencing Cohort for Non-Small Cell Cancer (MSK, Cancer Discovery 2017)
117                      MSK-IMPACT Clinical Sequencing Cohort in Prostate Cancer (MSK, JCO Precision Oncology 2017)
118                                                                         MSS Mixed Solid Tumors (Van Allen, 2018)
119                                                  Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
120                                                            Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
121                                                                        Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
122                                                                             Medulloblastoma (Broad, Nature 2012)
123                                                                              Medulloblastoma (ICGC, Nature 2012)
124                                                                              Medulloblastoma (PCGP, Nature 2012)
125                                                                          Medulloblastoma (Sickkids, Nature 2016)
126                                                                        Melanoma (Broad/Dana Farber, Nature 2012)
127                                                                   Merged Cohort of LGG and GBM (TCGA, Cell 2016)
128                                                                             Mesothelioma (TCGA, PanCancer Atlas)
129                                                                                 Mesothelioma (TCGA, Provisional)
130                                                 Metastatic Esophagogastric Cancer (MSKCC, Cancer Discovery 2017)
131                                                           Metastatic Prostate Adenocarcinoma (MCTP, Nature 2012)
132                                                      Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015)
133                                                                       Multiple Myeloma (Broad, Cancer Cell 2014)
134                                  Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014)
135                                                   Mutational profiles of metastatic breast cancer (France, 2016)
136                                                                              Myelodysplasia (Tokyo, Nature 2011)
137                                                                        NCI-60 Cell Lines (NCI, Cancer Res. 2012)
138              NGS in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas tumors (MSK, Neuro Oncol 2017)
139                                                             Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
140                                                                       Neuroblastoma (AMC Amsterdam, Nature 2012)
141                                                                             Neuroblastoma (Broad Institute 2013)
142                                                                            Neuroblastoma (Broad, Nat Genet 2013)
143                                                       Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
144 Next generation sequencing (NGS) of pre-treatment metastatic melanoma samples (MSK, JCO Precision Oncology 2017)
145                                                                        Non-Hodgkin Lymphoma (BCGSC, Nature 2011)
146                                                                       Non-Small Cell Lung Cancer (MSK, JCO 2018)
147                                                            Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017)
148                                                   Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
149                                                            Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
150                                                        Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)
151                                                            Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
152                                                Paired-exome sequencing of acral melanoma (TGEN, Genome Res 2017)
153                                                                           Pan-Lung Cancer (TCGA, Nat Genet 2016)
154                                                                    Pancreatic Adenocarcinoma (ICGC, Nature 2012)
155                                                                    Pancreatic Adenocarcinoma (QCMG, Nature 2016)
156                                                                Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)
157                                                                    Pancreatic Adenocarcinoma (TCGA, Provisional)
158                                                                        Pancreatic Cancer (UTSW, Nat Commun 2015)
159                                        Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
160                                                                    Papillary Thyroid Carcinoma (TCGA, Cell 2014)
161                                                      Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018)
162                                                                  Pediatric Acute Myeloid Leukemia (TARGET, 2018)
163                                                               Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
164                                                                            Pediatric Mixed Tumors (PIP-Seq 2017)
165                                                                           Pediatric Neuroblastoma (TARGET, 2018)
166                                                    Pediatric Pan-Cancer (DKFZ - German Cancer Consortium,  2017)
167                                                                          Pediatric Rhabdoid Tumor (TARGET, 2018)
168                                                                            Pediatric Wilms' Tumor (TARGET, 2018)
169                                                       Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)
170                                                           Pheochromocytoma and Paraganglioma (TCGA, Provisional)
171                                           Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
172                                      Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
173                                                               Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
174                                                          Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
175                                                                          Prostate Adenocarcinoma (EurUrol, 2017)
176                                                      Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
177                                                                Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
178                                                       Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018)
179                                                                        Prostate Adenocarcinoma (TCGA, Cell 2015)
180                                                                  Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
181                                                                      Prostate Adenocarcinoma (TCGA, Provisional)
182                                                             Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
183                                                             Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
184                                             Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016)
185                                                       Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
186                                                                        Rhabdoid Cancer (BCGSC, Cancer Cell 2016)
187                                                                       Rhabdomyosarcoma (NIH, Cancer Discov 2014)
188                                                                                            SUMMIT (Nature, 2018)
189                                                                            Sarcoma (MSKCC/Broad, Nat Genet 2010)
190                                                                                  Sarcoma (TCGA, PanCancer Atlas)
191                                                                                      Sarcoma (TCGA, Provisional)
192                                                                       Skin Cutaneous Melanoma (Broad, Cell 2012)
193                                                                  Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)
194                                                                      Skin Cutaneous Melanoma (TCGA, Provisional)
195                                                                   Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
196                                                               Skin Cutaneous Melanoma(Broad, Cancer Discov 2014)
197                                                        Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
198                                                                   Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
199                                                           Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
200                                                                  Small Cell Lung Cancer (U Cologne, Nature 2015)
201                                                                    Small-Cell Lung Cancer (Multi-Institute 2017)
202                                                     Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)
203                                                          Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
204                                                                       Stomach Adenocarcinoma (TCGA, Nature 2014)
205                                                                   Stomach Adenocarcinoma (TCGA, PanCancer Atlas)
206                                                                       Stomach Adenocarcinoma (TCGA, Provisional)
207                                                                 Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
208                                                                     Stomach Adenocarcinoma (UHK, Nat Genet 2011)
209                                                      TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
210           Targeted gene sequencing in 62 high-grade primary Unclassified Renal Cell Carcinoma (MSK, Nature 2016)
211            Targeted sequencing of 1134 samples from metastatic colorectal cancer samples (MSK, Cancer Cell 2018)
212                                Targeted sequencing of upper tract urothelial cancer samples (MSK, Eur Urol 2013)
213                                                                  Testicular Germ Cell Cancer (TCGA, Provisional)
214                                                              Testicular Germ Cell Tumors (TCGA, PanCancer Atlas)
215                                                           The Angiosarcoma Project (Provisional, September 2018)
216                                                 The Metastatic Breast Cancer Project (Provisional, October 2018)
217                                                                   Thymic Epithelial Tumors (NCI, Nat Genet 2014)
218                                                                                  Thymoma (TCGA, PanCancer Atlas)
219                                                                                      Thymoma (TCGA, Provisional)
220                                                                        Thyroid Carcinoma (TCGA, PanCancer Atlas)
221                                                                            Thyroid Carcinoma (TCGA, Provisional)
222                                                              Urothelial Carcinoma (Cornell/Trento, Nat Gen 2016)
223                                               Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
224                                                                   Uterine Carcinosarcoma (TCGA, PanCancer Atlas)
225                                                                       Uterine Carcinosarcoma (TCGA, Provisional)
226                                                                  Uterine Clear Cell Carcinoma (NIH, Cancer 2017)
227                                                         Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
228                                                     Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
229                                                         Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
230                                                                           Uveal Melanoma (QIMR, Oncotarget 2016)
231                                                                           Uveal Melanoma (TCGA, PanCancer Atlas)
232                                                                               Uveal Melanoma (TCGA, Provisional)
233                                       Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (Nature, 2017)
234                                    Whole-exome sequences (WES) of pretreatment melanoma tumors (UCLA, Cell 2016)
235                                       Whole-genome sequencing of pilocytic astrocytomasatic (Nat Genetics, 2013)
236                                                                                    miRNAs in HCA/HCC (MSK, 2018)
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1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Mutation data from whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation.
2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-genome and/or whole-exome sequencing was performed for ERG-altered B-ALL cases.
3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCGA Acute Myeloid Leukemia, analysis of 200 adult cases; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LAML&diseaseName=Acute%20Myeloid%20Leukemia">NCI</A>.
4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Acute Myeloid Leukemia; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LAML/20160128/gdac.broadinstitute.org_LAML.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive genomic profiling of 28 metastatic ACCs.
7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients).
8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome or whole-genome sequencing analysis of 60 ACC tumor/normal pairs
9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole exome sequencing of 24 ACCs.
10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 12 breast AdCCs.
11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Adrenocortical Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <A HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/ACC/20160128/gdac.broadinstitute.org_ACC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Mutation data from 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).
14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014).
15                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive profiling of 97 bladder cancer samples, including targeted sequencing of 15 cancer genes. Iyer et al., JCO in press.
16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive analysis of muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms.
17                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genomic profiling of plasmacytoid-variant (signet ring cell) tumors of the bladder, published set
18                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome and whole-genome sequencing of 99 bladder cancer samples. Generated by BGI.
19                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of 50 patients with muscle invasive urothelial carcinoma
20                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Bladder Cancer, containing 131 samples; raw data at the NCI.
21                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
22                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Bladder Urothelial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BLCA/20160128/gdac.broadinstitute.org_BLCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
23                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
24                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Brain Lower Grade Glioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LGG/20160128/gdac.broadinstitute.org_LGG.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
25                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          The genomic profiles (somatic mutations [targeted sequencing], copy number alterations, and gene expression) of 2509 breast cancers.
26                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted Sequencing of 1918 tumor and patient-matched normals.
27                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing of 22 phyllodes tumors
28                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 65 breast cancer samples. Generated by the British Columbia Cancer Research Centre.
29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 103 breast cancer samples. Generated by the Broad Institute.
30                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive profiling of 100 breast cancer samples. Generated by the Sanger Institute.
31                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 817 cases (TCGA Cell 2015).
32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <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>.
33                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
34                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Breast Invasive Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
35                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Dynamics of genomic clones in breast cancer patient xenografts.
36                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, containing 1020 samples.
37                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/CESC/20160128/gdac.broadinstitute.org_CESC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
39                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Exome sequencing of 15 cholangiocarcinoma cases from the National Cancer Centre of Singapore to study the somatic mutations.
40                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
41                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
42                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Cholangiocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/CHOL/20160128/gdac.broadinstitute.org_CHOL.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
43                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Exome sequencing of 160 CLL samples. Generated by the Broad Institute.
44                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Mutation data from whole-genome or whole-exome sequencing (WGS/WXS) of 428 CLL, 54 MBL, and 24 SLL samples.
45                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome Sequencing of CLL samples.
46                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Mutation data from whole genome and/or whole exome sequencing of 106 clear-cell renal cell carcinoma samples.
47                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations.
48                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive profiling of 72 colon cancer samples. Generated by Genentech.
49                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Colorectal Cancer project. <br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/coadread_2012/">Raw data via the TCGA Data Portal</a>.
50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
51                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCGA Colorectal Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COADREAD/20160128/gdac.broadinstitute.org_COADREAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
52                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Colon Trios data from 69 Patients each with a  primary and metastatic tumor. (Primary / Met) (David Solit / Evi Vakiani / Michael Berger, MSKCC)
53                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 39 cases aggressive cutaneous squamous cell carcinoma.
54                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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).
55                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 504 cancer-associated genes in 29 cutaneous squamous cell carcinoma samples
56                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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).
57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Mutation data from Exome/Whole Genome sequencing of 20 desmoplastic melanoma cases.
58                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-exome sequencing of tumor/matching normal sample pairs from 135 DLBCL patients.
59                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 58 DLBCL samples.
60                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Genomic profiling of 1,001 DLBCL patients, mutations reported in only 150 driver genes.
61                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
62                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole genome sequencing analysis of 40 DLBCL tumors and 13 cell lines.
63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Clinical Utility Of Prospective Molecular Characterization In Advanced Endometrial Cancer
64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Comprehensive profiling of 149 esophageal adenocarcinoma samples from the Broad Institute.
65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
66                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Esophageal Carcinoma ; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/ESCA/20160128/gdac.broadinstitute.org_ESCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              WGS and WES of 88 esophageal squamous cell carcinoma samples. Generated by ICGC.
68                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
69                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Mutation data from whole-genome sequencing of 112 Ewing sarcoma samples and matched germ line DNA. <a href="http://cancerdiscovery.aacrjournals.org/content/4/11/1342/suppl/DC1">
70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Mutation data from whole exome sequencing of 32 gallbladder carcinoma tumors with paired normals
71                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing on 78 Gastric Adenocarcinoma of differing histologies and anatomic locations
72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         The retrospective study using NGS approach for genetic characterization of NSCLC young adult patients
73                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Comprehensive genomic profiling of 477 Prostate Adenocarcinoma samples from CPC-GENE and public data sets, including TCGA-PRAD.
74                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 180 germ cell tumor samples.
75                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project.<br> <a href="http://tcga-data.nci.nih.gov/tcga/">Raw data via the TCGA Data Portal</a>.
76                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project. 206 primary glioblastoma samples.<br> <a href="https://tcga-data.nci.nih.gov/docs/publications/gbm_2008/">Raw data via the TCGA Data Portal</a>.
77                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
78                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Glioblastoma Multiforme; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/GBM/20160128/gdac.broadinstitute.org_GBM.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
79                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive profiling of 74 head and neck squamous cell carcinoma samples from the Broad Institute.
80                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Comprehensive profiling of 32 head and neck squamous cell carcinoma samples from Johns Hopkins.
81                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Head and Neck Squamous Cell Carcinoma, containing 279 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=HNSC&diseaseName=Head and Neck Squamous Cell Carcinoma">NCI</A>.
82                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
83                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Head and Neck Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/HNSC/20160128/gdac.broadinstitute.org_HNSC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
84                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Mutation data from whole-exome sequencing (WXS) of 46 liver tumor and corresponding nontumor DNA.
85                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Mutation data from whole-exome sequencing (WXS) of 243 liver tumors identified mutational signatures associated with specific risk factors.
86                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Exome sequencing of 44 ALL samples.
87                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole genome sequencing (WGS) of 22 infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) cases
88                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole exome sequencing of 10 benign insulinoma tumors. <A HREF="http://www.nature.com/ncomms/2013/131210/ncomms3810/extref/ncomms3810-s1.pdf">
89                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome Sequencing of 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
90                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KICH&diseaseName=Kidney Chromophobe">NCI</A>.
91                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
92                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KICH/20160128/gdac.broadinstitute.org_KICH.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
93                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive sequencing of 98 clear cell kidney cancer samples. Generated by BGI-Shenzhen.
94                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Kidney Renal Clear Cell Carcinoma, containing 499 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KIRC&diseaseName=Kidney Renal Clear Cell Carcinoma">NCI</A>.
95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
96                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Kidney Renal Clear Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRC/20160128/gdac.broadinstitute.org_KIRC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
97                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
98                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Kidney Renal Papillary Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRP/20160128/gdac.broadinstitute.org_KIRP.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
99                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Liver Hepatocellular Carcinoma from Asan Medical Center, Korea, containing 231 samples.
100                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-genome sequencing of 27 hepatocellular carcinoma samples from RIKEN.
101                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
102                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA Liver Hepatocellular Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LIHC/20160128/gdac.broadinstitute.org_LIHC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from whole exome sequencing of 23 grade II glioma patients.
104                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 183 lung adenocarcinoma samples. Generated by the Broad Institute.
105                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of non small cell lung cancers treated with pembrolizumab
106                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCGA Lung Adenocarcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LUAD&diseaseName=Lung Adenoarcinoma">NCI</A>.
107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
108                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Lung Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
109                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 163 lung adenocarcinoma samples. Generated by WashU/Broad.
110                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Lung Squamous Cell Carcinoma project. 178 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/lusc_2012/">Raw data via the TCGA Data Portal</a>.
111                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
112                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Lung Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUSC/20160128/gdac.broadinstitute.org_LUSC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/DLBC/20160128/gdac.broadinstitute.org_DLBC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
114                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Targeted sequencing of thoracic PDX lines to characterize genetic alterations clinical MSK-IMPACT cases. Data generated in Charles Rudin Lab.
115                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
116                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Prospective molecular characterization of lung adenocarcinomas for efficient patient matching.
117                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted sequencing of clinical cases via MSK-IMPACT for prostate cancer (Abida et al, JCO Precision Oncology 2017).
118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing molecular profiling of tumors across multiple cancer types including melanoma, non-small cell lung cancer, head and neck cancer, and bladder cancer. Generated by the Van Allen Lab, 2018.
119                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome profiling of 17 malignant peripheral nerve sheath tumors.
120                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Mutation data from whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) and matched blood samples.
121                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 29 primary mantle cell lymphomas.
122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 92 medulloblastoma samples from the Broad Institute.
123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive profiling of 125 matched tumor and germline medulloblastoma samples
124                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole genome sequencing of 37 medulloblastoma samples from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University.
125                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from whole-genome sequencing (WGS) of 46 recurrent medulloblastoma samples.
126                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Somatic Mutation data from 25 Whole Genome Sequenced metastatic melanoma samples
127                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing from TCGA LGG and GBM cases
128                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
129                                                                                                                                                                                                                                                                                                                                                    TCGA Mesothelioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data at the <A HREF="https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-MESO%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_format%22,%22value%22:%5B%22MAF%22%5D%7D%7D%5D%7D">GDC</A>.
130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Prospective genomic profiling of 341 samples from 305 metastatic esophagogastric cancer patients
131                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Comprehensive profiling of 61 prostate cancer samples, including 50 metastatic CRPCs and 11 high-grade localized prostate cancers. Generated by Arul Chinnaiyan's and Scott Tomlins' labs at the University of Michigan.
132                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive analysis of 150 metastatic prostate cancer samples by the SU2C/PCF Dream Team
133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome/genome sequencing of paired tumor/normal samples from multiple myeloma patients
134                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Mutation data from multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
135                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole-exome sequencing was performed on 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.
136                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 29 myelodysplasia samples from the University of Tokyo.
137                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Genomic characterization using next generation sequencing (NGS) in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.
139                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome sequencing of 56 NPC tumor / normal pairs. Generated by the Cancer Science Institute of Singapore, National University of Singapore.
140                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole genome sequencing of 87 neuroblastoma samples from the Academic Medical Center, Amsterdam.
141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole Genome and Whole Exome sequencing of 240 high-risk neuroblastoma cases.
142                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Mutation data from whole-genome sequencing of 56 neuroblastoma samples
143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome and RNA Seq data of castration resistant adenocarcinoma and castration resistant neuroendocrine prostate cancer (somatic mutations and copy number aberrations)
144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Next generation sequencing (NGS) of pre-treatment tumor to identify co-altered genes that predict for intrinsic resistance to BRAF inhibitor therapy in melanoma patients as a prelude to rational combination strategies.
145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole Genome/Exome sequencing of 14 NHL cases.
146                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               NGS sequencing of 240 NSCLC cases treated at MSKCC with anti-PD-(L)1 based therapy using the MSK-IMPACT assay.
147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genomic Landscape and Predictors of Response for High Risk NMIBC
148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive profiling of 40 oral squamous cell carcinoma samples from MD Anderson.
149                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <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>.
150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   TCGA Ovarian Serous Cystadenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/OV/20160128/gdac.broadinstitute.org_OV.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive genomic and transcriptomic analysis of ALM patients.
153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
154                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive profiling of 99 pancreatic cancer samples. Generated by ICGC.
155                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              342 primary tumours and 41 patient-derived cell lines underwent whole genome sequencing (WGS) when tumor cellularity was >40% (nâ??=â??179), or deep-exome sequencing (nâ??=â??204) for samples with a cellularity of 12â??40%.
156                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Pancreatic Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PAAD/20160128/gdac.broadinstitute.org_PAAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
158                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. <A HREF="https://www.sciencemag.org/content/331/6021/1199/suppl/DC1">
160                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       TCGA Papillary Thyroid Carcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=THCA&diseaseName=Thyroid%20carcinoma">NCI</A>.
161              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
162              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>
163                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
164                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 101 high-risk pediatric cancer patients
165                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>
166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive genomic profiling of 961 Pediatric Cancer samples. Data generated from Pfister Lab & DKFZ/German Cancer Consortium.
167 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>
168        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>
169                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
170                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA Pheochromocytoma and Paraganglioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PCPG/20160128/gdac.broadinstitute.org_PCPG.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
171                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, J Clin Invest 2016)
172                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Mutation data from whole exome sequencing (WXS) of 19 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
173                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 57 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
174                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive profiling of 112 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
175                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome and Transcriptome Sequencing of 65 Prostate Adenocarcinoma Patients. Generated by the Sun Lab 2017.
176                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of prostate cancer samples. Generated by Peter Nelson's lab at the Fred Hutchinson Cancer Research Center.
177                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  MSKCC Prostate Oncogenome Project. 181 primary, 37 metastatic prostate cancer samples, 12 prostate cancer cell lines and xenografts.<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>.
178                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole Exome Sequencing of 1013 prostate cancer samples.
179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Integrated profiling of 333 primary prostate adenocarcinoma samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/prad_2015/">NCI</A>.
180                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
181                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Prostate Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PRAD/20160128/gdac.broadinstitute.org_PRAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
182                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Copy-number profiling of 103 primary prostate cancer samples from MSKCC. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54691">Raw data via GEO (GSE54691)</a>.
183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome profiling of prostate cancer samples and matched organoids.
184                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome sequencing of 139 Renal Non-Clear Cell Carcinoma (NCCRCC) samples.
186                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole-genome sequencing of tumor-normal sample pairs from 40 patients with Malignant Rhabdoid Cancer.
187                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Mutation data from WGS and/or WXS of 43 rhabdomyosarcoma samples.
188                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Findings of a multi-histology, genomically selected, 'basket' study utilizing the pan-HER kinase inhibitor neratinib.
189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            The Sarcoma Genome Project, <a href="http://www.mskcc.org/">MSKCC</a> and <a href="http://www.broadinstitute.org/">The Broad Institute</a>. 207 high-grade adult soft tissue sarcomas across seven subtypes of disease.<br> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21124">Raw data via GEO (GSE21124)</a>.
190                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
191                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TCGA Sarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/SARC/20160128/gdac.broadinstitute.org_SARC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
192                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of 121 melanoma samples. Generated by the Broad Institute.
193                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
194                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Skin Cutaneous Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/SKCM/20160128/gdac.broadinstitute.org_SKCM.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
195                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Exome sequencing of 91 melanoma samples. Generated by Yale.
196                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Sequencing of 44 melanoma patients pre and post vemurafenib treatment. Generated by the Broad Institute.
197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Targeted sequencing of 12 SCCO samples.
198                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
199                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 36 primary human SCLC tumors and 17 matched SCLC and lymphoblastoid cell lines. Generated by Johns Hopkins.
200                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Comprehensive WGS profiling of 110 human SCLC specimens.
201                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole Exome Sequencing of paired chemosensitive and chemoresistant SCLC PDX.
202                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of tumor/normal pairs from 15 vulvar squamous cell carcinomas.
203                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole genome sequencing of 100 tumor-normal pairs from the University of Hong Kong and Pfizer.
204                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Stomach Adenocarcinoma, containing 295 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
205                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Stomach Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/STAD/20160128/gdac.broadinstitute.org_STAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
207                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples from the University of Tokyo.
208                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Exome sequencing of 22 gastric cancer samples.
209                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA data for Esophagus-Stomach Cancers.
210                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Molecular Analysis of Unclassified Renal Cell Carcinoma
211                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Genomic Characterization using next-generation sequencing of Upper Tract Urothelial Carcinoma.
213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Testicular Germ Cell Cancer; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/TGCT/20160128/gdac.broadinstitute.org_TGCT.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
214                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
215                                                                                                                                                                                                                                                                                                                                                                                                                      The Angiosarcoma Project is a patient-driven initiative. 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, 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.ascproject.org. Questions about these data can be directed to data@ascproject.org.
216                                                                                                                                                                             The Metastatic Breast Cancer Project is a patient-driven initiative. This study includes genomic data, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). All of the titles and descriptive text for the clinical data elements have been finalized in partnership with numerous patients in the project. 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.mbcproject.org. For questions about these data, including how to cite, please visit www.mbcproject.org/data-release or direct questions to data@mbcproject.org.
217                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 28 thymic epithelial tumors.
218                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
219                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TCGA Thymoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THYM/20160128/gdac.broadinstitute.org_THYM.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
220                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
221                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Thyroid Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THCA/20160128/gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
222                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-exome sequencing (Illumina HiSeq 2500) of 72 tumor samples in Urothelial Carcinoma.
223                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing (WXS) of 22 uterine carcinosarcoma/uterine malignant mixed Mullerian (UCS) tumors. <A HREF="http://www.nature.com/ncomms/2014/140919/ncomms6006/extref/ncomms6006-s1.pdf">
224                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
225                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Uterine Carcinosarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UCS/20160128/gdac.broadinstitute.org_UCS.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
226                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole exome sequencing of paired tumor-normal DNAs from 16 cases of clear cell endometrial tumors.
227                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Integrative genomic analysis of 373 endometrial carcinomas. TCGA Uterine Corpus Endometrial Carcinoma project; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/">NCI</A>.
228                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
229                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Uterine Corpus Endometrial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UCEC/20160128/gdac.broadinstitute.org_UCEC.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
230                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-genome or whole-exome sequencing of tumor/normal pairs from 28 uveal melanoma samples.
231                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive TCGA PanCanAtlas (https://gdc.cancer.gov/about-data/publications/pancanatlas) data from 11k cases and all TCGA tumor types (33). (PMID: 29625048, 29596782, 29622463, 29617662, 29625055, 29625050)
232                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Uveal Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>; source mutation data from <a HREF="http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/UVM/20160128/gdac.broadinstitute.org_UVM.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz">GDAC Firehose</A>.
233                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-genome sequencing of 102 primary PanNETs and the defined genomic events that characterize their pathogenesis.
234                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Genetic Characterization of 38 pretreatment (pembrolizumab and nivolumab) melanoma tumors.
235                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-genome sequencing of 96 pilocytic astrocytomasatic alterations in pilocytic astrocytoma conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
236                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Sequencing of miRNAs from hepatocellular carcinomas, hepatocellular adenomas and paired.
> 
> # 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)
                    BRCA1 BRCA2
SJBALL020595_D1       NaN   NaN
SJERG005_D            NaN   NaN
SJERG023_D_WES        NaN   NaN
SJERG028_D_WES        NaN   NaN
SJERG007_D_WES        NaN   NaN
SJERG020309_D1        NaN   NaN
SJBALL021405_D1_WES   NaN   NaN
SJBALL021514_D1_WES   NaN   NaN
SJBALL021372_D1_WES   NaN   NaN
SJERG016_D_WES        NaN   NaN
SJERG020305_D1        NaN   NaN
SJBALL021130_D1       NaN   NaN
SJBALL021324_D1_WES   NaN   NaN
SJBALL020340_D1       NaN   NaN
SJERG020050_D1_WES    NaN   NaN
SJBALL241_D_WES       NaN   NaN
SJBALL021427_D1_WES   NaN   NaN
SJERG018_D_WES        NaN   NaN
SJERG020303_D1        NaN   NaN
SJERG029_D_WES        NaN   NaN
SJBALL021336_D1_WES   NaN   NaN
SJERG020306_D1        NaN   NaN
SJERG021_D_WES        NaN   NaN
SJBALL021299_D1_WES   NaN   NaN
SJERG010_D            NaN   NaN
SJBALL020469_D1       NaN   NaN
SJERG020308_D1        NaN   NaN
SJERG020304_D1        NaN   NaN
SJERG020_D_WES        NaN   NaN
SJERG020053_D1_WES    NaN   NaN
SJBALL021512_D1_WES   NaN   NaN
SJERG020299_D1        NaN   NaN
SJERG031_D            NaN   NaN
SJERG006_D            NaN   NaN
SJERG020300_D1        NaN   NaN
SJERG020307_D1        NaN   NaN
SJERG026_D            NaN   NaN
SJERG001_D_WES        NaN   NaN
SJBALL218_D_WES       NaN   NaN
SJBALL227_D_WES       NaN   NaN
SJERG014_D_WES        NaN   NaN
SJERG002_D            NaN   NaN
SJBALL021081_D1_WES   NaN   NaN
SJERG030_D_WES        NaN   NaN
SJBALL021333_D1_WES   NaN   NaN
SJERG019_D_WES        NaN   NaN
SJBALL020635_D1       NaN   NaN
SJBALL020383_D1_WES   NaN   NaN
SJBALL087_D_WES       NaN   NaN
SJERG004_D_WES        NaN   NaN
SJERG013_D_WES        NaN   NaN
SJERG017_D_WES        NaN   NaN
SJERG020052_D1        NaN   NaN
SJERG020051_D1_WES    NaN   NaN
SJBALL215_D_WES       NaN   NaN
SJBALL020828_D1       NaN   NaN
SJERG022_D_WES        NaN   NaN
SJBALL230_D_WES       NaN   NaN
SJBALL021511_D1_WES   NaN   NaN
SJBALL199_D_WES       NaN   NaN
SJERG020054_D1_WES    NaN   NaN
SJERG020302_D1        NaN   NaN
SJERG008_D_WES        NaN   NaN
SJERG020_D            NaN   NaN
SJBALL021492_D1_WES   NaN   NaN
SJERG020051_D1        NaN   NaN
SJERG009_D            NaN   NaN
SJERG025_D_WES        NaN   NaN
SJERG003_D_WES        NaN   NaN
SJERG011_D            NaN   NaN
SJERG024_D            NaN   NaN
SJERG028_D            NaN   NaN
SJERG016_D            NaN   NaN
> 
> # Get data slice for a single gene
> getProfileData(mycgds,'HMGA2',mygeneticprofile,mycaselist)
                    HMGA2
SJBALL020595_D1       NaN
SJERG005_D            NaN
SJERG023_D_WES        NaN
SJERG028_D_WES        NaN
SJERG007_D_WES        NaN
SJERG020309_D1        NaN
SJBALL021405_D1_WES   NaN
SJBALL021514_D1_WES   NaN
SJBALL021372_D1_WES   NaN
SJERG016_D_WES        NaN
SJERG020305_D1        NaN
SJBALL021130_D1       NaN
SJBALL021324_D1_WES   NaN
SJBALL020340_D1       NaN
SJERG020050_D1_WES    NaN
SJBALL241_D_WES       NaN
SJBALL021427_D1_WES   NaN
SJERG018_D_WES        NaN
SJERG020303_D1        NaN
SJERG029_D_WES        NaN
SJBALL021336_D1_WES   NaN
SJERG020306_D1        NaN
SJERG021_D_WES        NaN
SJBALL021299_D1_WES   NaN
SJERG010_D            NaN
SJBALL020469_D1       NaN
SJERG020308_D1        NaN
SJERG020304_D1        NaN
SJERG020_D_WES        NaN
SJERG020053_D1_WES    NaN
SJBALL021512_D1_WES   NaN
SJERG020299_D1        NaN
SJERG031_D            NaN
SJERG006_D            NaN
SJERG020300_D1        NaN
SJERG020307_D1        NaN
SJERG026_D            NaN
SJERG001_D_WES        NaN
SJBALL218_D_WES       NaN
SJBALL227_D_WES       NaN
SJERG014_D_WES        NaN
SJERG002_D            NaN
SJBALL021081_D1_WES   NaN
SJERG030_D_WES        NaN
SJBALL021333_D1_WES   NaN
SJERG019_D_WES        NaN
SJBALL020635_D1       NaN
SJBALL020383_D1_WES   NaN
SJBALL087_D_WES       NaN
SJERG004_D_WES        NaN
SJERG013_D_WES        NaN
SJERG017_D_WES        NaN
SJERG020052_D1        NaN
SJERG020051_D1_WES    NaN
SJBALL215_D_WES       NaN
SJBALL020828_D1       NaN
SJERG022_D_WES        NaN
SJBALL230_D_WES       NaN
SJBALL021511_D1_WES   NaN
SJBALL199_D_WES       NaN
SJERG020054_D1_WES    NaN
SJERG020302_D1        NaN
SJERG008_D_WES        NaN
SJERG020_D            NaN
SJBALL021492_D1_WES   NaN
SJERG020051_D1        NaN
SJERG009_D            NaN
SJERG025_D_WES        NaN
SJERG003_D_WES        NaN
SJERG011_D            NaN
SJERG024_D            NaN
SJERG028_D            NaN
SJERG016_D            NaN
> 
> # Get data slice for multiple genetic profiles and single gene
> getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],mycaselist)
[1] No.genetic.profile.available.for.genetic_profile_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'],' '))
> getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],cases=cases)
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(file, "rt") : cannot open the connection
Calls: getProfileData ... processURL -> processURL.CGDS -> read.table -> file
Execution halted