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

> ### Name: cgdsr-plot
> ### Title: Generic plot function for CGDS API data.
> ### Aliases: cgdsr-plot plot plot.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                        brca_bccrc
28                        brca_broad
29                       brca_sanger
30                 brca_tcga_pub2015
31                     brca_tcga_pub
32      brca_tcga_pan_can_atlas_2018
33                         brca_tcga
34         brca_bccrc_xenograft_2014
35               cellline_ccle_broad
36      cesc_tcga_pan_can_atlas_2018
37                         cesc_tcga
38                    chol_nccs_2013
39                     chol_nus_2012
40      chol_tcga_pan_can_atlas_2018
41                         chol_tcga
42                   lcll_broad_2013
43                    cll_iuopa_2015
44                  cllsll_icgc_2011
45                 ccrcc_utokyo_2013
46      coad_tcga_pan_can_atlas_2018
47                coadread_dfci_2016
48                coadread_genentech
49                 coadread_tcga_pub
50                     coadread_tcga
51                    coadread_mskcc
52                cscc_hgsc_bcm_2014
53                ctcl_columbia_2015
54                 cscc_dfarber_2015
55                     pact_jhu_2011
56                   desm_broad_2015
57                   dlbc_broad_2012
58      dlbc_tcga_pan_can_atlas_2018
59                    nhl_bcgsc_2013
60                     ucec_msk_2018
61                        esca_broad
62      esca_tcga_pan_can_atlas_2018
63                         esca_tcga
64                         escc_icgc
65                    escc_ucla_2014
66                   es_iocurie_2014
67                 gbc_shanghai_2014
68                   egc_tmucih_2015
69                  nsclc_unito_2016
70                    prad_cpcg_2017
71                      gct_msk_2016
72                  mixed_allen_2018
73                  gbm_tcga_pub2013
74                      gbm_tcga_pub
75       gbm_tcga_pan_can_atlas_2018
76                          gbm_tcga
77                        hnsc_broad
78                          hnsc_jhu
79                     hnsc_tcga_pub
80      hnsc_tcga_pan_can_atlas_2018
81                         hnsc_tcga
82               liad_inserm_fr_2014
83                hcc_inserm_fr_2015
84                   all_stjude_2013
85                   all_stjude_2015
86               panet_shanghai_2013
87                     chol_jhu_2013
88                     kich_tcga_pub
89      kich_tcga_pan_can_atlas_2018
90                         kich_tcga
91                          kirc_bgi
92                     kirc_tcga_pub
93      kirc_tcga_pan_can_atlas_2018
94                         kirc_tcga
95      kirp_tcga_pan_can_atlas_2018
96                         kirp_tcga
97                      lihc_amc_prv
98                        lihc_riken
99      lihc_tcga_pan_can_atlas_2018
100                        lihc_tcga
101                    lgg_ucsf_2014
102                       luad_broad
103                  luad_mskcc_2015
104                    luad_tcga_pub
105     luad_tcga_pan_can_atlas_2018
106                        luad_tcga
107                         luad_tsp
108                    lusc_tcga_pub
109     lusc_tcga_pan_can_atlas_2018
110                        lusc_tcga
111                        dlbc_tcga
112                  msk_impact_2017
113                    lung_msk_2017
114                  prad_mskcc_2017
115                      mpnst_mskcc
116                  plmeso_nyu_2015
117                 mcl_idibips_2013
118                   mbl_broad_2012
119                         mbl_icgc
120                         mbl_pcgp
121                mbl_sickkids_2016
122               skcm_broad_dfarber
123                  lgggbm_tcga_pub
124     meso_tcga_pan_can_atlas_2018
125                        meso_tcga
126                     egc_msk_2017
127                        prad_mich
128                   prad_su2c_2015
129                         mm_broad
130                   ccrcc_irc_2014
131                    brca_igr_2015
132                   mds_tokyo_2011
133                   cellline_nci60
134                     odg_msk_2017
135                  npc_nusingapore
136                     nbl_amc_2012
137                   nbl_broad_2013
138                nbl_ucologne_2015
139                    nepc_wcm_2016
140       skcm_vanderbilt_mskcc_2015
141                   nhl_bcgsc_2011
142               nsclc_pd1_msk_2018
143                  blca_nmibc_2017
144             hnsc_mdanderson_2013
145                      ov_tcga_pub
146       ov_tcga_pan_can_atlas_2018
147                          ov_tcga
148              mel_tsam_liang_2017
149            nsclc_tcga_broad_2016
150                        paad_icgc
151                paad_qcmg_uq_2016
152     paad_tcga_pan_can_atlas_2018
153                        paad_tcga
154                   paad_utsw_2015
155                   panet_jhu_2011
156                    thca_tcga_pub
157       all_phase2_target_2018_pub
158              aml_target_2018_pub
159            es_dfarber_broad_2014
160                mixed_pipseq_2017
161              nbl_target_2018_pub
162              pediatric_dkfz_2017
163               rt_target_2018_pub
164               wt_target_2018_pub
165     pcpg_tcga_pan_can_atlas_2018
166                        pcpg_tcga
167               thyroid_mskcc_2016
168                  pcnsl_mayo_2015
169                  prad_broad_2013
170                       prad_broad
171                prad_eururol_2017
172                       prad_fhcrc
173                       prad_mskcc
174                       prad_p1000
175                    prad_tcga_pub
176     prad_tcga_pan_can_atlas_2018
177                        prad_tcga
178                  prad_mskcc_2014
179 prad_mskcc_cheny1_organoids_2014
180     read_tcga_pan_can_atlas_2018
181                   hnc_mskcc_2016
182            nccrcc_genentech_2014
183                     rms_nih_2014
184                      summit_2018
185                       sarc_mskcc
186     sarc_tcga_pan_can_atlas_2018
187                        sarc_tcga
188                       skcm_broad
189     skcm_tcga_pan_can_atlas_2018
190                        skcm_tcga
191                        skcm_yale
192       skcm_broad_brafresist_2012
193                       scco_mskcc
194                       sclc_clcgp
195                         sclc_jhu
196               sclc_ucologne_2015
197     sclc_cancercell_gardner_2017
198            stad_pfizer_uhongkong
199                    stad_tcga_pub
200     stad_tcga_pan_can_atlas_2018
201                        stad_tcga
202                      stad_utokyo
203                   stad_uhongkong
204                    stes_tcga_pub
205                  urcc_mskcc_2016
206                     crc_msk_2018
207                  utuc_mskcc_2013
208                        tgct_tcga
209     tgct_tcga_pan_can_atlas_2018
210        angs_project_painter_2018
211       brca_mbcproject_wagle_2017
212                     tet_nci_2014
213     thym_tcga_pan_can_atlas_2018
214                        thym_tcga
215     thca_tcga_pan_can_atlas_2018
216                        thca_tcga
217                     ucs_jhu_2014
218      ucs_tcga_pan_can_atlas_2018
219                         ucs_tcga
220                    ucec_tcga_pub
221     ucec_tcga_pan_can_atlas_2018
222                        ucec_tcga
223      uvm_tcga_pan_can_atlas_2018
224                         uvm_tcga
225                panet_arcnet_2017
226                   skcm_ucla_2016
227        past_dkfz_heidelberg_2013
228            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 Invasive Carcinoma (British Columbia, Nature 2012)
28                                                                           Breast Invasive Carcinoma (Broad, Nature 2012)
29                                                                          Breast Invasive Carcinoma (Sanger, Nature 2012)
30                                                                              Breast Invasive Carcinoma (TCGA, Cell 2015)
31                                                                            Breast Invasive Carcinoma (TCGA, Nature 2012)
32                                                                        Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
33                                                                            Breast Invasive Carcinoma (TCGA, Provisional)
34                                                         Breast cancer patient xenografts (British Columbia, Nature 2014)
35                                                              Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
36                                                                 Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
37                                     Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
38                                                 Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
39                                                    Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
40                                                                               Cholangiocarcinoma (TCGA, PanCancer Atlas)
41                                                                                   Cholangiocarcinoma (TCGA, Provisional)
42                                                                          Chronic Lymphocytic Leukemia (Broad, Cell 2013)
43                                                                        Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
44                                                                            Chronic lymphocytic leukemia (ICGA, Nat 2011)
45                                                                Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
46                                                                             Colon Adenocarcinoma (TCGA, PanCancer Atlas)
47                                                                      Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
48                                                                       Colorectal Adenocarcinoma (Genentech, Nature 2012)
49                                                                            Colorectal Adenocarcinoma (TCGA, Nature 2012)
50                                                                            Colorectal Adenocarcinoma (TCGA, Provisional)
51                                                             Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
52                                                    Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014)
53                                                                   Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
54                                                           Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
55                                                                   Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011
56                                                                  Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
57                                                                         Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
58                                                                    Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)
59                                                                        Diffuse Large B-cell Lymphoma (BCGSC, Blood 2013)
60                                                                                           Endometrial Cancer (MSK, 2018)
61                                                                        Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
62                                                                        Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)
63                                                                                 Esophageal Carcinoma (TCGA, Provisional)
64                                                                   Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
65                                                                Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
66                                                                       Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
67                                                                         Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
68                                                                               Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
69                          Genetic Characterization of NSCLC young adult patients ( University of Turin, Lung Cancer 2016)
70                                                     Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
71                                              Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016).
72  Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors (Van Allen Lab 2018)
73                                                                                           Glioblastoma (TCGA, Cell 2013)
74                                                                                         Glioblastoma (TCGA, Nature 2008)
75                                                                          Glioblastoma Multiforme (TCGA, PanCancer Atlas)
76                                                                              Glioblastoma Multiforme (TCGA, Provisional)
77                                                              Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
78                                                      Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
79                                                                Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
80                                                            Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
81                                                                Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
82                                                                        Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
83                                                                       Hepatocellular Carcinomas (Inserm, Nat Genet 2015)
84                                                            Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
85                                             Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
86                                                                                   Insulinoma (Shanghai, Nat Commun 2013)
87                                               Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
88                                                                              Kidney Chromophobe (TCGA, Cancer Cell 2014)
89                                                                               Kidney Chromophobe (TCGA, PanCancer Atlas)
90                                                                                   Kidney Chromophobe (TCGA, Provisional)
91                                                                  Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
92                                                                    Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
93                                                                Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)
94                                                                    Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
95                                                            Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)
96                                                                Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
97                                                                    Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
98                                                                   Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
99                                                                   Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)
100                                                                      Liver Hepatocellular Carcinoma (TCGA, Provisional)
101                                                                                 Low-Grade Gliomas (UCSF, Science 2014).
102                                                                                  Lung Adenocarcinoma (Broad, Cell 2012)
103                                                                                        Lung Adenocarcinoma (MSKCC 2015)
104                                                                                 Lung Adenocarcinoma (TCGA, Nature 2014)
105                                                                             Lung Adenocarcinoma (TCGA, PanCancer Atlas)
106                                                                                 Lung Adenocarcinoma (TCGA, Provisional)
107                                                                                  Lung Adenocarcinoma (TSP, Nature 2008)
108                                                                        Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
109                                                                    Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
110                                                                        Lung Squamous Cell Carcinoma (TCGA, Provisional)
111                                                     Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
112                                                             MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
113                            MSK-IMPACT Clinical Sequencing Cohort for Non-Small Cell Cancer (MSK, Cancer Discovery 2017)
114                             MSK-IMPACT Clinical Sequencing Cohort in Prostate Cancer (MSK, JCO Precision Oncology 2017)
115                                                         Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
116                                                                   Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
117                                                                               Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
118                                                                                    Medulloblastoma (Broad, Nature 2012)
119                                                                                     Medulloblastoma (ICGC, Nature 2012)
120                                                                                     Medulloblastoma (PCGP, Nature 2012)
121                                                                                 Medulloblastoma (Sickkids, Nature 2016)
122                                                                               Melanoma (Broad/Dana Farber, Nature 2012)
123                                                                          Merged Cohort of LGG and GBM (TCGA, Cell 2016)
124                                                                                    Mesothelioma (TCGA, PanCancer Atlas)
125                                                                                        Mesothelioma (TCGA, Provisional)
126                                                           Metastatic Esophagogastric Cancer (MSKCC, Cancer Discov 2017)
127                                                                  Metastatic Prostate Adenocarcinoma (MCTP, Nature 2012)
128                                            Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015)
129                                                                              Multiple Myeloma (Broad, Cancer Cell 2014)
130                                         Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014)
131                                                          Mutational profiles of metastatic breast cancer (France, 2016)
132                                                                                     Myelodysplasia (Tokyo, Nature 2011)
133                                                                               NCI-60 Cell Lines (NCI, Cancer Res. 2012)
134                     NGS in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas tumors (MSK, Neuro Oncol 2017)
135                                                                    Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
136                                                                              Neuroblastoma (AMC Amsterdam, Nature 2012)
137                                                                                    Neuroblastoma (Broad Institute 2013)
138                                                                                   Neuroblastoma (Broad, Nat Genet 2013)
139                                                              Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
140        Next generation sequencing (NGS) of pre-treatment metastatic melanoma samples (MSK, JCO Precision Oncology 2017)
141                                                                               Non-Hodgkin Lymphoma (BCGSC, Nature 2011)
142                                                                              Non-Small Cell Lung Cancer (MSK, JCO 2018)
143                                                                   Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017)
144                                                          Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
145                                                                   Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
146                                                               Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)
147                                                                   Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
148                                                       Paired-exome sequencing of acral melanoma (TGEN, Genome Res 2017)
149                                                                                  Pan-Lung Cancer (TCGA, Nat Genet 2016)
150                                                                           Pancreatic Adenocarcinoma (ICGC, Nature 2012)
151                                                                           Pancreatic Adenocarcinoma (QCMG, Nature 2016)
152                                                                       Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)
153                                                                           Pancreatic Adenocarcinoma (TCGA, Provisional)
154                                                                               Pancreatic Cancer (UTSW, Nat Commun 2015)
155                                               Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
156                                                                           Papillary Thyroid Carcinoma (TCGA, Cell 2014)
157                                                             Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018)
158                                                                         Pediatric Acute Myeloid Leukemia (TARGET, 2018)
159                                                                      Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
160                                                                                   Pediatric Mixed Tumors (PIP-Seq 2017)
161                                                                                  Pediatric Neuroblastoma (TARGET, 2018)
162                                                           Pediatric Pan-Cancer (DKFZ - German Cancer Consortium,  2017)
163                                                                                 Pediatric Rhabdoid Tumor (TARGET, 2018)
164                                                                                   Pediatric Wilms' Tumor (TARGET, 2018)
165                                                              Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)
166                                                                  Pheochromocytoma and Paraganglioma (TCGA, Provisional)
167                                                  Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
168                                             Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
169                                                                      Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
170                                                                 Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
171                                                                                 Prostate Adenocarcinoma (EurUrol, 2017)
172                                                             Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
173                                                                       Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
174                                                              Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018)
175                                                                               Prostate Adenocarcinoma (TCGA, Cell 2015)
176                                                                         Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
177                                                                             Prostate Adenocarcinoma (TCGA, Provisional)
178                                                                    Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
179                                                                    Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
180                                                                           Rectum Adenocarcinoma (TCGA, PanCancer Atlas)
181                                                    Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016)
182                                                              Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
183                                                                              Rhabdomyosarcoma (NIH, Cancer Discov 2014)
184                                                                                                   SUMMIT (Nature, 2018)
185                                                                                   Sarcoma (MSKCC/Broad, Nat Genet 2010)
186                                                                                         Sarcoma (TCGA, PanCancer Atlas)
187                                                                                             Sarcoma (TCGA, Provisional)
188                                                                              Skin Cutaneous Melanoma (Broad, Cell 2012)
189                                                                         Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)
190                                                                             Skin Cutaneous Melanoma (TCGA, Provisional)
191                                                                          Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
192                                                                      Skin Cutaneous Melanoma(Broad, Cancer Discov 2014)
193                                                               Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
194                                                                          Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
195                                                                  Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
196                                                                         Small Cell Lung Cancer (U Cologne, Nature 2015)
197                                                                           Small-Cell Lung Cancer (Multi-Institute 2017)
198                                                                 Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
199                                                                              Stomach Adenocarcinoma (TCGA, Nature 2014)
200                                                                          Stomach Adenocarcinoma (TCGA, PanCancer Atlas)
201                                                                              Stomach Adenocarcinoma (TCGA, Provisional)
202                                                                        Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
203                                                                            Stomach Adenocarcinoma (UHK, Nat Genet 2011)
204                                                             TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
205                  Targeted gene sequencing in 62 high-grade primary Unclassified Renal Cell Carcinoma (MSK, Nature 2016)
206                   Targeted sequencing of 1134 samples from metastatic colorectal cancer samples (MSK, Cancer Cell 2018)
207                                       Targeted sequencing of upper tract urothelial cancer samples (MSK, Eur Urol 2013)
208                                                                         Testicular Germ Cell Cancer (TCGA, Provisional)
209                                                                     Testicular Germ Cell Tumors (TCGA, PanCancer Atlas)
210                                                                   The Angiosarcoma Project (Provisional, February 2018)
211                                                          The Metastatic Breast Cancer Project (Provisional, April 2018)
212                                                                          Thymic Epithelial Tumors (NCI, Nat Genet 2014)
213                                                                                         Thymoma (TCGA, PanCancer Atlas)
214                                                                                             Thymoma (TCGA, Provisional)
215                                                                               Thyroid Carcinoma (TCGA, PanCancer Atlas)
216                                                                                   Thyroid Carcinoma (TCGA, Provisional)
217                                                      Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
218                                                                          Uterine Carcinosarcoma (TCGA, PanCancer Atlas)
219                                                                              Uterine Carcinosarcoma (TCGA, Provisional)
220                                                                Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
221                                                            Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
222                                                                Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
223                                                                                  Uveal Melanoma (TCGA, PanCancer Atlas)
224                                                                                      Uveal Melanoma (TCGA, Provisional)
225                                              Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (Nature, 2017)
226                                           Whole-exome sequences (WES) of pretreatment melanoma tumors (UCLA, Cell 2016)
227                                              Whole-genome sequencing of pilocytic astrocytomasatic (Nat Genetics, 2013)
228                                                                                           miRNAs in HCA/HCC (MSK, 2018)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     description
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         The genomic landscape of endocrine resistant advanced breast cancers.
27                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 65 breast cancer samples. Generated by the British Columbia Cancer Research Centre.
28                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 103 breast cancer samples. Generated by the Broad Institute.
29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive profiling of 100 breast cancer samples. Generated by the Sanger Institute.
30                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 817 cases (TCGA Cell 2015).
31                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    <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>.
32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
33                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
34                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Dynamics of genomic clones in breast cancer patient xenografts.
35                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, containing 1020 samples.
36                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
37                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Exome sequencing of 15 cholangiocarcinoma cases from the National Cancer Centre of Singapore to study the somatic mutations.
39                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
40                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
41                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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>.
42                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Exome sequencing of 160 CLL samples. Generated by the Broad Institute.
43                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Mutation data from whole-genome or whole-exome sequencing (WGS/WXS) of 428 CLL, 54 MBL, and 24 SLL samples.
44                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome Sequencing of CLL samples.
45                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Mutation data from whole genome and/or whole exome sequencing of 106 clear-cell renal cell carcinoma samples.
46                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                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>.
51                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Colon Trios data from 69 Patients each with a  primary and metastatic tumor. (Primary / Met) (David Solit / Evi Vakiani / Michael Berger, MSKCC)
52                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole-exome sequencing of 39 cases aggressive cutaneous squamous cell carcinoma.
53                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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).
54                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 504 cancer-associated genes in 29 cutaneous squamous cell carcinoma samples
55                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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).
56                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Mutation data from Exome/Whole Genome sequencing of 20 desmoplastic melanoma cases.
57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 58 DLBCL samples.
58                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
59                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole genome sequencing analysis of 40 DLBCL tumors and 13 cell lines.
60                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Clinical Utility Of Prospective Molecular Characterization In Advanced Endometrial Cancer
61                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Comprehensive profiling of 149 esophageal adenocarcinoma samples from the Broad Institute.
62                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              WGS and WES of 88 esophageal squamous cell carcinoma samples. Generated by ICGC.
65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
66                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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">
67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Mutation data from whole exome sequencing of 32 gallbladder carcinoma tumors with paired normals
68                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing on 78 Gastric Adenocarcinoma of differing histologies and anatomic locations
69                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         The retrospective study using NGS approach for genetic characterization of NSCLC young adult patients
70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Comprehensive genomic profiling of 477 Prostate Adenocarcinoma samples from CPC-GENE and public data sets, including TCGA-PRAD.
71                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 180 germ cell tumor samples.
72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing molecular profiling of tumors and corresponding clinical outcomes from patients treated with immune checkpoint inhibitors across multiple cancer types including melanoma, non-small cell lung cancer, head and neck cancer, and bladder cancer. Generated by the Van Allen Lab, 2018.
73                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       <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>.
74                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <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>.
75                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
76                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
77                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive profiling of 74 head and neck squamous cell carcinoma samples from the Broad Institute.
78                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Comprehensive profiling of 32 head and neck squamous cell carcinoma samples from Johns Hopkins.
79                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
80                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
81                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
82                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Mutation data from whole-exome sequencing (WXS) of 46 liver tumor and corresponding nontumor DNA.
83                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Mutation data from whole-exome sequencing (WXS) of 243 liver tumors identified mutational signatures associated with specific risk factors.
84                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Exome sequencing of 44 ALL samples.
85                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole genome sequencing (WGS) of 22 infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) cases
86                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole exome sequencing of 10 benign insulinoma tumors. <A HREF="http://www.nature.com/ncomms/2013/131210/ncomms3810/extref/ncomms3810-s1.pdf">
87                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome Sequencing of 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
88                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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>.
89                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
90                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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>.
91                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive sequencing of 98 clear cell kidney cancer samples. Generated by BGI-Shenzhen.
92                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
93                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
94                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
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 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>.
97                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Liver Hepatocellular Carcinoma from Asan Medical Center, Korea, containing 231 samples.
98                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole-genome sequencing of 27 hepatocellular carcinoma samples from RIKEN.
99                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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)
100                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
101                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from whole exome sequencing of 23 grade II glioma patients.
102                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 183 lung adenocarcinoma samples. Generated by the Broad Institute.
103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-exome sequencing of non small cell lung cancers treated with pembrolizumab
104                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                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>.
105                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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)
106                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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>.
107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Targeted sequencing of 163 lung adenocarcinoma samples. Generated by WashU/Broad.
108                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <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>.
109                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
110                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
111                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
112                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Prospective molecular characterization of lung adenocarcinomas for efficient patient matching.
114                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted sequencing of clinical cases via MSK-IMPACT for prostate cancer (Abida et al, JCO Precision Oncology 2017).
115                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Exome profiling of 17 malignant peripheral nerve sheath tumors.
116                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Mutation data from whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) and matched blood samples.
117                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 29 primary mantle cell lymphomas.
118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 92 medulloblastoma samples from the Broad Institute.
119                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive profiling of 125 matched tumor and germline medulloblastoma samples
120                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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.
121                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from whole-genome sequencing (WGS) of 46 recurrent medulloblastoma samples.
122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Somatic Mutation data from 25 Whole Genome Sequenced metastatic melanoma samples
123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-exome sequencing from TCGA LGG and GBM cases
124                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
125                                                                                                                                                                                                                                                                                                                                                    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>.
126                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Prospective genomic profiling of 341 samples from 305 metastatic esophagogastric cancer patients
127                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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.
128                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive analysis of 150 metastatic prostate cancer samples by the SU2C/PCF Dream Team
129                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome sequencing of 205 multiple myeloma samples.
130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Mutation data from multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
131                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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.
132                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 29 myelodysplasia samples from the University of Tokyo.
133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
134                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Genomic characterization using next generation sequencing (NGS) in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.
135                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole genome sequencing of 56 NPC tumor / normal pairs. Generated by the Cancer Science Institute of Singapore, National University of Singapore.
136                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole genome sequencing of 87 neuroblastoma samples from the Academic Medical Center, Amsterdam.
137                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole Genome and Whole Exome sequencing of 240 high-risk neuroblastoma cases.
138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Mutation data from whole-genome sequencing of 56 neuroblastoma samples
139                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole exome and RNA Seq data of castration resistant adenocarcinoma and castration resistant neuroendocrine prostate cancer (somatic mutations and copy number aberrations)
140                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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.
141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole Genome/Exome sequencing of 14 NHL cases.
142                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               NGS sequencing of 240 NSCLC cases treated at MSKCC with anti-PD-(L)1 based therapy using the MSK-IMPACT assay.
143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genomic Landscape and Predictors of Response for High Risk NMIBC
144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive profiling of 40 oral squamous cell carcinoma samples from MD Anderson.
145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            <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>.
146                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive genomic and transcriptomic analysis of ALM patients.
149                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive profiling of 99 pancreatic cancer samples. Generated by ICGC.
151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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%.
152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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>.
154                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
155                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. <A HREF="https://www.sciencemag.org/content/331/6021/1199/suppl/DC1">
156                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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>.
157              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
158              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>
159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
160                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 101 high-risk pediatric cancer patients
161                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>
162                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive genomic profiling of 961 Pediatric Cancer samples. Data generated from Pfister Lab & DKFZ/German Cancer Consortium.
163 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>
164        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>
165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
167                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, J Clin Invest 2016)
168                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Mutation data from whole exome sequencing (WXS) of 19 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
169                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 57 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
170                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive profiling of 112 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
171                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole-genome and Transcriptome Sequencing of 65 Prostate Adenocarcinoma Patients. Generated by the Sun Lab 2017.
172                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of prostate cancer samples. Generated by Peter Nelson's lab at the Fred Hutchinson Cancer Research Center.
173                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  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>.
174                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole Exome Sequencing of 1013 prostate cancer samples.
175                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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>.
176                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
177                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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>.
178                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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>.
179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome profiling of prostate cancer samples and matched organoids.
180                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
181                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
182                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome sequencing of 139 Renal Non-Clear Cell Carcinoma (NCCRCC) samples.
183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Mutation data from WGS and/or WXS of 43 rhabdomyosarcoma samples.
184                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Findings of a multi-histology, genomically selected, 'basket' study utilizing the pan-HER kinase inhibitor neratinib.
185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
186                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
187                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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>.
188                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of 121 melanoma samples. Generated by the Broad Institute.
189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
190                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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>.
191                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Exome sequencing of 91 melanoma samples. Generated by Yale.
192                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Sequencing of 44 melanoma patients pre and post vemurafenib treatment. Generated by the Broad Institute.
193                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Targeted sequencing of 12 SCCO samples.
194                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
195                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 36 primary human SCLC tumors and 17 matched SCLC and lymphoblastoid cell lines. Generated by Johns Hopkins.
196                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Comprehensive WGS profiling of 110 human SCLC specimens.
197                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole Exome Sequencing of paired chemosensitive and chemoresistant SCLC PDX.
198                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Whole genome sequencing of 100 tumor-normal pairs from the University of Hong Kong and Pfizer.
199                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Stomach Adenocarcinoma, containing 295 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
200                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
201                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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>.
202                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples from the University of Tokyo.
203                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Exome sequencing of 22 gastric cancer samples.
204                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA data for Esophagus-Stomach Cancers.
205                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Molecular Analysis of Unclassified Renal Cell Carcinoma
206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
207                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Genomic Characterization using next-generation sequencing of Upper Tract Urothelial Carcinoma.
208                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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>.
209                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
210                                                                                                                                                                                                                                                                                                                                                                                                                      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.
211                                                                                                                                                                                                                                                          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. Questions about these data can be directed to data@mbcproject.org.
212                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 28 thymic epithelial tumors.
213                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
214                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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>.
215                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
216                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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>.
217                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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">
218                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
219                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
220                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
221                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
222                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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>.
223                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA PanCanAtlas genomic data from 11k cases and all TCGA tumor types (33). The data is expected to be updated.
224                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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>.
225                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole-genome sequencing of 102 primary PanNETs and the defined genomic events that characterize their pathogenesis.
226                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Genetic Characterization of 38 pretreatment (pembrolizumab and nivolumab) melanoma tumors.
227                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole-genome sequencing of 96 pilocytic astrocytomasatic alterations in pilocytic astrocytoma conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
228                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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)[4,1]
> 
> # histogram of genetic profile data for gene
> plot(mycgds,mycancerstudy,'MDM2',mygeneticprofile,mycaselist)
[1] "Error: empty data frame returned :\n Error..Problem.when.identifying.a.cancer.study.for.the.request."
> 
> # scatter plot of genetic profile data for two genes
> plot(mycgds,mycancerstudy,c('MDM2','MDM4'),mygeneticprofile,mycaselist)
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(file, "rt") : cannot open the connection
Calls: plot ... processURL -> processURL.CGDS -> read.table -> file
Execution halted