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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgdsr-getProfileData
> ### Title: Retrieves genomic profile data for genes and genetic profiles.
> ### Aliases: cgdsr-getProfileData getProfileData getProfileData.CGDS
> 
> ### ** Examples
> 
> # Create CGDS object
> mycgds = CGDS("http://www.cbioportal.org/")
> 
> # Get list of cancer studies at server
> getCancerStudies(mycgds)
                     cancer_study_id
1                      paac_jhu_2014
2                      laml_tcga_pub
3                          laml_tcga
4                      acyc_fmi_2014
5                      acyc_mda_2015
6                    acyc_mskcc_2013
7                   acyc_sanger_2013
8                    acbc_mskcc_2015
9                           acc_tcga
10                    ampca_bcm_2016
11             blca_mskcc_solit_2014
12             blca_mskcc_solit_2012
13      blca_plasmacytoid_mskcc_2016
14                          blca_bgi
15           blca_dfarber_mskcc_2014
16                     blca_tcga_pub
17                         blca_tcga
18                          lgg_tcga
19                     brca_metabric
20                        brca_bccrc
21                        brca_broad
22                       brca_sanger
23                 brca_tcga_pub2015
24                     brca_tcga_pub
25                         brca_tcga
26         brca_bccrc_xenograft_2014
27               cellline_ccle_broad
28                         cesc_tcga
29                    chol_nccs_2013
30                     chol_nus_2012
31                         chol_tcga
32                   lcll_broad_2013
33                    cll_iuopa_2015
34                 ccrcc_utokyo_2013
35                coadread_dfci_2016
36                coadread_genentech
37                 coadread_tcga_pub
38                     coadread_tcga
39                    coadread_mskcc
40                ctcl_columbia_2015
41                 cscc_dfarber_2015
42                     pact_jhu_2011
43                   desm_broad_2015
44                   dlbc_broad_2012
45                        esca_broad
46                         esca_tcga
47                         escc_icgc
48                    escc_ucla_2014
49                   es_iocurie_2014
50                 gbc_shanghai_2014
51                   egc_tmucih_2015
52                  nsclc_unito_2016
53                    prad_cpcg_2017
54                      gct_msk_2016
55                  gbm_tcga_pub2013
56                      gbm_tcga_pub
57                          gbm_tcga
58                        hnsc_broad
59                          hnsc_jhu
60                     hnsc_tcga_pub
61                         hnsc_tcga
62               liad_inserm_fr_2014
63                hcc_inserm_fr_2015
64                   all_stjude_2013
65                   all_stjude_2015
66               panet_shanghai_2013
67                     chol_jhu_2013
68                     kich_tcga_pub
69                         kich_tcga
70                          kirc_bgi
71                     kirc_tcga_pub
72                         kirc_tcga
73                         kirp_tcga
74                      lihc_amc_prv
75                        lihc_riken
76                         lihc_tcga
77                     lgg_ucsf_2014
78                        luad_broad
79                   luad_mskcc_2015
80                     luad_tcga_pub
81                         luad_tcga
82                          luad_tsp
83                     lusc_tcga_pub
84                         lusc_tcga
85                         dlbc_tcga
86                   msk_impact_2017
87                     lung_msk_2017
88                   prad_mskcc_2017
89                       mpnst_mskcc
90                   plmeso_nyu_2015
91                  mcl_idibips_2013
92                    mbl_broad_2012
93                          mbl_icgc
94                          mbl_pcgp
95                 mbl_sickkids_2016
96                skcm_broad_dfarber
97                   lgggbm_tcga_pub
98                         meso_tcga
99                    prad_su2c_2015
100                         mm_broad
101                   ccrcc_irc_2014
102                    brca_igr_2015
103                   mds_tokyo_2011
104                   cellline_nci60
105                     odg_msk_2017
106                  npc_nusingapore
107                     nbl_amc_2012
108                nbl_ucologne_2015
109                    nepc_wcm_2016
110       skcm_vanderbilt_mskcc_2015
111             hnsc_mdanderson_2013
112                      ov_tcga_pub
113                          ov_tcga
114              mel_tsam_liang_2017
115            nsclc_tcga_broad_2016
116                        paad_icgc
117                paad_qcmg_uq_2016
118                        paad_tcga
119                   paad_utsw_2015
120                   panet_jhu_2011
121                    thca_tcga_pub
122            es_dfarber_broad_2014
123                        pcpg_tcga
124               thyroid_mskcc_2016
125                  pcnsl_mayo_2015
126                  prad_broad_2013
127                       prad_broad
128                       prad_fhcrc
129                       prad_mskcc
130                    prad_tcga_pub
131                        prad_tcga
132                  prad_mskcc_2014
133 prad_mskcc_cheny1_organoids_2014
134                        prad_mich
135                   hnc_mskcc_2016
136            nccrcc_genentech_2014
137                     rms_nih_2014
138                       sarc_mskcc
139                        sarc_tcga
140                       skcm_broad
141                        skcm_tcga
142                        skcm_yale
143                       scco_mskcc
144                       sclc_clcgp
145                         sclc_jhu
146               sclc_ucologne_2015
147            stad_pfizer_uhongkong
148                    stad_tcga_pub
149                        stad_tcga
150                      stad_utokyo
151                   stad_uhongkong
152                    stes_tcga_pub
153                     egc_msk_2017
154                  urcc_mskcc_2016
155                        tgct_tcga
156       brca_mbcproject_wagle_2017
157                     tet_nci_2014
158                        thym_tcga
159                        thca_tcga
160                     ucs_jhu_2014
161                         ucs_tcga
162                    ucec_tcga_pub
163                        ucec_tcga
164                         uvm_tcga
165                panet_arcnet_2017
166                   skcm_ucla_2016
167        past_dkfz_heidelberg_2013
                                                                                                                name
1                                               Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
2                                                                           Acute Myeloid Leukemia (TCGA, NEJM 2013)
3                                                                         Acute Myeloid Leukemia (TCGA, Provisional)
4                                                              Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
5                                                               Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
6                                                                   Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
7                                                                    Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
8                                                     Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
9                                                                       Adrenocortical Carcinoma (TCGA, Provisional)
10                                               Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016)
11                                                                             Bladder Cancer (MSKCC, Eur Urol 2014)
12                                                                                  Bladder Cancer (MSKCC, JCO 2013)
13                                                      Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016)
14                                                                Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
15                                            Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discov 2014)
16                                                                  Bladder Urothelial Carcinoma (TCGA, Nature 2014)
17                                                                  Bladder Urothelial Carcinoma (TCGA, Provisional)
18                                                                      Brain Lower Grade Glioma (TCGA, Provisional)
19                                                           Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
20                                                         Breast Invasive Carcinoma (British Columbia, Nature 2012)
21                                                                    Breast Invasive Carcinoma (Broad, Nature 2012)
22                                                                   Breast Invasive Carcinoma (Sanger, Nature 2012)
23                                                                       Breast Invasive Carcinoma (TCGA, Cell 2015)
24                                                                     Breast Invasive Carcinoma (TCGA, Nature 2012)
25                                                                     Breast Invasive Carcinoma (TCGA, Provisional)
26                                                  Breast cancer patient xenografts (British Columbia, Nature 2014)
27                                                       Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
28                              Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
29                                          Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
30                                             Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
31                                                                            Cholangiocarcinoma (TCGA, Provisional)
32                                                                   Chronic Lymphocytic Leukemia (Broad, Cell 2013)
33                                                                 Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
34                                                         Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
35                                                               Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
36                                                                Colorectal Adenocarcinoma (Genentech, Nature 2012)
37                                                                     Colorectal Adenocarcinoma (TCGA, Nature 2012)
38                                                                     Colorectal Adenocarcinoma (TCGA, Provisional)
39                                                      Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
40                                                            Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
41                                                    Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
42                                                            Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011
43                                                           Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
44                                                                  Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
45                                                                 Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
46                                                                          Esophageal Carcinoma (TCGA, Provisional)
47                                                            Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
48                                                         Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
49                                                                Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
50                                                                  Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
51                                                                        Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
52                   Genetic Characterization of NSCLC young adult patients ( University of Turin, Lung Cancer 2016)
53                                              Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
54                                       Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016).
55                                                                                    Glioblastoma (TCGA, Cell 2013)
56                                                                                  Glioblastoma (TCGA, Nature 2008)
57                                                                       Glioblastoma Multiforme (TCGA, Provisional)
58                                                       Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
59                                               Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
60                                                         Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
61                                                         Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
62                                                                 Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
63                                                                Hepatocellular Carcinomas (Inserm, Nat Genet 2015)
64                                                     Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
65                                      Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
66                                                                            Insulinoma (Shanghai, Nat Commun 2013)
67                                        Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
68                                                                       Kidney Chromophobe (TCGA, Cancer Cell 2014)
69                                                                            Kidney Chromophobe (TCGA, Provisional)
70                                                           Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
71                                                             Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
72                                                             Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
73                                                         Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
74                                                             Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
75                                                            Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
76                                                                Liver Hepatocellular Carcinoma (TCGA, Provisional)
77                                                                           Low-Grade Gliomas (UCSF, Science 2014).
78                                                                            Lung Adenocarcinoma (Broad, Cell 2012)
79                                                                                  Lung Adenocarcinoma (MSKCC 2015)
80                                                                           Lung Adenocarcinoma (TCGA, Nature 2014)
81                                                                           Lung Adenocarcinoma (TCGA, Provisional)
82                                                                            Lung Adenocarcinoma (TSP, Nature 2008)
83                                                                  Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
84                                                                  Lung Squamous Cell Carcinoma (TCGA, Provisional)
85                                               Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
86                                                       MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
87                      MSK-IMPACT Clinical Sequencing Cohort for Non-Small Cell Cancer (MSK, Cancer Discovery 2017)
88                       MSK-IMPACT Clinical Sequencing Cohort in Prostate Cancer (MSK, JCO Precision Oncology 2017)
89                                                   Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
90                                                             Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
91                                                                         Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
92                                                                              Medulloblastoma (Broad, Nature 2012)
93                                                                               Medulloblastoma (ICGC, Nature 2012)
94                                                                               Medulloblastoma (PCGP, Nature 2012)
95                                                                           Medulloblastoma (Sickkids, Nature 2016)
96                                                                         Melanoma (Broad/Dana Farber, Nature 2012)
97                                                                    Merged Cohort of LGG and GBM (TCGA, Cell 2016)
98                                                                                  Mesothelioma (TCGA, Provisional)
99                                      Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015)
100                                                                       Multiple Myeloma (Broad, Cancer Cell 2014)
101                                  Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014)
102                                                   Mutational profiles of metastatic breast cancer (France, 2016)
103                                                                              Myelodysplasia (Tokyo, Nature 2011)
104                                                                        NCI-60 Cell Lines (NCI, Cancer Res. 2012)
105              NGS in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas tumors (MSK, Neuro Oncol 2017)
106                                                             Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
107                                                                       Neuroblastoma (AMC Amsterdam, Nature 2012)
108                                                                            Neuroblastoma (Broad, Nat Genet 2013)
109                                                       Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
110 Next generation sequencing (NGS) of pre-treatment metastatic melanoma samples (MSK, JCO Precision Oncology 2017)
111                                                   Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
112                                                            Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
113                                                            Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
114                                                Paired-exome sequencing of acral melanoma (TGEN, Genome Res 2017)
115                                                                           Pan-Lung Cancer (TCGA, Nat Genet 2016)
116                                                                    Pancreatic Adenocarcinoma (ICGC, Nature 2012)
117                                                                    Pancreatic Adenocarcinoma (QCMG, Nature 2016)
118                                                                    Pancreatic Adenocarcinoma (TCGA, Provisional)
119                                                                        Pancreatic Cancer (UTSW, Nat Commun 2015)
120                                        Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
121                                                                    Papillary Thyroid Carcinoma (TCGA, Cell 2014)
122                                                               Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
123                                                           Pheochromocytoma and Paraganglioma (TCGA, Provisional)
124                                           Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
125                                      Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
126                                                               Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
127                                                          Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
128                                                      Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
129                                                                Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
130                                                                        Prostate Adenocarcinoma (TCGA, Cell 2015)
131                                                                      Prostate Adenocarcinoma (TCGA, Provisional)
132                                                             Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
133                                                             Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
134                                                      Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)
135                                             Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016)
136                                                       Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
137                                                                       Rhabdomyosarcoma (NIH, Cancer Discov 2014)
138                                                                            Sarcoma (MSKCC/Broad, Nat Genet 2010)
139                                                                                      Sarcoma (TCGA, Provisional)
140                                                                       Skin Cutaneous Melanoma (Broad, Cell 2012)
141                                                                      Skin Cutaneous Melanoma (TCGA, Provisional)
142                                                                   Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
143                                                        Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
144                                                                   Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
145                                                           Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
146                                                                  Small Cell Lung Cancer (U Cologne, Nature 2015)
147                                                          Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
148                                                                       Stomach Adenocarcinoma (TCGA, Nature 2014)
149                                                                       Stomach Adenocarcinoma (TCGA, Provisional)
150                                                                 Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
151                                                                     Stomach Adenocarcinoma (UHK, Nat Genet 2011)
152                                                      TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
153   Targeted Sequencing of 341 samples from metastatic esophagogastric cancer patients (MSK,Cancer Discovery 2017)
154           Targeted gene sequencing in 62 high-grade primary Unclassified Renal Cell Carcinoma (MSK, Nature 2016)
155                                                                  Testicular Germ Cell Cancer (TCGA, Provisional)
156                                                 The Metastatic Breast Cancer Project (Provisional, October 2017)
157                                                                   Thymic Epithelial Tumors (NCI, Nat Genet 2014)
158                                                                                      Thymoma (TCGA, Provisional)
159                                                                            Thyroid Carcinoma (TCGA, Provisional)
160                                               Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
161                                                                       Uterine Carcinosarcoma (TCGA, Provisional)
162                                                         Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
163                                                         Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
164                                                                               Uveal Melanoma (TCGA, Provisional)
165                                       Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (Nature, 2017)
166                                    Whole-exome sequences (WES) of pretreatment melanoma tumors (UCLA, Cell 2016)
167                                       Whole-genome sequencing of pilocytic astrocytomasatic (Nat Genetics, 2013)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            description
1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Mutation data from whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation.
2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         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>.
3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Acute Myeloid Leukemia; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive genomic profiling of 28 metastatic ACCs.
5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients).
6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Exome profiling of 60 adenoid cystic carcinoma samples
7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 24 ACCs.
8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 12 breast AdCCs.
9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Adrenocortical Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
10                                                                                                                                                                                                                                                                                                                                                                                                             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).
11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014).
12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Comprehensive profiling of 97 bladder cancer samples, including targeted sequencing of 15 cancer genes. Iyer et al., JCO in press.
13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Genomic profiling of plasmacytoid-variant (signet ring cell) tumors of the bladder, published set
14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Exome and whole-genome sequencing of 99 bladder cancer samples. Generated by BGI.
15                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole exome sequencing of 50 patients with muscle invasive urothelial carcinoma
16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Bladder Cancer, containing 131 samples; raw data at the NCI.
17                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Bladder Urothelial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
18                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Brain Lower Grade Glioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
19                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 The genomic profiles (somatic mutations [targeted sequencing], copy number alterations, and gene expression) of 2509 breast cancers.
20                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Comprehensive profiling of 65 breast cancer samples. Generated by the British Columbia Cancer Research Centre.
21                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 103 breast cancer samples. Generated by the Broad Institute.
22                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Comprehensive profiling of 100 breast cancer samples. Generated by the Sanger Institute.
23                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 817 cases (TCGA Cell 2015).
24                                                                                                                                                                                                                                                                                                                                                                                                                                           <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>.
25                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Breast Invasive Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
26                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Dynamics of genomic clones in breast cancer patient xenografts.
27                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, containing 883 samples; raw data at the <A HREF="http://www.broadinstitute.org/ccle/data/browseData?conversationPropagation=begin">CCLE</A>.
28                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Exome sequencing of 15 cholangiocarcinoma cases from the National Cancer Centre of Singapore to study the somatic mutations.
30                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
31                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Cholangiocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Exome sequencing of 160 CLL samples. Generated by the Broad Institute.
33                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Mutation data from whole-genome or whole-exome sequencing (WGS/WXS) of 428 CLL, 54 MBL, and 24 SLL samples.
34                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Mutation data from whole genome and/or whole exome sequencing of 106 clear-cell renal cell carcinoma samples.
35                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations.
36                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive profiling of 72 colon cancer samples. Generated by Genentech.
37                                                                                                                                                                                                                                                                                                                                                                                                                                                         <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>.
38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Colorectal Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
39                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Colon Trios data from 69 Patients each with a  primary and metastatic tumor. (Primary / Met) (David Solit / Evi Vakiani / Michael Berger, MSKCC)
40                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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).
41                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Targeted sequencing of 504 cancer-associated genes in 29 cutaneous squamous cell carcinoma samples
42                                                                                                                                                                                                                                                                                                                                                                                                                                                           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).
43                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Mutation data from Exome/Whole Genome sequencing of 20 desmoplastic melanoma cases.
44                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole exome sequencing of 58 DLBCL samples.
45                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Comprehensive profiling of 149 esophageal adenocarcinoma samples from the Broad Institute.
46                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Esophageal Carcinoma ; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
47                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     WGS and WES of 88 esophageal squamous cell carcinoma samples. Generated by ICGC.
48                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
49                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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">
50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Mutation data from whole exome sequencing of 32 gallbladder carcinoma tumors with paired normals
51                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Whole-exome sequencing on 78 Gastric Adenocarcinoma of differing histologies and anatomic locations
52                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                The retrospective study using NGS approach for genetic characterization of NSCLC young adult patients
53                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive genomic profiling of 477 Prostate Adenocarcinoma samples from CPC-GENE and public data sets, including TCGA-PRAD.
54                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 180 germ cell tumor samples.
55                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              <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>.
56                                                                                                                                                                                                                                                                                                                                                                                                                                                     <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>.
57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Glioblastoma Multiforme; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
58                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 74 head and neck squamous cell carcinoma samples from the Broad Institute.
59                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive profiling of 32 head and neck squamous cell carcinoma samples from Johns Hopkins.
60                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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>.
61                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Head and Neck Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
62                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from whole-exome sequencing (WXS) of 46 liver tumor and corresponding nontumor DNA.
63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Mutation data from whole-exome sequencing (WXS) of 243 liver tumors identified mutational signatures associated with specific risk factors.
64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Exome sequencing of 44 ALL samples.
65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Whole genome sequencing (WGS) of 22 infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) cases
66                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Whole exome sequencing of 10 benign insulinoma tumors. <A HREF="http://www.nature.com/ncomms/2013/131210/ncomms3810/extref/ncomms3810-s1.pdf">
67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Exome Sequencing of 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
68                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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>.
69                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive sequencing of 98 clear cell kidney cancer samples. Generated by BGI-Shenzhen.
71                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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>.
72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA Kidney Renal Clear Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
73                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Kidney Renal Papillary Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
74                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Liver Hepatocellular Carcinoma from Asan Medical Center, Korea, containing 231 samples.
75                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Whole-genome sequencing of 27 hepatocellular carcinoma samples from RIKEN.
76                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TCGA Liver Hepatocellular Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
77                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Mutation data from whole exome sequencing of 23 grade II glioma patients.
78                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Comprehensive profiling of 183 lung adenocarcinoma samples. Generated by the Broad Institute.
79                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Whole-exome sequencing of non small cell lung cancers treated with pembrolizumab
80                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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>.
81                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Lung Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
82                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Targeted sequencing of 163 lung adenocarcinoma samples. Generated by WashU/Broad.
83                                                                                                                                                                                                                                                                                                                                                                                                                                        <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>.
84                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Lung Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
85                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
86                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay
87                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Prospective molecular characterization of lung adenocarcinomas for efficient patient matching.
88                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Targeted sequencing of clinical cases via MSK-IMPACT for prostate cancer (Abida et al, JCO Precision Oncology 2017).
89                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Exome profiling of 17 malignant peripheral nerve sheath tumors.
90                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Mutation data from whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) and matched blood samples.
91                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Whole exome sequencing of 29 primary mantle cell lymphomas.
92                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive profiling of 92 medulloblastoma samples from the Broad Institute.
93                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      125 Medulloblastoma tumor / normal pairs. ICGC.
94                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           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.
95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Mutation data from whole-genome sequencing (WGS) of 46 recurrent medulloblastoma samples.
96                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Somatic Mutation data from 25 Whole Genome Sequenced metastatic melanoma samples
97                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole-exome sequencing from TCGA LGG and GBM cases
98                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Mesothelioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
99                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive analysis of 150 metastatic prostate cancer samples by the SU2C/PCF Dream Team
100                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Exome sequencing of 205 multiple myeloma samples.
101                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Mutation data from multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
102                                                                                                                                                                                                                                                                                                                                                                                                              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.
103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole exome sequencing of 29 myelodysplasia samples from the University of Tokyo.
104                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
105                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Genomic characterization using next generation sequencing (NGS) in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.
106                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Whole genome sequencing of 56 NPC tumor / normal pairs. Generated by the Cancer Science Institute of Singapore, National University of Singapore.
107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole genome sequencing of 87 neuroblastoma samples from the Academic Medical Center, Amsterdam.
108                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Mutation data from whole-genome sequencing of 56 neuroblastoma samples
109                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Whole exome and RNA Seq data of castration resistant adenocarcinoma and castration resistant neuroendocrine prostate cancer (somatic mutations and copy number aberrations)
110                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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.
111                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Comprehensive profiling of 40 oral squamous cell carcinoma samples from MD Anderson.
112                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <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>.
113                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Ovarian Serous Cystadenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
114                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive genomic and transcriptomic analysis of ALM patients.
115                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
116                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Comprehensive profiling of 99 pancreatic cancer samples. Generated by ICGC.
117                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  342 primary tumours and 41 patient-derived cell lines underwent whole genome sequencing (WGS) when tumour cellularity was >40% (n=179), or deep-exome sequencing (n=204) for samples with a cellularity of 12-40%.
118                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   TCGA Pancreatic Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
119                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
120                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. <A HREF="https://www.sciencemag.org/content/331/6021/1199/suppl/DC1">
121                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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>.
122                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
123                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TCGA Pheochromocytoma and Paraganglioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
124                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Next generation sequencing (MSK-IMPACT) of 84 poorly-differentiated (PDTC) and 33 anaplastic thyroid cancers (ATC)
125                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Mutation data from whole exome sequencing (WXS) of 10 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
126                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Comprehensive profiling of 57 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
127                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Comprehensive profiling of 112 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
128                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive profiling of prostate cancer samples. Generated by Peter Nelson's lab at the Fred Hutchinson Cancer Research Center.
129                                                                                                                                                                                                                                                                                                                                                         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>.
130                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  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>.
131                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Prostate Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
132                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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>.
133                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Exome profiling of prostate cancer samples and matched organoids.
134                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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.
135                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
136                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Exome sequencing of 139 Renal Non-Clear Cell Carcinoma (NCCRCC) samples.
137                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Mutation data from WGS and/or WXS of 43 rhabdomyosarcoma samples.
138                                                                                                                                                                                                                                                                                                                                                                   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>.
139                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Sarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
140                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Comprehensive profiling of 121 melanoma samples. Generated by the Broad Institute.
141                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Skin Cutaneous Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
142                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Exome sequencing of 91 melanoma samples. Generated by Yale.
143                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Targeted sequencing of 12 SCCO samples.
144                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Comprehensive profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
145                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Comprehensive profiling of 36 primary human SCLC tumors and 17 matched SCLC and lymphoblastoid cell lines. Generated by Johns Hopkins.
146                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Comprehensive WGS profiling of 110 human SCLC specimens.
147                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Whole genome sequencing of 100 tumor-normal pairs from the University of Hong Kong and Pfizer.
148                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCGA Stomach Adenocarcinoma, containing 295 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
149                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Stomach Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples from the University of Tokyo.
151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Exome sequencing of 22 gastric cancer samples.
152                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TCGA data for Esophagus-Stomach Cancers.
153                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Prospective genomic profiling of 341 samples from 305 metastatic esophagogastric cancer patients
154                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Molecular Analysis of Unclassified Renal Cell Carcinoma
155                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCGA Testicular Germ Cell Cancer; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
156 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.
157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Whole exome sequencing of 28 thymic epithelial tumors.
158                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TCGA Thymoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
159                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TCGA Thyroid Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
160                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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">
161                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCGA Uterine Carcinosarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
162                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TCGA Uterine Corpus Endometrial Carcinoma, containing 373 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/">NCI</A>.
163                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        TCGA Uterine Corpus Endometrial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
164                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TCGA Uveal Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Whole-genome sequencing of 102 primary PanNETs and the defined genomic events that characterize their pathogenesis.
166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Genetic Characterization of 38 pretreatment (pembrolizumab and nivolumab) melanoma tumors.
167                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Whole-genome sequencing of 96 pilocytic astrocytomasatic alterations in pilocytic astrocytoma conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project.
> 
> # Get available case lists (collection of samples) for a given cancer study  
> mycancerstudy = getCancerStudies(mycgds)[2,1]
> mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]
> 
> # Get available genetic profiles
> mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[1,1]
> 
> # Get data slices for a specified list of genes, genetic profile and case list
> getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get data slice for a single gene
> getProfileData(mycgds,'HMGA2',mygeneticprofile,mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get data slice for multiple genetic profiles and single gene
> getProfileData(mycgds,'HMGA2',getGeneticProfiles(mycgds,mycancerstudy)[c(1,2),1],mycaselist)
[1] Error..Invalid.case_set_id...NA.
<0 rows> (or 0-length row.names)
> 
> # Get the same dataset from a vector of case IDs
> cases = unlist(strsplit(getCaseLists(mycgds,mycancerstudy)[1,'case_ids'],' '))
Error in strsplit(getCaseLists(mycgds, mycancerstudy)[1, "case_ids"],  : 
  non-character argument
Calls: unlist -> strsplit
Execution halted