* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/cgdsr.Rcheck’ * using R Under development (unstable) (2022-04-01 r82052) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘cgdsr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cgdsr’ version ‘1.3.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cgdsr’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/12s] OK * checking examples with --run-donttest ... ERROR Running examples in ‘cgdsr-Ex.R’ failed The error most likely occurred in: > ### Name: cgdsr-getMutationData > ### Title: Get mutation data for cancer study > ### Aliases: cgdsr-getMutationData getMutationData getMutationData.CGDS > > ### ** Examples > > # Create CGDS object > mycgds = CGDS("http://www.cbioportal.org/") > > getCancerStudies(mycgds) cancer_study_id 1 paac_jhu_2014 2 mel_tsam_liang_2017 3 all_stjude_2015 4 all_stjude_2016 5 aml_ohsu_2018 6 laml_tcga 7 laml_tcga_pub 8 laml_tcga_pan_can_atlas_2018 9 mnm_washu_2016 10 acyc_fmi_2014 11 acyc_jhu_2016 12 acyc_mda_2015 13 acyc_mgh_2016 14 acyc_mskcc_2013 15 acyc_sanger_2013 16 acc_2019 17 acbc_mskcc_2015 18 acc_tcga 19 acc_tcga_pan_can_atlas_2018 20 sarc_tcga_pub 21 ampca_bcm_2016 22 odg_msk_2017 23 bcc_unige_2016 24 blca_msk_tcga_2020 25 blca_mskcc_solit_2014 26 blca_mskcc_solit_2012 27 blca_plasmacytoid_mskcc_2016 28 blca_tcga_pub_2017 29 blca_bgi 30 blca_dfarber_mskcc_2014 31 blca_tcga 32 blca_tcga_pub 33 blca_tcga_pan_can_atlas_2018 34 lgg_tcga 35 lgg_tcga_pan_can_atlas_2018 36 gbm_mayo_pdx_sarkaria_2019 37 brca_hta9_htan_2022 38 brca_metabric 39 breast_msk_2018 40 brca_pareja_msk_2020 41 breast_alpelisib_2020 42 brca_mskcc_2019 43 brca_smc_2018 44 brca_bccrc_xenograft_2014 45 bfn_duke_nus_2015 46 brca_bccrc 47 brca_broad 48 brca_sanger 49 brca_tcga_pub2015 50 brca_tcga 51 brca_tcga_pub 52 brca_tcga_pan_can_atlas_2018 53 ccle_broad_2019 54 cellline_ccle_broad 55 msk_ch_ped_2021 56 msk_ch_2020 57 cesc_tcga_pan_can_atlas_2018 58 cesc_tcga 59 pan_origimed_2020 60 chol_icgc_2017 61 chol_msk_2018 62 chol_nccs_2013 63 chol_nus_2012 64 chol_tcga 65 chol_tcga_pan_can_atlas_2018 66 lcll_broad_2013 67 cll_broad_2015 68 cll_iuopa_2015 69 cllsll_icgc_2011 70 ccrcc_dfci_2019 71 coad_caseccc_2015 72 coad_cptac_2019 73 coadread_dfci_2016 74 coadread_genentech 75 coadread_tcga 76 coadread_tcga_pub 77 coadread_tcga_pan_can_atlas_2018 78 coadread_mskcc 79 crc_dd_2022 80 crc_apc_impact_2020 81 hccihch_pku_2019 82 cscc_dfarber_2015 83 cscc_hgsc_bcm_2014 84 cscc_ucsf_2021 85 ctcl_columbia_2015 86 pact_jhu_2011 87 desm_broad_2015 88 difg_glass_2019 89 dlbcl_dfci_2018 90 dlbc_broad_2012 91 dlbcl_duke_2017 92 dlbc_tcga_pan_can_atlas_2018 93 nhl_bcgsc_2013 94 crc_nigerian_2020 95 ucec_msk_2018 96 ucec_cptac_2020 97 esca_broad 98 esca_tcga_pan_can_atlas_2018 99 egc_trap_msk_2020 100 esca_tcga 101 stes_tcga_pub 102 escc_icgc 103 escc_ucla_2014 104 egc_mskcc_2020 105 es_iocurie_2014 106 gbc_msk_2018 107 gbc_shanghai_2014 108 egc_tmucih_2015 109 stad_oncosg_2018 110 gct_msk_2016 111 gct_msk_2020 112 gbm_cptac_2021 113 gbm_columbia_2019 114 gbm_tcga_pub2013 115 gbm_tcga_pub 116 gbm_tcga 117 gbm_tcga_pan_can_atlas_2018 118 glioma_msk_2018 119 glioma_mskcc_2019 120 hnsc_broad 121 hnsc_jhu 122 hnsc_tcga 123 hnsc_tcga_pub 124 hnsc_tcga_pan_can_atlas_2018 125 liad_inserm_fr_2014 126 hcc_mskimpact_2018 127 hcc_inserm_fr_2015 128 hgsoc_msk_2021 129 histiocytosis_cobi_msk_2019 130 all_stjude_2013 131 panet_shanghai_2013 132 chol_jhu_2013 133 ihch_mskcc_2020 134 ihch_msk_2021 135 ihch_ismms_2015 136 ihch_smmu_2014 137 brca_jup_msk_2020 138 kich_tcga_pub 139 kich_tcga 140 kich_tcga_pan_can_atlas_2018 141 kirc_bgi 142 ccrcc_irc_2014 143 kirc_tcga 144 kirc_tcga_pub 145 kirc_tcga_pan_can_atlas_2018 146 kirp_tcga 147 kirp_tcga_pan_can_atlas_2018 148 hcc_msk_venturaa_2018 149 lihc_amc_prv 150 lihc_riken 151 lihc_tcga 152 lihc_tcga_pan_can_atlas_2018 153 lgg_ucsf_2014 154 luad_broad 155 luad_cptac_2020 156 luad_mskcc_2020 157 luad_mskimpact_2021 158 luad_mskcc_2015 159 luad_msk_npjpo_2021 160 luad_oncosg_2020 161 luad_tcga 162 luad_tcga_pub 163 luad_tcga_pan_can_atlas_2018 164 luad_tsp 165 lung_smc_2016 166 lusc_cptac_2021 167 lusc_tcga 168 lusc_tcga_pub 169 lusc_tcga_pan_can_atlas_2018 170 dlbc_tcga 171 lymphoma_cellline_msk_2020 172 brca_mapk_hp_msk_2021 173 msk_met_2021 174 msk_impact_2017 175 msk_access_2021 176 mixed_allen_2018 177 mpnst_mskcc 178 mcl_idibips_2013 179 mbn_mdacc_2013 180 mbl_broad_2012 181 mbl_dkfz_2017 182 mbl_icgc 183 mbl_pcgp 184 mbl_sickkids_2016 185 skcm_broad_dfarber 186 mel_mskimpact_2020 187 skcm_mskcc_2014 188 skcm_tcga_pub_2015 189 lgggbm_tcga_pub 190 meso_tcga 191 meso_tcga_pan_can_atlas_2018 192 mbc_msk_2021 193 brca_igr_2015 194 breast_ink4_msk_2021 195 crc_msk_2017 196 egc_msk_2017 197 mel_dfci_2019 198 skcm_dfci_2015 199 skcm_vanderbilt_mskcc_2015 200 mel_ucla_2016 201 prad_mich 202 prad_su2c_2019 203 prad_su2c_2015 204 metastatic_solid_tumors_mich_2017 205 prad_mcspc_mskcc_2020 206 mixed_kunga_msk_2022 207 cfdna_msk_2019 208 mixed_cfdna_msk_2020 209 mm_broad 210 mds_tokyo_2011 211 mds_mskcc_2020 212 mpn_cimr_2013 213 cellline_nci60 214 npc_nusingapore 215 nbl_amc_2012 216 nbl_broad_2013 217 nbl_ucologne_2015 218 nepc_wcm_2016 219 nhl_bcgsc_2011 220 lung_msk_2017 221 nsclc_mskcc_2018 222 nsclc_pd1_msk_2018 223 nsclc_tracerx_2017 224 nsclc_unito_2016 225 nsclc_mskcc_2015 226 blca_nmibc_2017 227 hnsc_mdanderson_2013 228 ov_tcga 229 ov_tcga_pub 230 ov_tcga_pan_can_atlas_2018 231 nsclc_tcga_broad_2016 232 pancan_pcawg_2020 233 paad_icgc 234 paad_qcmg_uq_2016 235 paad_tcga 236 paad_tcga_pan_can_atlas_2018 237 paad_utsw_2015 238 paad_cptac_2021 239 panet_jhu_2011 240 panet_arcnet_2017 241 thca_tcga_pub 242 all_phase2_target_2018_pub 243 aml_target_2018_pub 244 brain_cptac_2020 245 es_dfarber_broad_2014 246 nbl_target_2018_pub 247 pediatric_dkfz_2017 248 mixed_pipseq_2017 249 pptc_2019 250 rt_target_2018_pub 251 wt_target_2018_pub 252 pcpg_tcga_pub 253 pcpg_tcga 254 pcpg_tcga_pan_can_atlas_2018 255 past_dkfz_heidelberg_2013 256 plmeso_nyu_2015 257 thyroid_mskcc_2016 258 pcnsl_mayo_2015 259 prad_broad_2013 260 prad_broad 261 prad_cpcg_2017 262 prad_fhcrc 263 prad_cdk12_mskcc_2020 264 prad_mskcc 265 prad_mskcc_2014 266 prad_p1000 267 prad_eururol_2017 268 prad_tcga_pub 269 prad_tcga 270 prad_tcga_pan_can_atlas_2018 271 prad_mskcc_cheny1_organoids_2014 272 prostate_dkfz_2018 273 prad_msk_2019 274 prad_mskcc_2017 275 brca_cptac_2020 276 mixed_msk_tcga_2021 277 prad_msk_stopsack_2021 278 rectal_msk_2019 279 hnc_mskcc_2016 280 ccrcc_utokyo_2013 281 nccrcc_genentech_2014 282 rbl_mskcc_2020 283 rbl_cfdna_msk_2020 284 mrt_bcgsc_2016 285 rms_nih_2014 286 summit_2018 287 sarcoma_mskcc_2022 288 sarc_mskcc 289 sarc_tcga 290 sarc_tcga_pan_can_atlas_2018 291 skcm_broad 292 skcm_tcga 293 skcm_tcga_pan_can_atlas_2018 294 skcm_yale 295 skcm_broad_brafresist_2012 296 scco_mskcc 297 sclc_clcgp 298 sclc_jhu 299 sclc_ucologne_2015 300 sclc_cancercell_gardner_2017 301 vsc_cuk_2018 302 stad_pfizer_uhongkong 303 stad_tcga 304 stad_tcga_pub 305 stad_tcga_pan_can_atlas_2018 306 stad_utokyo 307 stad_uhongkong 308 tmb_mskcc_2018 309 tgct_tcga 310 tgct_tcga_pan_can_atlas_2018 311 angs_painter_2020 312 angs_project_painter_2018 313 brca_mbcproject_wagle_2017 314 mpcproject_broad_2021 315 lung_pdx_msk_2021 316 lung_msk_pdx 317 tet_nci_2014 318 thym_tcga 319 thym_tcga_pan_can_atlas_2018 320 thca_tcga 321 thca_tcga_pan_can_atlas_2018 322 ntrk_msk_2019 323 urcc_mskcc_2016 324 utuc_mskcc_2015 325 utuc_cornell_baylor_mdacc_2019 326 utuc_igbmc_2021 327 utuc_msk_2019 328 utuc_pdx_msk_2019 329 blca_cornell_2016 330 ucs_jhu_2014 331 ucs_tcga 332 ucs_tcga_pan_can_atlas_2018 333 uccc_nih_2017 334 ucec_tcga 335 ucec_tcga_pub 336 ucec_tcga_pan_can_atlas_2018 337 usarc_msk_2020 338 um_qimr_2016 339 uvm_tcga 340 uvm_tcga_pan_can_atlas_2018 name 1 Acinar Cell Carcinoma of the Pancreas (JHU, J Pathol 2014) 2 Acral Melanoma (TGEN, Genome Res 2017) 3 Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015) 4 Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2016) 5 Acute Myeloid Leukemia (OHSU, Nature 2018) 6 Acute Myeloid Leukemia (TCGA, Firehose Legacy) 7 Acute Myeloid Leukemia (TCGA, NEJM 2013) 8 Acute Myeloid Leukemia (TCGA, PanCancer Atlas) 9 Acute myeloid leukemia or myelodysplastic syndromes (WashU, 2016) 10 Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014) 11 Adenoid Cystic Carcinoma (JHU, Cancer Prev Res 2016) 12 Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015) 13 Adenoid Cystic Carcinoma (MGH, Nat Gen 2016) 14 Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013) 15 Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013) 16 Adenoid Cystic Carcinoma Project (J Clin Invest 2019) 17 Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015) 18 Adrenocortical Carcinoma (TCGA, Firehose Legacy) 19 Adrenocortical Carcinoma (TCGA, PanCancer Atlas) 20 Adult Soft Tissue Sarcomas (TCGA, Cell 2017) 21 Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016) 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytoma (MSKCC, Neuro Oncol 2017) 23 Basal Cell Carcinoma (UNIGE, Nat Genet 2016) 24 Bladder Cancer (MSK/TCGA, 2020) 25 Bladder Cancer (MSKCC, Eur Urol 2014) 26 Bladder Cancer (MSKCC, J Clin Onco 2013) 27 Bladder Cancer (MSKCC, Nat Genet 2016) 28 Bladder Cancer (TCGA, Cell 2017) 29 Bladder Urothelial Carcinoma (BGI, Nat Genet 2013) 30 Bladder Urothelial Carcinoma (DFCI/MSKCC, Cancer Discov 2014) 31 Bladder Urothelial Carcinoma (TCGA, Firehose Legacy) 32 Bladder Urothelial Carcinoma (TCGA, Nature 2014) 33 Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas) 34 Brain Lower Grade Glioma (TCGA, Firehose Legacy) 35 Brain Lower Grade Glioma (TCGA, PanCancer Atlas) 36 Brain Tumor PDXs (Mayo Clinic, 2019) 37 Breast Cancer (HTAN, Cell Rep Med 2022) 38 Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016) 39 Breast Cancer (MSK, Cancer Cell 2018) 40 Breast Cancer (MSK, Clinical Cancer Res 2020) 41 Breast Cancer (MSK, Nature Cancer 2020) 42 Breast Cancer (MSKCC, NPJ Breast Cancer 2019) 43 Breast Cancer (SMC 2018) 44 Breast Cancer Xenografts (British Columbia, Nature 2015) 45 Breast Fibroepithelial Tumors (Duke-NUS, Nat Genet 2015) 46 Breast Invasive Carcinoma (British Columbia, Nature 2012) 47 Breast Invasive Carcinoma (Broad, Nature 2012) 48 Breast Invasive Carcinoma (Sanger, Nature 2012) 49 Breast Invasive Carcinoma (TCGA, Cell 2015) 50 Breast Invasive Carcinoma (TCGA, Firehose Legacy) 51 Breast Invasive Carcinoma (TCGA, Nature 2012) 52 Breast Invasive Carcinoma (TCGA, PanCancer Atlas) 53 Cancer Cell Line Encyclopedia (Broad, 2019) 54 Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012) 55 Cancer Therapy and Clonal Hematopoiesis (MSK, 2021) 56 Cancer Therapy and Clonal Hematopoiesis (MSK, Nat Genet 2020) 57 Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas) 58 Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Firehose Legacy) 59 China Pan-cancer (OrigiMed2020) 60 Cholangiocarcinoma (ICGC, Cancer Discov 2017) 61 Cholangiocarcinoma (MSK, Clin Cancer Res 2018) 62 Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013) 63 Cholangiocarcinoma (National University of Singapore, Nat Genet 2012) 64 Cholangiocarcinoma (TCGA, Firehose Legacy) 65 Cholangiocarcinoma (TCGA, PanCancer Atlas) 66 Chronic Lymphocytic Leukemia (Broad, Cell 2013) 67 Chronic Lymphocytic Leukemia (Broad, Nature 2015) 68 Chronic Lymphocytic Leukemia (IUOPA, Nature 2015) 69 Chronic lymphocytic leukemia (ICGC, Nature Genetics 2011) 70 Clear Cell Renal Cell Carcinoma (DFCI, Science 2019) 71 Colon Adenocarcinoma (CaseCCC, PNAS 2015) 72 Colon Cancer (CPTAC-2 Prospective, Cell 2019) 73 Colorectal Adenocarcinoma (DFCI, Cell Reports 2016) 74 Colorectal Adenocarcinoma (Genentech, Nature 2012) 75 Colorectal Adenocarcinoma (TCGA, Firehose Legacy) 76 Colorectal Adenocarcinoma (TCGA, Nature 2012) 77 Colorectal Adenocarcinoma (TCGA, PanCancer Atlas) 78 Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014) 79 Colorectal Cancer (MSK, 2022) 80 Colorectal Cancer (MSK, Gastroenterology 2020) 81 Combined Hepatocellular and Intrahepatic Cholangiocarcinoma (Peking University, Cancer Cell 2019) 82 Cutaneous Squamous Cell Carcinoma (DFCI, Clin Cancer Res 2015) 83 Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014) 84 Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021) 85 Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015) 86 Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011) 87 Desmoplastic Melanoma (Broad Institute, Nat Genet 2015) 88 Diffuse Glioma (GLASS Consortium, Nature 2019) 89 Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018) 90 Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012) 91 Diffuse Large B-Cell Lymphoma (Duke, Cell 2017) 92 Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas) 93 Diffuse Large B-cell Lymphoma (BCGSC, Blood 2013) 94 Disparities in metastatic colorectal cancer between Africans and Americans (MSK, 2020) 95 Endometrial Cancer (MSK, 2018) 96 Endometrial Carcinoma (CPTAC, Cell 2020) 97 Esophageal Adenocarcinoma (DFCI, Nat Genet 2013) 98 Esophageal Adenocarcinoma (TCGA, PanCancer Atlas) 99 Esophageal Cancer-TRAP Project (MSK, Lancet Oncol 2020) 100 Esophageal Carcinoma (TCGA, Firehose Legacy) 101 Esophageal Carcinoma (TCGA, Nature 2017) 102 Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014) 103 Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014) 104 Esophageal/Stomach Cancer (MSK, 2020) 105 Ewing Sarcoma (Institut Curie, Cancer Discov 2014) 106 Gallbladder Cancer (MSK, Cancer 2018) 107 Gallbladder Carcinoma (Shanghai, Nat Genet 2014) 108 Gastric Adenocarcinoma (TMUCIH, PNAS 2015) 109 Gastric Cancer (OncoSG, 2018) 110 Germ Cell Tumors (MSKCC, J Clin Oncol 2016) 111 Germ Cell Tumors and Shared Leukemias (MSK, 2020) 112 Glioblastoma (CPTAC, Cell 2021) 113 Glioblastoma (Columbia, Nat Med. 2019) 114 Glioblastoma (TCGA, Cell 2013) 115 Glioblastoma (TCGA, Nature 2008) 116 Glioblastoma Multiforme (TCGA, Firehose Legacy) 117 Glioblastoma Multiforme (TCGA, PanCancer Atlas) 118 Glioma (MSK, Nature 2019) 119 Glioma (MSKCC, Clin Cancer Res 2019) 120 Head and Neck Squamous Cell Carcinoma (Broad, Science 2011) 121 Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011) 122 Head and Neck Squamous Cell Carcinoma (TCGA, Firehose Legacy) 123 Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015) 124 Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas) 125 Hepatocellular Adenoma (INSERM, Cancer Cell 2014) 126 Hepatocellular Carcinoma (MSK, Clin Cancer Res 2018) 127 Hepatocellular Carcinomas (INSERM, Nat Genet 2015) 128 High-Grade Serous Ovarian Cancer (MSK, 2021) 129 Histiocytosis Cobimetinib (MSK, Nature 2019) 130 Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013) 131 Insulinoma (Shanghai, Nat Commun 2013) 132 Intrahepatic Cholangiocarcinoma (JHU, Nat Genet 2013) 133 Intrahepatic Cholangiocarcinoma (MSK, 2020) 134 Intrahepatic Cholangiocarcinoma (MSK, Hepatology 2021) 135 Intrahepatic Cholangiocarcinoma (Mount Sinai 2015) 136 Intrahepatic Cholangiocarcinoma (Shanghai, Nat Commun 2014) 137 Juvenile Papillomatosis and Breast Cancer (MSK, 2020) 138 Kidney Chromophobe (TCGA, Cancer Cell 2014) 139 Kidney Chromophobe (TCGA, Firehose Legacy) 140 Kidney Chromophobe (TCGA, PanCancer Atlas) 141 Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012) 142 Kidney Renal Clear Cell Carcinoma (IRC, Nat Genet 2014) 143 Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy) 144 Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013) 145 Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas) 146 Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy) 147 Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas) 148 Liver Hepatocellular Adenoma and Carcinomas (MSK, PLOS One 2018) 149 Liver Hepatocellular Carcinoma (AMC, Hepatology 2014) 150 Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012) 151 Liver Hepatocellular Carcinoma (TCGA, Firehose Legacy) 152 Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas) 153 Low-Grade Gliomas (UCSF, Science 2014) 154 Lung Adenocarcinoma (Broad, Cell 2012) 155 Lung Adenocarcinoma (CPTAC, Cell 2020) 156 Lung Adenocarcinoma (MSKCC, 2020) 157 Lung Adenocarcinoma (MSKCC, 2021) 158 Lung Adenocarcinoma (MSKCC, Science 2015) 159 Lung Adenocarcinoma (NPJ Precision Oncology, MSK 2021) 160 Lung Adenocarcinoma (OncoSG, Nat Genet 2020) 161 Lung Adenocarcinoma (TCGA, Firehose Legacy) 162 Lung Adenocarcinoma (TCGA, Nature 2014) 163 Lung Adenocarcinoma (TCGA, PanCancer Atlas) 164 Lung Adenocarcinoma (TSP, Nature 2008) 165 Lung Cancer (SMC, Cancer Research 2016) 166 Lung Squamous Cell Carcinoma (CPTAC, Cell 2021) 167 Lung Squamous Cell Carcinoma (TCGA, Firehose Legacy) 168 Lung Squamous Cell Carcinoma (TCGA, Nature 2012) 169 Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas) 170 Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Firehose Legacy) 171 Lymphoma Cell Lines (MSKCC, 2020) 172 MAPK on resistance to anti-HER2 therapy for breast cancer (MSKCC, Nat Comm 2021) 173 MSK MetTropism (MSK, Cell 2021) 174 MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017) 175 MSK-IMPACT and MSK-ACCESS Mixed Cohort (MSK, 2021) 176 MSS Mixed Solid Tumors (Broad/Dana-Farber, Nat Genet 2018) 177 Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014) 178 Mantle Cell Lymphoma (IDIBIPS, PNAS 2013) 179 Mature B-cell malignancies (MD Anderson Cancer Center) 180 Medulloblastoma (Broad, Nature 2012) 181 Medulloblastoma (DKFZ, Nature 2017) 182 Medulloblastoma (ICGC, Nature 2012) 183 Medulloblastoma (PCGP, Nature 2012) 184 Medulloblastoma (Sickkids, Nature 2016) 185 Melanoma (Broad/Dana Farber, Nature 2012) 186 Melanoma (MSKCC, Clin Cancer Res 2021) 187 Melanoma (MSKCC, NEJM 2014) 188 Melanomas (TCGA, Cell 2015) 189 Merged Cohort of LGG and GBM (TCGA, Cell 2016) 190 Mesothelioma (TCGA, Firehose Legacy) 191 Mesothelioma (TCGA, PanCancer Atlas) 192 Metaplastic Breast Cancer (MSK, 2021) 193 Metastatic Breast Cancer (INSERM, PLoS Med 2016) 194 Metastatic Breast Cancer (MSK, Cancer Discovery 2021) 195 Metastatic Colorectal Cancer (MSKCC, Cancer Cell 2018) 196 Metastatic Esophagogastric Cancer (MSKCC, Cancer Discovery 2017) 197 Metastatic Melanoma (DFCI, Nature Medicine 2019) 198 Metastatic Melanoma (DFCI, Science 2015) 199 Metastatic Melanoma (MSKCC, JCO Precis Oncol 2017) 200 Metastatic Melanoma (UCLA, Cell 2016) 201 Metastatic Prostate Adenocarcinoma (MCTP, Nature 2012) 202 Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019) 203 Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015) 204 Metastatic Solid Cancers (UMich, Nature 2017) 205 Metastatic castration-sensitive prostate cancer (MSK, Clin Cancer Res 2020) 206 Mixed Tumors (MSK, 2022) 207 Mixed cfDNA (MSK, Nature Medicine 2019) 208 Mixed cfDNA (MSKCC, 2020) 209 Multiple Myeloma (Broad, Cancer Cell 2014) 210 Myelodysplasia (UTokyo, Nature 2011) 211 Myelodysplastic (MSKCC, 2020) 212 Myeloproliferative Neoplasms (CIMR, NEJM 2013) 213 NCI-60 Cell Lines (NCI, Cancer Res 2012) 214 Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014) 215 Neuroblastoma (AMC Amsterdam, Nature 2012) 216 Neuroblastoma (Broad, Nat Genet 2013) 217 Neuroblastoma (Broad, Nature 2015) 218 Neuroendocrine Prostate Cancer (Multi-Institute, Nat Med 2016) 219 Non-Hodgkin Lymphoma (BCGSC, Nature 2011) 220 Non-Small Cell Cancer (MSKCC, Cancer Discov 2017) 221 Non-Small Cell Lung Cancer (MSK, Cancer Cell 2018) 222 Non-Small Cell Lung Cancer (MSKCC, J Clin Oncol 2018) 223 Non-Small Cell Lung Cancer (TRACERx, NEJM & Nature 2017) 224 Non-Small Cell Lung Cancer (University of Turin, Lung Cancer 2017) 225 Non-small cell lung cancer (MSK, Science 2015) 226 Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017) 227 Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013) 228 Ovarian Serous Cystadenocarcinoma (TCGA, Firehose Legacy) 229 Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011) 230 Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas) 231 Pan-Lung Cancer (TCGA, Nat Genet 2016) 232 Pan-cancer analysis of whole genomes (ICGC/TCGA, Nature 2020) 233 Pancreatic Adenocarcinoma (ICGC, Nature 2012) 234 Pancreatic Adenocarcinoma (QCMG, Nature 2016) 235 Pancreatic Adenocarcinoma (TCGA, Firehose Legacy) 236 Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas) 237 Pancreatic Cancer (UTSW, Nat Commun 2015) 238 Pancreatic Ductal Adenocarcinoma (CPTAC, Cell 2021) 239 Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011) 240 Pancreatic Neuroendocrine Tumors (Multi-Institute, Nature 2017) 241 Papillary Thyroid Carcinoma (TCGA, Cell 2014) 242 Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018) 243 Pediatric Acute Myeloid Leukemia (TARGET, 2018) 244 Pediatric Brain Cancer (CPTAC/CHOP, Cell 2020) 245 Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014) 246 Pediatric Neuroblastoma (TARGET, 2018) 247 Pediatric Pan-Cancer (DKFZ, Nature 2017) 248 Pediatric Pan-cancer (Columbia U, Genome Med 2016) 249 Pediatric Preclinical Testing Consortium (CHOP, Cell Rep 2019) 250 Pediatric Rhabdoid Tumor (TARGET, 2018) 251 Pediatric Wilms' Tumor (TARGET, 2018) 252 Pheochromocytoma and Paraganglioma (TCGA, Cell 2017) 253 Pheochromocytoma and Paraganglioma (TCGA, Firehose Legacy) 254 Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas) 255 Pilocytic Astrocytoma (ICGC, Nature Genetics 2013) 256 Pleural Mesothelioma (NYU, Cancer Res 2015) 257 Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016) 258 Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015) 259 Prostate Adenocarcinoma (Broad/Cornell, Cell 2013) 260 Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012) 261 Prostate Adenocarcinoma (CPC-GENE, Nature 2017) 262 Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016) 263 Prostate Adenocarcinoma (MSK, Eur Urol 2020) 264 Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010) 265 Prostate Adenocarcinoma (MSKCC, PNAS 2014) 266 Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018) 267 Prostate Adenocarcinoma (SMMU, Eur Urol 2017) 268 Prostate Adenocarcinoma (TCGA, Cell 2015) 269 Prostate Adenocarcinoma (TCGA, Firehose Legacy) 270 Prostate Adenocarcinoma (TCGA, PanCancer Atlas) 271 Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014) 272 Prostate Cancer (DKFZ, Cancer Cell 2018) 273 Prostate Cancer (MSK, Cell Metab 2020) 274 Prostate Cancer (MSKCC, JCO Precis Oncol 2017) 275 Proteogenomic landscape of breast cancer (CPTAC, Cell 2020) 276 RAD51B Associated Mixed Cancers (Mandelker 2021) 277 Race Differences in Prostate Cancer (MSK, 2021) 278 Rectal Cancer (MSK,Nature Medicine 2019) 279 Recurrent and Metastatic Head & Neck Cancer (MSKCC, JAMA Oncol 2016) 280 Renal Clear Cell Carcinoma (UTokyo, Nat Genet 2013) 281 Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014) 282 Retinoblastoma (MSK, Cancers 2021) 283 Retinoblastoma cfDNA (MSKCC 2020) 284 Rhabdoid Cancer (BCGSC, Cancer Cell 2016) 285 Rhabdomyosarcoma (NIH, Cancer Discov 2014) 286 SUMMIT - Neratinib Basket Study (Multi-Institute, Nature 2018) 287 Sarcoma (MSK, 2022) 288 Sarcoma (MSKCC/Broad, Nat Genet 2010) 289 Sarcoma (TCGA, Firehose Legacy) 290 Sarcoma (TCGA, PanCancer Atlas) 291 Skin Cutaneous Melanoma (Broad, Cell 2012) 292 Skin Cutaneous Melanoma (TCGA, Firehose Legacy) 293 Skin Cutaneous Melanoma (TCGA, PanCancer Atlas) 294 Skin Cutaneous Melanoma (Yale, Nat Genet 2012) 295 Skin Cutaneous Melanoma(Broad, Cancer Discov 2014) 296 Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014) 297 Small Cell Lung Cancer (CLCGP, Nat Genet 2012) 298 Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012) 299 Small Cell Lung Cancer (U Cologne, Nature 2015) 300 Small-Cell Lung Cancer (Multi-Institute, Cancer Cell 2017) 301 Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018) 302 Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014) 303 Stomach Adenocarcinoma (TCGA, Firehose Legacy) 304 Stomach Adenocarcinoma (TCGA, Nature 2014) 305 Stomach Adenocarcinoma (TCGA, PanCancer Atlas) 306 Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014) 307 Stomach Adenocarcinoma (UHK, Nat Genet 2011) 308 TMB and Immunotherapy (MSKCC, Nat Genet 2019) 309 Testicular Germ Cell Cancer (TCGA, Firehose Legacy) 310 Testicular Germ Cell Tumors (TCGA, PanCancer Atlas) 311 The Angiosarcoma Project (Provisional, July 2020) 312 The Angiosarcoma Project - Count Me In (Nature Medicine, 2020) 313 The Metastatic Breast Cancer Project (Provisional, February 2020) 314 The Metastatic Prostate Cancer Project (Provisional, June 2021) 315 Thoracic Cancer (MSK, 2021) 316 Thoracic PDX (MSK, Provisional) 317 Thymic Epithelial Tumors (NCI, Nat Genet 2014) 318 Thymoma (TCGA, Firehose Legacy) 319 Thymoma (TCGA, PanCancer Atlas) 320 Thyroid Carcinoma (TCGA, Firehose Legacy) 321 Thyroid Carcinoma (TCGA, PanCancer Atlas) 322 Tumors with TRK fusions (MSK, Clin Cancer Res 2020) 323 Unclassified Renal Cell Carcinoma (MSK, Nature 2016) 324 Upper Tract Urothelial Cancer (MSK, Eur Urol 2015) 325 Upper Tract Urothelial Carcinoma (Cornell/Baylor/MDACC, Nat Commun 2019) 326 Upper Tract Urothelial Carcinoma (IGBMC, Genome Biology 2021) 327 Upper Tract Urothelial Carcinoma (MSK, Nat Commun 2020) 328 Upper Tract Urothelial Carcinoma PDX (MSK, Nat Commun 2020) 329 Urothelial Carcinoma (Cornell/Trento, Nat Gen 2016) 330 Uterine Carcinosarcoma (Johns Hopkins, Nat Commun 2014) 331 Uterine Carcinosarcoma (TCGA, Firehose Legacy) 332 Uterine Carcinosarcoma (TCGA, PanCancer Atlas) 333 Uterine Clear Cell Carcinoma (NIH, Cancer 2017) 334 Uterine Corpus Endometrial Carcinoma (TCGA, Firehose Legacy) 335 Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013) 336 Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas) 337 Uterine Sarcoma/Mesenchymal (MSK, Clin Cancer Res 2020) 338 Uveal Melanoma (QIMR, Oncotarget 2016) 339 Uveal Melanoma (TCGA, Firehose Legacy) 340 Uveal Melanoma (TCGA, PanCancer Atlas) description 1 Whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation and their matched normals. 2 Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals). 3 Comprehensive profiling of infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) 4 Whole-genome and/or whole-exome sequencing of ERG-altered B-ALL tumor/normal pairs. 5 Whole-exome sequencing of 672 acute myeloid leukemia samples (with 454 matched normals) from the Beat AML program. 6 TCGA Acute Myeloid Leukemia. Source data from GDAC Firehose. Previously known as TCGA Provisional. 7 Whole-genome or whole-exome sequencing analysis of 200 adult de novo AML tumor/normal pairs. TCGA Acute Myeloid Leukemia Project; raw data at the NCI. 8 Acute Myeloid Leukemia TCGA PanCancer data. The original data is here. The publications are here. 9 Enhanced exome or targeted sequencing of 116 acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS) patients' tumor/normal pairs . 10 Targeted Sequencing of 28 metastatic Adenoid Cystic Carcinoma samples. 11 Whole-genome or whole-exome sequencing of 25 adenoid cystic carcinoma tumor/normal pairs. 12 WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients). 13 Whole-genome/exome sequencing of 10 ACC PDX models. 14 Whole-exome or whole-genome sequencing analysis of 60 ACC tumor/normal pairs 15 Whole exome sequencing of 24 ACCs. 16 Multi-Institute Cohort of 1045 Adenoid Cystic Carcinoma patients. 17 Whole exome sequencing of 12 breast AdCCs. 18 TCGA Adrenocortical Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 19 Adrenocortical Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 20 Whole-exome sequencing of 206 Adult Soft Tissue Sarcoma tumor/normal pairs. 21 Exome sequencing analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44) or the duodenum (n = 18) and 98 for which the epithelium of origin could not be clearly defined morphologically (AMPCA). 22 IMPACT sequencing of 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas. 23 Whole-exome sequencing of 126 basal cell carcinoma tumor/normal pairs; targeted sequencing of 163 sporadic samples (40 tumor/normal pairs) and 4 Gorlin symdrome basal cell carcinomas. 24 Whole-exome or targeted sequencing of 476 muscle-invasive bladder tumor/normal pairs via TCGA or MSK-IMPACT sequencing. 25 Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014). 26 Comprehensive profiling of 97 high-grade bladder tumors, including targeted sequencing of 15 cancer genes 27 Whole exome and targeted sequencing of 34 plasmacytoid-variant (signet ring cell) tumors of the bladder 28 Whole-exome sequencing of 412 muscle-invasive bladder tumors and matched normal samples. 29 Whole-exome and whole-genome sequencing of 99 bladder cancer tumor/normal pairs. Generated by BGI. 30 Whole exome sequencing of tumor/normal samples from 50 patients treated with cisplatin-based chemotherapy for muscle invasive urothelial carcinoma. 31 TCGA Bladder Urothelial Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 32 Whole-exome sequencing of 131 high-grade muscle-invasive urothelial bladder carcinomas 33 Bladder Urothelial Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 34 TCGA Brain Lower Grade Glioma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 35 Brain Lower Grade Glioma TCGA PanCancer data. The original data is here. The publications are here. 36 WES on a total of 83 PDXs and 55 PDXs have the matched germline (blood) samples sequenced. A total of 66 PDXs have RNASeq available 37 Sequencing data from breast cancer patient from HTAN 38 Targeted sequencing of 2509 primary breast tumors with 548 matched normals. 39 Targeted Sequencing of tumor/normal sample pairs from 1918 Breast cancers. 40 Whole-exome and MSK-IMPACT sequencing of 60 tumor/normal matched samples. 41 Targeted sequencing of pre- and post-treatment tumor/cfDNA samples from 51 Breast Cancer patients to understand the mechanisms of resistance to Alepelisib. 42 Targeted Sequencing of buparlisib + letrozole and alpelisib + letrozole-treated metastatic ER+ unmatched breast tumors. 43 Whole-exome sequencing of 187 primary tumors from a Korean breast cancer cohort (SMC). 44 Whole genome/targeted sequencing to evaluate the clonal dynamics in 116 breast cancer patient xenografts. 45 Whole exome sequencing of 22 phyllodes tumors 46 Whole genome/exome sequencing analysis of 65 breast cancer samples 47 Whole-exome sequencing of 103 breast cancer tumor/normal sample pairs. Generated by the Broad Institute. 48 Whole exome sequencing from 100 breast cancer tumor/normal sample pairs. Generated by the Sanger Institute. 49 Whole-exome sequencing of 817 Breast Invasive Carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma Project. 50 TCGA Breast Invasive Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 51 Whole-exome sequencing (510 samples with matched normals), genomic DNA copy number arrays, DNA methylation, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays analysis on 825 primary breast cancer samples. The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma project. 825 cases.
Nature 2012. Raw data via the TCGA Data Portal. 52 Breast Invasive Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 53 Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, updated 2019. Data downloaded from the Broad CCLE Portal. For more info about the proteomics data, see the README. 54 Targeted sequencing of 1020 samples from Cancer Cell Line Encyclopedia from the Broad Institute and Novartis. 55 Clonal hematopoiesis mutations identified in blood samples from patients whose tumor-blood pairs were analyzed using MSK-IMPACT. 56 Clonal hematopoiesis mutations identified in blood samples from 24,146 patients whose tumor-blood pairs were analyzed using MSK-IMPACT. 57 Cervical Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 58 TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 59 Landscape of genomic alterations in 10,194 solid tumors from the Chinese population 60 Whole-exome sequencing and Targeted/Exome sequencing of 489 Cholangiocarcinoma samples from 10 countries. 61 Targeted sequencing (MSK-IMPACT) of 195 tumor samples (194 with matched normals) from 192 cholangiocarcinoma patients. 62 Exome sequencing of 15 cholangiocarcinoma cases. 63 Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue. 64 TCGA Cholangiocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 65 Cholangiocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 66 Whole-exome sequencing of 160 CLL tumor/normal pairs. 67 Whole exome sequencing of 537 chronic lymphocytic leukemia tumor/normal pairs. 68 Mutation data from whole-genome or whole-exome sequencing of 428 CLL, 54 MBL, and 24 SLL tumor/normal pairs. 69 Whole-exome sequencing of 105 Chronic Lymphocytic Leukemia samples. 70 Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 35 tumor/normal pairs. 71 Whole-exome sequencing of tumor/normal pairs from 29 African American Colon Cancers. 72 Proteogenomic analysis of prospectively collected 110 human colon adenocarcinoma tumor normal pairs. Data generated by CPTAC. 73 Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations. 74 Whole-genome sequencing of 74 paired colon tumor-normal samples. 75 TCGA Colorectal Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 76 Whole exome sequencing in 224 of the 276 colorectal carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Colorectal Cancer project. 77 Colorectal Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 78 Targeted sequencing of primary, metastatic, and normal tissues from 69 colorectal adenocarcinoma patients. 79 Molecular characterization of 47 BRAF inhibitor-naive colorectal cancer patients with dual RAS hotspot/BRAF V600E mutations. 80 Targeted sequencing of 471 unresectable colorectal tumor/normal pairs via MSK-IMPACT. 81 Whole-exome sequencing of 121 combined hepatocellular and intrahepatic cholangiocarcinoma (cHCC-ICC) patients with matched normal pairs (whole-genome sequenced samples are not included here). 82 Targeted sequencing of 29 metastatic cutaneous squamous cell carcinoma samples. 83 Whole-exome sequencing of tumor/normal pairs from 39 aggressive cutaneous squamous cell carcinoma cases. 84 Catalogue of driver genes in cutaneous squamous cell carcinoma. Meta-analysis of 105 normal/tumor pairs. 85 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). 86 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). 87 Exome/Whole Genome sequencing of 20 desmoplastic melanoma tumor/normal pairs. 88 Whole genome or whole exome sequencing analysis of temporally separated diffuse glioma tumor/normal pairs from 222 adult patients. 89 Whole-exome sequencing of tumor/matching normal sample pairs from 135 DLBCL patients. 90 Whole exome sequencing of 58 primary DLBCL samples and their matched normals. 91 Whole-exome sequencing of 1,001 Diffuse Large B Cell Lymphoma (DLBCL) tumors (N = 1001) and paired-normal tissue (N = 400). 92 Diffuse Large B-Cell Lymphoma TCGA PanCancer data. The original data is here. The publications are here. 93 Whole genome sequencing of 40 DLBCL tumor/normal pairs and 13 cell lines. 94 Targeted sequencing of 64 colorectal tumor/normal pairs via MSK-IMPACT to determine the epigenetic differences seen in Nigerian patients. 95 MSK-IMPACT sequencing of 197 advanced-staged endometrial cancer tumor samples with matched normals, from 189 patients treated at MSK. 96 Proteogenomic Characterization of Endometrial Carcinoma. Generated by CPTAC. 97 Whole-exome sequencing of 149 tumor/normal pairs and whole-genome sequencing of 16 pairs from 149 esophageal adenocarcinoma patients. 98 Esophageal Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 99 Targeted and WES recapture sequencing of tumor/normal samples from 37 Esophageal Cancer patients. 100 TCGA Esophageal Carcinoma . Source data from GDAC Firehose. Previously known as TCGA Provisional. 101 Whole exome sequencing of 559 esophageal and gastric carcinoma tumors with matched normals. 102 Whole-genome or whole-exome sequencing of 88 esophageal squamous cell carcinoma tumor/normal pairs. 103 Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients. 104 Targeted sequencing of 487 Esophageal/stomach cancer tumor-normal pairs via MSK-IMPACT. 105 Whole-genome sequencing of 112 Ewing sarcoma samples and matched germ line DNA. 106 Targeted Sequencing of 103 samples with matched normals from 101 Gallbladder cancer patients. 107 Whole exome sequencing of 32 gallbladder carcinoma tumor/normal pairs. 108 Whole-exome sequencing of 78 Gastric Adenocarcinomas and their matched normal samples. 109 Whole-genome sequencing of 147 gastric cancer tumors with matched normals. Courtesy of OncoSG. 110 Whole-exome and Targeted sequencing of 19 samples and Targeted sequencing of 161 samples from 180 Germ Cell Tumor patients. 111 Targeted and WES sequencing of germ cell tumor and shared leukemia samples. 112 Proteogenomic and metabolomic characterization of human glioblastoma. Whole genome or whole exome sequencing of 99 samples. Generated by CPTAC. 113 Whole-exome sequencing of 32 out of 42 glioblastomas patients with matched normals. 114 Whole-exome and/or whole-genome sequencing of 291 of the 577 glioblastoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Glioblastoma Project. 115 Targeted sequencing in 91 of the 206 primary glioblastoma tumors (143 with matched normals) from the Cancer Genome Atlas (TCGA) Glioblastoma Project. 116 TCGA Glioblastoma Multiforme. Source data from GDAC Firehose. Previously known as TCGA Provisional. 117 Glioblastoma Multiforme TCGA PanCancer data. The original data is here. The publications are here. 118 Targeted Sequencing of CSF samples (91 samples with 86 matched normals) from 42 glioma patients. 119 Targeted sequencing on MSK-IMPACT and FMI Panels of 1004 samples (837 with matched normals) from 923 glioma patients. 120 Whole-exome sequencing of 74 head and neck squamous cell carcinoma tumor/normal pairs. 121 Exome sequencing of 32 head and neck squamous cell carcinoma tumor/normal sample pairs. 122 TCGA Head and Neck Squamous Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 123 Whole-exome sequencing and/or whole-genome sequencing of 279 head and neck squamous cell carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma Project. 124 Head and Neck Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 125 Whole-exome sequencing of 46 liver tumor/normal pairs. 126 MSK-IMPACT sequencing of 127 Hepatocellular Carcinoma tumor samples with matched normals. 127 Whole-exome sequencing of 243 liver tumors and matched normals. 128 Targeted Sequencing of 45 Serous Ovarian Cancer tumor/normal pairs from 45 patients. 129 Targeted and whole exome sequencing of 52 histiocytosis tumor/normal pairs. 130 Whole genome or exome sequencing of 44 (20 whole genome, 20 exome) ALL tumor/normal pairs. 131 Whole exome sequencing of 10 benign insulinoma tumor/normal pairs. 132 Exome sequencing of tumor/normal pairs from 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases. 133 Targeted sequencing of IMPACT and CMO samples 134 Targeted sequencing of 412 intrahepatic cholangiocarcinoma tumor/normal sample pairs. 135 Whole-exome sequencing of 8 tumor-normal paired iCCA samples by Liver Cancer Program at the Icahn School of Medicine at Mount Sinai, in collaboration with Barcelona-Clínic Liver Cancer Group. 136 Whole exome sequencing of 103 tumor/normal sample pairs in 103 intrahepatic cholangiocarcinoma patients. 137 Whole-exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma. 138 Whole-exome sequencing of 66 chromophobe renal cell carcinoma (ChRCCs) tumor/normal pairs. 139 TCGA Kidney Chromophobe. Source data from GDAC Firehose. Previously known as TCGA Provisional. 140 Kidney Chromophobe TCGA PanCancer data. The original data is here. The publications are here. 141 Whole-exome sequencing of 10 ccRCC tumor/normal pairs and targeted sequencing of 88 clear cell carcinoma tumor/normal pairs. Generated by BGI-Shenzhen. 142 Multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs) 143 TCGA Kidney Renal Clear Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 144 Whole-exome sequencing in 417 of 446 clear cell renal cell carcinoma tumor/normal pairs. 145 Kidney Renal Clear Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 146 TCGA Kidney Renal Papillary Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 147 Kidney Renal Papillary Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 148 Targeted sequencing of tumor/normal pairs of 9 LIAD and 10 HCC patients via MSK-IMPACT platform. 149 Whole exome sequencing of 231 hepatocellular carcinomas and matched normal tissue pairs. 150 Whole-genome sequencing of 27 hepatocellular carcinoma tumor/norma pairs from RIKEN. 151 TCGA Liver Hepatocellular Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 152 Liver Hepatocellular Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 153 Whole exome sequencing of 23 grade II glioma tumor/normal pairs. 154 Whole-exome and/or whole-genome sequencing of 183 lung adenocarcinomas and matched normal tissue pairs. 155 Whole genome (WGS) or whole exome sequencing (WES) of 110 tumors and 101 matched normal adjacent tissues in lung adenocarcinoma. Proteogenomic characterization generated by CPTAC. 156 Targeted sequencing of 604 lung adenocarcinoma tumor/normal pairs via MSK-IMPACT. 157 Targeted sequencing of 186 matched normal samples from 186 lung adenocarcinoma patient via MSK-IMPACT. 158 Whole-exome sequencing of 34 non small cell lung cancer tumor/normal pairs. 159 Targeted sequencing of 426 matched normal samples from 426 lung adenocarcinoma patients. 160 Whole-exome and transcriptome sequencing of 305 east asian lung adenocarcinomas with matched normals. Courtesy of OncoSG. Lung Cancer Consortium Singapore (LCCS). 161 TCGA Lung Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 162 Whole exome sequencing of 230 lung adenocarcinoma tumor/normal pairs. Raw data via the TCGA Data Portal. 163 Lung Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 164 Targeted sequencing of 163 lung adenocarcinoma tumor/normal pairs. Generated by WashU/Broad. 165 Whole exome and whole transcriptome sequencing of primary and multiple metastatic lymph node samples from 6 lung cancer patients with their matched normals. 166 Whole genome / whole exome sequencing and proteogenomic portrait of 108 prospectively collected, treatment-naive, primary LSCC tumors and 99 paired normal adjacent tissues. Generated by CPTAC. 167 TCGA Lung Squamous Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 168 Whole exome sequencing of 178 lung squamous cell carcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Lung Squamous Cell Carcinoma project. 169 Lung Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 170 TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 171 Targeted sequencing of 34 lymphoma cell lines using HemePACT_v3 172 MSK-IMPACT targeted sequencing of 145 breast tumors with matched normal samples. 173 MSK-MET (Memorial Sloan Kettering - Metastatic Events and Tropisms) is an integrated pan-cancer cohort of tumor genomic and clinical outcome data from 25,000 patients. We analyzed this dataset to identify associations between tumor genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR+/HER2+ breast ductal carcinoma, but not in others, such as colorectal MSS, pancreatic adenocarcinoma and high-grade serous ovarian cancer. We also identified specific somatic alterations associated with increased metastatic burden and specific routes of metastatic spread. Our data offer a unique resource for the investigation of the biologic basis for metastatic spread and highlight the crucial role of chromosomal instability in cancer progression. PubMed 174 Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay 175 Targeted sequencing of 1446 Tumor and cfDNA samples (1440 with matched normals) from MSK-IMPACT and MSK-ACCESS. 176 Whole exome sequencing of tumor/normal pairs and corresponding clinical outcomes from patients treated with immune checkpoint inhibitors across multiple cancer types including melanoma, non-small cell lung cancer, head and neck cancer, and bladder cancer. 177 Whole exome sequencing of 15 malignant peripheral nerve sheath tumor/normal pairs. 178 Whole exome sequencing of 29 primary mantle cell lymphomas and their matched normals. 179 We performed targeted deep sequencing of 380 recurrently mutated genes across a cohort of 755 mature B-cell malignancies to define conserved and disease-specific patterns of genomic alterations.PubMed 180 Whole exome sequencing of 92 primary medulloblastoma tumor/normal pairs. 181 Whole genome or whole exome sequencing of 491 previously untreated Medulloblastoma tumor/normal pairs. 182 Comprehensive profiling of 125 matched tumor and germline medulloblastoma samples 183 Whole genome sequencing of 37 medulloblastoma tumors and their matched normals from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University. 184 Whole-genome sequencing of 46 recurrent medulloblastoma samples. 185 Whole Genome Sequencing of 25 metastatic melanoma samples with matched normals 186 Targeted sequencing (MSK-IMPACT) of 696 melanoma tumor/normal pairs. 187 Whole-exome sequencing of 64 pretreated (ipilimumab or tremelimumab) melanoma tumor-normal pairs. 188 Whole-exome sequencing of 333 primary and/or metastatic melanomas. 189 Whole exome sequencing of 1,122 LGG and GBM tumor/normal pairs. 190 TCGA Mesothelioma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 191 Mesothelioma TCGA PanCancer data. The original data is here. The publications are here. 192 Targeted or whole-exome sequencing of 19 Metaplastic Breast Cancer tumor/normal pairs. 193 Whole exome sequencing of 216 tumor/normal (blood) pairs from metastatic breast cancer patients who underwent a biopsy in the context of the SAFIR01/SAFIR02 (Unicancer, France), SHIVA (Institut Curie, France) or MOSCATO (Gustave Roussy, France) prospective trials. 194 Targeted Sequencing of 1365 metastatic Breast Cancer tumor/normal pairs via MSK-IMPACT to understand the role of INK4 on CDK4/6 resistance. 195 Targeted sequencing of 1134 metastatic colorectal tumor/normal pairs. 196 Targeted sequencing of 341 samples from 305 metastatic esophagogastric cancer patients 197 Whole-exome sequencing of 144 pre-treatment samples from 144 patients with metastatic melanoma treated with anti-PD1 ICB. 198 Whole-exome sequencing of 110 metastatic melanoma tumor-normal pairs. 199 Targeted sequencing of pre-treatment 66 Melanoma tumor samples. PubMed 200 Whole-exome sequencing of 38 pretreated (pembrolizumab, nivolumab) melanoma tumor-normal pairs. 201 Exome sequencing of 61 prostate cancer tumor/normal pairs (50 metastatic CRPCs and 11 high-grade localized prostate cancers). Generated by Arul Chinnaiyan's and Scott Tomlins' labs at the University of Michigan. 202 Whole exome sequencing of 444 castrate resistant prostate cancer tumor/normal pairs. SU2C-PCF Dream Team: Precision Therapy for Advanced Prostate Cancer. 203 Whole-exome sequencing of 150 metastatic prostate cancer tumor/normal pairs by the SU2C/PCF Dream Team. 204 Whole-exome and -transcriptome sequencing of 500 adult patients with metastatic solid tumor/primary normal pairs of diverse lineage and biopsy site. 205 MSK-IMPACT sequencing of 424 matched tumor-normal samples from patients with metastatic castration-sensitive prostate cancer. Germline alterations are not shown here. 206 Targeted NGS of mixed tumors from MSK-IMPACT testing. 207 Targeted sequencing of 248 samples from 124 patients' cfDNA/WBC and tumor/normal pairs. 208 IMPACT sequencing of 229 cell-free DNA (cfDNA) and associated tumor samples with matched normal 209 Whole-exome or whole-genome sequencing of 203 multiple myeloma paired tumor/normal sample pairs. 210 Whole exome sequencing of 29 myelodysplasia tumor/normal pairs. 211 Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms 212 Whole exome sequencing of paired tumor/normal pairs from 151 cases of Myeloproliferative Neoplasms. 213 Whole-exome sequencing of 67 samples by NCI-60 cell line project; raw data at CellMiner. 214 Whole exome sequencing of 56 NPC tumor/normal pairs. 215 Whole genome sequencing of 87 primary neuroblastoma tumors and their matched normals. 216 Whole Genome and Whole Exome sequencing of 240 high-risk neuroblastoma tumor/normal pairs. 217 Whole-genome sequencing of 56 neuroblastoma tumor/normal pairs. 218 Whole exome sequencing of 114 metastatic tumor/normal pairs to understand genomic overlap between castration resistant adenocarcinoma (CRPC-Adeno) and neuroendocrine histologies (CRPC-NE). 219 Whole genome or whole exome sequencing of 14 NHL tumors and their matched normals. 220 Targeted sequencing of 860 patients with metastatic lung adenocarcinoma 221 Whole-exome sequencing of 75 tumor/normal NSCLC pairs treated with PD-1 plus CTLA-4 blockade.. 222 IMPACT sequencing of 240 NSCLC tumor/normal pairs treated at MSKCC with anti-PD-(L)1 based therapy. 223 Whole-exome sequencing of 327 primary tumors with matched germline samples, and phylogenetic ctDNA sequencing of 96 pre- and 24 postoperative samples from 100 NSCLC TRACERx patients. 224 Targeted next-generation sequencing of 41 NSCLC samples. 225 Whole-exome sequencing of tumor-normal tissue pairs from 16 non-small cell lung cancer samples. 226 IMPACT sequencing of 105 High Risk Nonmuscle Invasive Bladder Cancer samples. 227 Whole-exome sequencing of 40 oral squamous cell carcinoma tumor/normal sample pairs. 228 TCGA Ovarian Serous Cystadenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 229 Whole exome sequencing of 489 high-grade serous ovarian adenocarcinoma tumor/normal pairs. The Cancer Genome Atlas (TCGA) Serous Ovarian Cancer project. 489 cases.
Raw data via the TCGA Data Portal. 230 Ovarian Serous Cystadenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 231 Whole-exome sequencing of 660 lung ADC and 484 lung SqCC tumor/normal pairs. 232 WGS changes cataloged in 2,583 whole-cancer genomes and their matched normal tissues across 38 tumor types. Source data from UCSC Xena and ICGC Data Portal. 233 Whole-exome sequencing of 99 pancreatic samples and their matched normals. 234 Whole-genome and deep-exome sequencing analysis of 456 pancreatic ductal adenocarcinomas 235 TCGA Pancreatic Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 236 Pancreatic Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 237 Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue. 238 Whole-genome sequencing (WGS) and whole-exome sequencing (WES) of 140 pancreatic cancers with 67 normal adjacent tissues. Proteogenomic characterization generated by CPTAC. 239 Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. 240 Whole-genome sequencing of 98 pancreatic neuroendocrine tumours (PanNETs) and matched normal DNA pairs. 241 Exome and whole genome sequencing of 496 papillary thyroid carcinoma tumor/normal pairs 242 Whole genome or whole exome sequencing on 298 Pediatric Acute Lymphoid Leukemia - Phase II samples. Comprehensive profiling of ALL Phase 2 samples.

TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see Using TARGET Data section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the TARGET Publication Guidelines.

TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see Using TARGET Data section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the TARGET Publication Guidelines.

244 Integrated proteogenomic characterization across major histological types of pediatric brain cancer . We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglio-glioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. 245 Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines. 246 Whole genome or whole exome sequencing on 1089 NBL samples. Comprehensive profiling of 1089 NBL samples.

TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see Using TARGET Data section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the TARGET Publication Guidelines.

247 Whole-genome/exome sequencing of 961 Pediatric Cancer samples. Data generated from Pfister Lab & DKFZ/German Cancer Consortium. 248 Whole exome sequencing of 103 samples (88 with matched normals) from 88 high-risk pediatric cancer patients. 249 Whole-exome sequencing of 261 patient derived xenografts (PDXs) samples from high-risk childhood cancers (with no matched normals). Website: PPTC 250 Whole-genome sequencing 72 patients with Rhabdoid Tumor. Comprehensive profiling of 72 patients with Rhabdoid Tumor.

TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see Using TARGET Data section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the TARGET Publication Guidelines.

251 Whole-exome sequencing of 657 Wilms' tumor samples. Comprehensive profiling of 657 Wilms' Tumor samples.

TARGET data is intended exclusively for biomedical research using pediatric data (i.e., the research objectives cannot be accomplished using data from adults) that focus on the development of more effective treatments, diagnostic tests, or prognostic markers for childhood cancers. Moreover, TARGET data can be used for research relevant to the biology, causes, treatment and late complications of treatment of pediatric cancers, but is not intended for the sole purposes of methods and/or tool development (please see Using TARGET Data section of the OCG website). If you are interested in using TARGET data for publication or other research purposes, you must follow the TARGET Publication Guidelines.

252 Whole-exome sequencing of 178 Pheochromocytoma or Paraganglioma tumor/normal pairs. 253 TCGA Pheochromocytoma and Paraganglioma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 254 Pheochromocytoma and Paraganglioma TCGA PanCancer data. The original data is here. The publications are here. 255 Whole-genome sequencing of 96 pilocytic astrocytoma tumor/normal pairs. Conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. 256 Whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) tumor/normal pairs. 257 Targeted sequencing of 341 cancer genes from 117 patient-derived PDTCs and ATCs 258 Exome sequencing of 19 immunocompetent primary central nervous system lymphoma (PCNSL) samples. 259 Whole genome sequencing of 57 prostate tumor and matches normal tissues. 260 Whole-exome sequencing of 112 prostate adenocarcinomas and matched normal samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell. 261 Whole-genome/exome sequencing of 477 prostate samples from CPC-GENE and public data sets, including TCGA-PRAD. 262 Whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling of 176 tumors from 63 patients with disseminated prostate cancer with matched normals. 263 Targeted sequencing of 1465 prostate adenocarcinoma tumor/normal pairs via MSK-IMPACT. 264 Comprehensive profiling of 218 prostate tumors (181 primaries, 37 metastases) and 14 prostate cancer cell lines and xenografts. MSKCC Prostate Oncogenome Project.
Normalized flat data files. Raw data via GEO (GSE21032). 265 Genome-wide copy number profiling in 104 primary prostate cancer tumor/normal pairs. Raw data via GEO (GSE54691). 266 Whole exome Sequencing of 1013 prostate cancer samples and their matched normals. 267 Whole-genome and transcriptome sequencing of 65 Prostate Adenocarcinoma tumor/normal pairs. 268 Whole exome and/or whole genome sequencing of 333 primary prostate adenocarcinoma tumor/normal pairs; raw data at the NCI. 269 TCGA Prostate Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 270 Prostate Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 271 Exome sequencing of 12 advanced prostate cancer samples and matched organoids 272 Whole genome and transcriptome sequencing of tumor/normal pairs from 292 prostate cancer patients. 273 MSK-IMPACT Sequencing of 18 prostate cancer tumor/normal pairs. 274 IMPACT sequencing of 504 prostate cancer tumor/normal pairs. 275 Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy. Whole exome sequencing 122 samples. Generated by CPTAC. 276 Germline RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in homologous recombination-deficient tumors 277 Targeted sequencing of 2,069 prostate cancers from different races via MSK-IMPACT. 278 MSK-IMPACT targeted sequencing of matched rectal cancer tumor and tumoroid samples. 279 Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors 280 Whole exome and/or whole genome sequencing of 106 clear cell renal cell carcinoma tumor/normal pairs. 281 Exome sequencing of 139 samples with matched normals and RNA-sequencing of 7 samples (5 samples with matched normals) from 145 Renal Non-Clear Cell Carcinoma (nccRCC) patients. 282 Targeted sequencing of 83 Retinoblastoma tumor-normal pairs via MSK-IMPACT. Genomic data provided is limited to somatic alterations. 283 Cell-free DNA profiling in 14 retinoblastoma patients with advanced intraocular disease: An MSKCC experience 284 Whole-genome sequencing of tumor-normal sample pairs from 40 patients with Malignant Rhabdoid Cancer. 285 Whole-genome or whole-exome sequencing of 43 rhabdomyosarcoma tumor/normal pairs. 286 MSK-IMPACT sequencing of 86 patients with HER2- and HER3-mutant cancers 287 Targeted Sequencing of 2138 Sarcoma sample and matched normals via MSK-IMPACT. 288 Sanger-sequenced 226 protein-coding genes (3,849 exons and adjacent intronic) on 207 samples (with 205 matched normals) encompassing 7 major sarcoma subtypes. 289 TCGA Sarcoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 290 Sarcoma TCGA PanCancer data. The original data is here. The publications are here. 291 Whole-exome sequencing of 121 melanoma samples with matched normals. 292 TCGA Skin Cutaneous Melanoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 293 Skin Cutaneous Melanoma TCGA PanCancer data. The original data is here. The publications are here. 294 Exome sequencing of 147 melanoma samples with 99 matched normals. 295 Exome Sequencing of tumors (with matched normals) from 45 patients with BRAFV600-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy. 296 Targeted sequencing of 12 SCCO paired tumor and normal samples. 297 Comprehensive whole exam profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project. 298 Whole exome-sequencing of 80 human SCLCs, including 36 primary SCLC human tumor and adjacent normal sample pairs and 17 paired SCLC cell lines and their patient-matched lymphoblastoid lines, as well as 4 primary SCLC tumors and 23 SCLC cell lines without matched normal controls. 299 Whole-genome sequencing of 120 small cell lung cancer(SCLC) tumour samples and matched normal material. 300 Whole Exome Sequencing of 10 paired chemosensitive and chemoresistant SCLC PDX. 301 Whole exome sequencing of tumor/normal pairs from 15 vulvar squamous cell carcinomas. 302 Whole genome sequencing of 100 gastric cancer tumor-normal pairs from the University of Hong Kong and Pfizer. 303 TCGA Stomach Adenocarcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 304 Whole-exome sequencing of 295 primary gastric adenocarcinomas tumors with matched normals. TCGA Stomach Adenocarcinoma Project; raw data at the NCI. 305 Stomach Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. 306 Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples (with matched normals) from the University of Tokyo. 307 Exome sequencing of 22 gastric cancer samples with matched normals. 308 Genomic and survival data from 1661 tumor-normal pairs from 1661 patients with various cancer types sequenced with the MSK-IMPACT assay. 309 TCGA Testicular Germ Cell Cancer. Source data from GDAC Firehose. Previously known as TCGA Provisional. 310 Testicular Germ Cell Tumors TCGA PanCancer data. The original data is here. The publications are here. 311 The Angiosarcoma Project (www.ascproject.org) is an ongoing patient-driven initiative. This provisional dataset is currently derived from 83 samples, including tumor specimens (FFPE and cfDNA) from 62 angiosarcoma patients subjected to WES (along with matched germline WES). This study includes genomic data, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). As these data were generated in a research laboratory, not a clinical laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. For questions about these data, including how to cite, please visit www.ascproject.org/data-release or direct questions to data@ascproject.org. 312 The Angiosarcoma Project is an ongoing patient-driven initiative. This archived Angiosarcoma Project dataset was analyzed in the linked Nature Medicine 2020 manuscript, and is derived from 48 samples from 36 angiosarcoma patients. Angiosarcoma tumor specimens (FFPE) were subjected to whole-exome sequencing (along with matched germline whole-exome sequencing). In addition to genomic data, this study includes patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). All annotations have been de-identified. Questions about these data can be directed to data@ascproject.org. 313 The Metastatic Breast Cancer Project (www.mbcproject.org) is an ongoing patient-driven initiative. This dataset release is derived from 237 samples, including both primary and/or metastatic tumor specimens (FFPE) from 180 patients who developed metastatic breast cancer. 237 samples have undergone whole-exome sequencing (along with matched germline whole-exome sequencing) and 146 of those samples have also undergone RNA-sequencing. This study includes genomic data, patient-reported data (prepended as PRD), medical record data (MedR), and pathology report data (PATH). All annotations have been de-identified. As these data were generated in a research laboratory, not a clinical laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. For questions about these data, including how to cite, please visit www.mbcproject.org/data-release or direct questions to data@mbcproject.org. 314 The Metastatic Prostate Cancer Project is a patient-driven initiative. This study includes genomic data, cfDNA tumor fractions, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). As these data were generated in a research, not a clinical, laboratory, they are for research purposes only and cannot be used to inform clinical decision-making. All annotations have been de-identified. More information is available at www.mpcproject.org. For questions about these data, including how to cite, please visit www.mpcproject.org/data-release or direct questions to data@mpcproject.org. 315 Targeted sequencing of tumor and PDX thoracic samples. 316 Targeted sequencing of thoracic PDX lines to characterize genetic alterations in 318 tumor/normal pairs via MSK-IMPACT. 317 Whole exome sequencing of 28 thymic epithelial tumors (TETs) with matched normals 318 TCGA Thymoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 319 Thymoma TCGA PanCancer data. The original data is here. The publications are here. 320 TCGA Thyroid Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 321 Thyroid Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 322 Tumors with TRK fusions based on MSK-IMPACT targeted sequencing. 323 Targeted sequencing of 62 high-grade primary Unclassified Renal Cell Carcinoma tumor samples with matched normals. 324 Next-generation sequencing (MSK-IMPACT) on all protein-coding exons of 300 cancer associated genes of 85 Upper Tract Urothelial Carcinoma tumor samples and paired normals. 325 Whole exome sequencing (37 samples) and RNA-seq analysis (32 samples) of 47 upper tract urothelial carcinoma patients. 326 Whole-exome sequencing of 30 upper-tract urothelial carcinoma patients and their matched normals. 327 Targeted Sequencing of 119 upper tract urothelial carcinoma tumor/normal pairs. 328 MSK-IMPACT sequencing of 34 upper tract urothelial patients and the matching PDX or PDC generated from 17 patient tumors. 329 Whole-exome sequencing of 72 tumor samples (with 32 matched normals) in Urothelial Carcinoma. 330 Whole exome sequencing (WXS) of 22 uterine carcinosarcoma/uterine malignant mixed Mullerian (UCS) tumors with matched normals. 331 TCGA Uterine Carcinosarcoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 332 Uterine Carcinosarcoma TCGA PanCancer data. The original data is here. The publications are here. 333 Whole exome sequencing of paired tumor-normal DNAs from 16 cases of clear cell endometrial tumors. 334 TCGA Uterine Corpus Endometrial Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 335 Whole exome sequencing of 373 endometrial carcinoma tumors with matched normals. TCGA Uterine Corpus Endometrial Carcinoma project; raw data at the NCI. 336 Uterine Corpus Endometrial Carcinoma TCGA PanCancer data. The original data is here. The publications are here. 337 Targeted Sequencing of 108 Uterine Sarcoma/Mesenchymal tumor/normal pairs from 107 patients. 338 Whole-genome or whole-exome sequencing of tumor/normal pairs from 28 uveal melanoma samples. 339 TCGA Uveal Melanoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. 340 Uveal melanoma TCGA PanCancer data. The original data is here. The publications are here. > > # Get available case lists (collection of samples) for a given cancer study > # Get Extended Mutation Data for EGFR and PTEN in TCGA GBM > > ## No test: > getMutationData(mycgds,gbm_tcga_all,gbm_tcga_mutations,c('EGFR','PTEN')) Error in paste(x$.url, "webservice.do?cmd=getMutationData", "&case_set_id=", : object 'gbm_tcga_all' not found Calls: getMutationData -> getMutationData.CGDS -> paste Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/cgdsr.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 0:56.22, 32.98 + 7.36