{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2500;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001001047"],"sample_count":["31"],"description":["EGA dataset EGAD00001001047"],"repository":["EGA"],"title":["nccRCC targeted exome sequencing of 375 genes"],"pubmed_abstract":["To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non-clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors."],"pubmed_title":["Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes."],"pubmed_authors":["Durinck Steffen S, Stawiski Eric W EW, Pavía-Jiménez Andrea A, Modrusan Zora Z, Kapur Payal P, Jaiswal Bijay S BS, Zhang Na N, Toffessi-Tcheuyap Vanina V, Nguyen Thong T TT, Pahuja Kanika Bajaj KB, Chen Ying-Jiun YJ, Saleem Sadia S, Chaudhuri Subhra S, Heldens Sherry S, Jackson Marlena M, Peña-Llopis Samuel S, Guillory Joseph J, Toy Karen K, Ha Connie C, Harris Corissa J CJ, Holloman Eboni E, Hill Haley M HM, Stinson Jeremy J, Rivers Celina Sanchez CS, Janakiraman Vasantharajan V, Wang Weiru W, Kinch Lisa N LN, Grishin Nick V NV, Haverty Peter M PM, Chow Bernard B, Gehring Julian S JS, Reeder Jens J, Pau Gregoire G, Wu Thomas D TD, Margulis Vitaly V, Lotan Yair Y, Sagalowsky Arthur A, Pedrosa Ivan I, de Sauvage Frederic J FJ, Brugarolas James J, Seshagiri Somasekar S"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["WES, Complete Transcriptome, Complete, Complete Transcriptome Sequencing, Exome Sequencings, Materials, Complete Exome Sequencings, Genetic, Complete Exome, Complete Exome Sequencing, Whole Transcriptome Sequencing, Exome, Gene, Cistrons, Sequencing, Exome Sequencing, Whole Exome, Material, Whole, Whole Exome Sequencing, Genetic Materials, Cistron, Whole Transcriptome, Transcriptome Sequencing, Genetic Material., Transcriptome Sequencings"],"pubmed_title_synonyms":["Adenocarcinoma, Carcinoma, Adenocarcinoma Of, Collecting Duct, Clear Cell Renal Carcinoma., Chromophil Renal Cell Carcinoma, Collecting Duct Carcinomas, Renal Cell Cancers, Renal Cell Carcinomas, Renal Cell Adenocarcinoma, Renal Adenocarcinoma, Renal Adenocarcinomas, Adenocarcinoma Of Kidney, Tumor, Papillary Renal Cell Carcinoma, Renal Cell Carcinoma, Adenocarcinomas, clear-cell metastatic renal cell carcinoma, Chromophobe Renal Cell Carcinoma, Collecting Duct Carcinoma of the Kidney, Hypernephroid, Clear Cell Renal Cell Carcinoma, Adenocarcinoma Of Kidneys, Renal Cell Adenocarcinomas, Sarcomatoid Renal Cell Carcinoma, Hypernephroid Carcinomas, Nephroid Carcinomas, Renal Carcinomas, Hypernephroid Carcinoma, Hypernephroma, hypernephroma, Grawitz Tumor, Carcinomas, Hypernephromas, Renal Cell, Renal Carcinoma, Kidney, Collecting Duct Carcinoma, Renal, Nephroid, Renal Cell Cancer, Papillary, Collecting Duct Carcinoma (Kidney), Collecting Duct (Kidney), Renal Collecting Duct Carcinoma, Collecting Duct Carcinomas (Kidney), Nephroid Carcinoma, Grawitz, Cancer"],"pubmed_abstract_synonyms":["type 2, E130019N06, Materials, RNA Sequence Determination, actg1a, Sequence Determination, RNA Sequence, KIDNEY NEOPL, DPTEN, adenocarcinoma of kidney, Profiles, Tumor, 2210010A19Rik, vit, Mutations, 5730420M11Rik, hierarchy, systematics, bbl, neoplasm of kidney, HEL-176, RCC, renal tumour, 2-amino-3-mercaptopropanoic acid, TEP1, Analysis, Kidney Cancer, C, SET, Hypernephromas, AI854243, BCC7, Analyses, M, BCC2, Vitiligo, bw, Clear Cells, Renal Cancer, MLIAP, KIPP1184, Sequence Determinations, Signatures, DmelCG4299, set, Expression Signature, tumor of the kidney, ACN, MNCb-5687, Role Concepts, malignant tumor of the kidney, ACT, Renal Collecting Duct Carcinoma, RG7MT1, malignant kidney tumour, Tumors, chromophobe renal cell adenocarcinoma, PDHBD, 2210013N15Rik, Systematics, Renal Cell Adenocarcinoma, Adenocarcinoma Of Kidney, Renal Cell Carcinoma, Collecting Duct Carcinoma of the Kidney, Clear Cell Renal Cell Carcinoma, Benign, Role Concept, PTEN3, PTEN1, Expression Signatures, Role, Methionin, bfy, renal tumor, Hmet, PHE1B, (2R)-2-amino-3-sulfanylpropanoic acid, Expression Profile, Hypernephroma, Carcinomas, HGF/SF receptor, C81408, kidney adenocarcinoma, HLA-DR-associated protein II, DI-2, LP8165, Kidney, PDC, I-2Dm, Benign Neoplasms, INSDC_feature:gene, WS2, hCMT1c, Nephroid, NEOPL KIDNEY, c-Met, PTENa, human, Malignant Neoplasms, I-2PP1, Papillary, Pgcp, E1beta, TAF-IBETA, kidney (renal) cancer, Material, Collecting Duct Carcinoma (Kidney), renal cell carcinoma, bhy, malignant neoplasm of kidney, TAF-Ibeta, Nephroid Carcinoma, oncocytoma renal, Clear Cell Renal Carcinoma, 2310035O07Rik, kidney neoplasm (disease), Adenocarcinoma, whole exome, 2-amino-4-(methylsulfanyl)butanoic acid, ectopic, GLM2, RNF50, Neoplasms, LIVIN, CRCC, number, L-Zystein, oncocytoma kidney, CG 11876, renal neoplasm, Renal Adenocarcinomas, LFS1, Human, Kidney Neoplasms, Renal cancer, Hypernephroid, AI463227, RCCP1, Hypernephroid Carcinomas, Renal Carcinomas, Hypernephroid Carcinoma, RCCP2, actg1, Man, Livin, malignant renal neoplasm, central type, F15E12_6, RGD1562597, kidney chromophobe, scatter factor receptor, Profile, E-920, BRWS2, Collecting Duct Carcinoma, 2pp2a, Renal, Hcys, Expressions, DmelCG5671, CG10574, Sequencing, Neoplasias, 2-amino-4-(methylthio)butanoic acid, 2PP2A, CYSTEINE, malignant tumor of kidney, B430203M17Rik, dSET, dSet, FREE CYSTEINE, bHLHe32, Expression, LAL, (2R)-2-amino-3-mercaptopropanoic acid, malignant neoplasm of the kidney, Collecting Duct Carcinomas (Kidney), metionina, NF2, Cancer, Grawitz, Sequence Analyses, RNA, Malignant Neoplasm, PTEN, TPRC, RNA Sequence Determinations, Chromophil Renal Cell Carcinoma, renal tumors, Kidney Neoplasm, Renal Cell Carcinomas, dPten, Renal Adenocarcinoma, DYT8, pten, MI, mi, E51, Concept, Chromophobe Renal Cell Carcinoma, dpten, Cancer of Kidney, chromophobe cell, acoustic Schwannomas, I-2PP2A, CWS1, Gene Expression Signatures, chemical analysis, Dm I-2, 2810403H05Rik, Neoplasm, merlin, dPTEN, cancer of kidney, Met, MET, ATCMPG1, ATCMPG2, Renal Neoplasms, Mmac, CG5671, ensemble, PDHB, Renal Cell, tyrosine-protein kinase Met, (R)-2-amino-3-mercaptopropanoic acid, Cancers, 2-Amino-3-mercaptopropionic acid, kidney neoplasm, kidney tumor, Gsfbcc2, PKND1, Gene Expression Profiles, E920, chromophobe cell carcinoma of the kidney, 5730455C01Rik, Renal Neoplasm, malignant neoplasm of kidney except pelvis, Neoplasia, WS2A, IPP2A2, E 920, PDHE1-B, Collecting Duct, Hgfr, determination, ACTG, chromophobe carcinoma of the kidney, AL024199, AA415817, Gene Expression Profile, 5730555F13Rik, kidney tumour, Papillary Renal Cell Carcinoma, Tp53, Classifications, renal tumours, kidney (including renal cell) cancer, hierarchies, Actl, Adenocarcinoma Of Kidneys, Renal Cell Adenocarcinomas, BANF, HGFR, Actg, Roles, MR-1, KIAP, Renal oncocytoma, Concepts, Kidney Cancers, Cystein, DmelCG11876, chromophobe adenocarcinoma, malignant tumour of kidney, Man (Taxonomy), Gene Expressions, tumour of the kidney, MUB3_18, TAF-I, Determination, cisteina, MUB3.18, IGAAD, DmelCG10574, ChRCC, Transcriptomes, Malignancies, malignant kidney neoplasm, TL, Racemethionine, CHRCC, chromophobe carcinoma, phapii, Carcinoma, Adenocarcinoma Of, proto-oncogene c-Met, PRO, Modern, Expression Profiles, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, FPD1, 9130215G10Rik, Adenocarcinomas, CYS, Cys, Determinations, neurofibromatosis central type, Gene Expression, Taxonomies, ML-IAP, XPrcc, mislocalized, tumour of kidney, acoustic schwannomas bilateral, TAHCCP2, DFNA26, Genetic Materials, and GLY protein 2, DFNA20, Genetic Material, Transcriptome Profiles, HGF receptor, and GLY protein 1, renal cancer, tumor of kidney, MMAC1, Exomes, CG4299, chromophobe cell carcinoma of kidney, Renal Cell Cancer, L-Cystein, type II, Tahccp2, P53, p44, Wh, Cistron, BZS, i2pp2a, human being, acoustic neurinoma bilateral, Transcriptome Profile, taxonomy, AL023024, malignant tumour of the kidney, p53, malignant kidney tumor, Benign Neoplasm, Renal Cell Cancers, neoplasm of the kidney, Gene, translocation-associated renal cell carcinoma, Bhlhe32, neurofibromatosis, Malignant, presence, PHAPII, Cancer of the Kidney, MHAM, HGF, Homo sapiens, Sarcomatoid Renal Cell Carcinoma, MR1, kidney cancer, neurofibromatosis type II, malignant renal tumour, F15E12.6, acoustic neurinoma, hypernephroma, Grawitz Tumor, Taxonomy, Genetic, Malignancy, LIVIN., ipp2a2, ROCY, bilateral, AUTS9, lal-1, chromophobe carcinoma of kidney, Trp53, RNA Sequence Analyses, 2610103L06Rik, taf-ibeta, CMM8, RNA Sequencing, AI838057, TRP53, Transcriptome, DL-Methionine, Collecting Duct Carcinomas, igaad, chromophobe renal cell carcinoma, chromophobe renal cell cancer, Cistrons, Xp53, group, count in organism, renal cell adenocarcinoma, I2PP2A, Gene Expression Signature, Nephroid Carcinomas, Renal Cancers, Zystein, RENAL NEOPL, 10q23del, 2-amino-3-sulfanylpropanoic acid, Renal Carcinoma, L-2-Amino-3-mercaptopropionic acid, chromophobe type, A130070J02Rik, DEC, dSET/TAF-Ibeta, 2610030F17Rik, Kiaa0251-hp, Modern Man, Collecting Duct (Kidney), RNA Sequence Analysis, cardinality, BRP17, alpha-amino-gamma-methylmercaptobutyric acid, Brp17, assay, Par4, malignant renal tumor, Signature, SCH, AA407739, SF receptor"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-Genentech-27-10-2014-16:49:10:053-281 - samples","description":"Targeted exome sequencing of  375 genes","dates":{"updated":"2019-10-01 16:52:42"},"accession":"EGAD00001001047","cross_references":{"TAXONOMY":["9606"],"pubmed":["25401301"],"EGA":["EGAC00001000247","EGAS00001000926"]}}