Cholangiocarcinoma whole genome sequencing data

EGAGenomicsHiSeq X Ten;ILLUMINA, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINAhttps://ega-archive.org/datasets/EGAD00001001988118EGA dataset EGAD00001001988EGACholangiocarcinoma whole genome sequencing dataCholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters-fluke-positive CCAs (clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3' untranslated region deletion as a mechanism of FGFR2 upregulation. Integration of noncoding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores-mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.Significance: Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. Cancer Discov; 7(10); 1116-35. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1047.Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.Jusakul Apinya A, Cutcutache Ioana I, Yong Chern Han CH, Lim Jing Quan JQ, Huang Mi Ni MN, Padmanabhan Nisha N, Nellore Vishwa V, Kongpetch Sarinya S, Ng Alvin Wei Tian AWT, Ng Ley Moy LM, Choo Su Pin SP, Myint Swe Swe SS, Thanan Raynoo R, Nagarajan Sanjanaa S, Lim Weng Khong WK, Ng Cedric Chuan Young CCY, Boot Arnoud A, Liu Mo M, Ong Choon Kiat CK, Rajasegaran Vikneswari V, Lie Stefanus S, Lim Alvin Soon Tiong AST, Lim Tse Hui TH, Tan Jing J, Loh Jia Liang JL, McPherson John R JR, Khuntikeo Narong N, Bhudhisawasdi Vajaraphongsa V, Yongvanit Puangrat P, Wongkham Sopit S, Totoki Yasushi Y, Nakamura Hiromi H, Arai Yasuhito Y, Yamasaki Satoshi S, Chow Pierce Kah-Hoe PK, Chung Alexander Yaw Fui AYF, Ooi London Lucien Peng Jin LLPJ, Lim Kiat Hon KH, Dima Simona S, Duda Dan G DG, Popescu Irinel I, Broet Philippe P, Hsieh Sen-Yung SY, Yu Ming-Chin MC, Scarpa Aldo A, Lai Jiaming J, Luo Di-Xian DX, Carvalho André Lopes AL, Vettore André Luiz AL, Rhee Hyungjin H, Park Young Nyun YN, Alexandrov Ludmil B LB, Gordân Raluca R, Rozen Steven G SG, Shibata Tatsuhiro T, Pairojkul Chawalit C, Teh Bin Tean BT, Tan Patrick PVasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASPCholangiocellular Carcinoma, Carcinomas, intrahepatic bile duct cancer (cholangiocarcinoma), Intrahepatic Cholangiocarcinoma, Carcinoma, Extrahepatic Cholangiocarcinoma, Complete., Complete Genome, Whole Genome, bile duct cancer, Cholangiocellular Carcinomas, Whole, Cholangiocarcinomas, Intrahepatic Cholangiocarcinomas, Extrahepatic, Complete Genome Sequencing, Genome Sequencing, Extrahepatic Cholangiocarcinomas, Intrahepatic, Cholangiocellular, Sequencing, CholangiocarcinomaCholangiocellular Carcinoma, Carcinomas, intrahepatic bile duct cancer (cholangiocarcinoma), Intrahepatic Cholangiocarcinoma, Carcinoma, Extrahepatic Cholangiocarcinoma, Genomes, bile duct cancer, Cholangiocellular Carcinomas, Epigenetic, Cholangiocarcinomas, Intrahepatic Cholangiocarcinomas, Extrahepatic, whole genome, Epigenetics, Extrahepatic Cholangiocarcinomas, Intrahepatic, Cholangiocellular, Intrahepatic., Epigenomic, CholangiocarcinomaErbb-2, ring1b, DmelCG8445, Materials, odd(Oz), Incidences, lambdatop, CT22273, CFD1, Intrahepatic Cholangiocarcinomas, Person-time Rates, Gukmi1, dev, Proportion, AIP3, DNA Methylations, 2300006C11Rik, sci, Tumor, type 9, Mutations, DmelCG7223, RPL23, FGF receptor activity, Kiaa3023, PDCD1L2, Regions, hucep-13, bbl, ten-m, HOW, How, Himasthla, Analysis, Id-1, PICD, Fgf-r, organ, Digenea, l(3)rP126, Genomes, Analyses, BCC7, Idpc, plant peltate hair, stru, l(3)S053606, BcDNA:AT25108, Epigenomic, 3'UTR, BTL/FGFR2, Fgfr7, intrahepatic bile duct cancer (cholangiocarcinoma), contractures, BEK, Bek, IDPC, Cholangiocarcinomas, Btdc, Infections and Infestations, RING1B, Tk2, Tk1, Tumors, Ten-mc, uch-x4, CpG-Rich Islands, anatomical protrusion, CG5723, Up-Regulation (Physiology), MLN19, HIPI3, Incidence Rates, Benign, RING2, JWS, bfy, Person-time Rate, PD1, c-neu, Carcinomas, HD-38, 3'UTRs, Htl, Idh-1, Fr1, EMS2, Upregulation, BBDS, ding, Benign Neoplasms, Infection and Infestation, whole genome, i100, surveillance, Islands, DING, Malignant Neoplasms, FR1, bap-1, AW553466, Untranslated Regions, Material, WWP3, hSLE1, bhy, distal, 2017, l(3)00208, DNA, Secondary Attack Rates, Epigenetics, 3' UTR, uchl2, whole exome, 5301, i79, AA989761, Neoplasms, peltate hair, number, protein-containing complex, LFS1, jecur, Odz, Rate, Digeneas, multiple with arachnodactyly, Island, Gene Products, CEK3, fibroblast growth factor-activated receptor activity, Attack Rates, HER-2/neu, CD273, Ly101, odz, occurrence, Receptor Up-Regulation, plasmid binding, prevalence, MAGI1c, hipi3, Magi-1, Paryphostomums, clinical infection, Expressions, CpG, l(3)rJ307, CD279, CG6714, Neoplasias, Cumulative, HUCEP-13, l(3)05301, Intrahepatic Cholangiocarcinoma, Pdc1, UTRs, Himasthlas, anatomical unit, FGFR, Person-time, body organ, Person time Rate, BFR-1, Expression, Methylations, Cancer, Neu, NEU, SSY2, Malignant Neoplasm, HER-2|neu, arthrogryposis, Proteins, UTR, j372, Secondary Attack, dtk2, dtk1, qkr, l(3)S090417, xfgfr2, Ten79E, Cumulative Incidences, MT, fgf-r, native protein, KH93F, chemical analysis, DNA Rearrangements, Neoplasm, NGL, i150, scales, Extrahepatic Cholangiocarcinomas, outbreaks, Cluster Analyses, INSDC_feature:regulatory, primary cancer, CT16449, c-erbB2, Aspidogastrea, DFR1/DFGF-R2, 60S ribosomal protein L23, Cancers, 3' UTRs, Petasigers, malignant tumor, CG32134, CpG Rich Islands, CT20816, Gene Proteins, Incidence Proportion, Fluke, BAIAP1, epidemics, ten(m), Dtk1, Dtk2, Neoplasia, CpG-Rich, CG11452, Dfr1, scale tissue, Troglotrema, determination, Infestations and Infections, dFGFR, Paryphostomum, protein, Intrahepatic, Tp53, CD332, element, CD340, DmelCG5723, DFGF-R2, congenital, Troglotremas, AI314845, DFGF-R1, Flukes, pathogenesis, Incidence Rate, FGF-R2, protein aggregate, contractural arachnodactyly, Btl, l(3)j5D5, DFR2, DFR1, arachnodactyly, 24B, Ear anomalies-contractures-dysplasia of bone with kyphoscoliosis, DNA methylation maintenance, FGF-activated receptor activity, Gene Expressions, l(3)rL201, Trematodas, Extrahepatic, iecur, CT39172, 3', ten-m/odz, DNA methylation, Dfr-1, ten[m], TNRC19, Dfr-2, CG10293, l(3)j5B5, CpG Clusters, malignant neoplasm, DFR-1, bap1, Environmental Carcinogens, svs, Malignancies, ring2, BAP1, PDL2, MAGI-1, Carcinoma, 0904/17, Magi1d, bA574F11.2, SLEB2, IDH, frequency, IDP, BAP-1, CG7223, F730015O22Rik, Clusters, Fgfr-7, l(3)05309, Cholangiocellular, Fgfr-2, IDCD, mKIAA0272, Feature., Petasiger, rpl17a, Cholangiocellular Carcinomas, SZ1, pd-1, B7-DC, UCHL2, Genetic Materials, CG8445, Region, Genetic Material, PD-1, Untranslated Region, Clusterings, DNA Rearrangement, 3' Untranslated Region, Epigenetic, DmelCG32134, Exomes, rpl23, Features, morbidity, TK25, hPD-1, CpG-Rich Island, MLN 19, hPD-l, Cluster, spine, Clustering, rpl17, P53, TKR1, p44, DmHD-38, anon-EST:Liang-2.39, Cistron, Echinochasmus, Methylation, DTRK(FR1), TK14, Gene Rearrangements, AU043015, Extrahepatic Cholangiocarcinoma, KGFR, K-SAM, P62, Rearrangements, p53, Benign Neoplasm, Gene, Ten[m], Malignant, presence, protrusion, Secondary Attack Rate, heredity, HEL-216, AI788952, Cholangiocellular Carcinoma, CpG Cluster, 0844/01, l(3)s2612, Genetic, Malignancy, HER-2, AW556123, Up Regulation, causes, PD-L2, E030024J03Rik, hucep-6, ECT1, Ect1, DA9, Infestation and Infection, Trp53, microtubule/chromatin interaction, B7DC, odz/ten-m, DmelCG10293, causality, L17, Incidence Proportions, Characteristics, TRP53, AIP-3, incidence, FGFR2, FGFR1, Rearrangement, structure-specific DNA binding, bile duct cancer, protein complex, clone 2.39, DPR3, Attack Rate, Cumulative Incidence, Incidence, mKIAA3023, D-FGFR, l17, Cistrons, Xp53, Baiap1, contractural Beals type, count in organism, Characteristic, DmHD-311, Protein, HEL-S-26, Infection, structure specific DNA binding, mKIAA4129, KSAM, who, KGFRTr, Exhibit, CpG Island, scale, Aspidogastreas, Who/How, endemics, Cholangiocarcinoma, HTL/FGFR1, CCA, Protein Gene Products, EOMD, Secondary, Livers, 3' Untranslated, DEL, Attack, cardinality, qkr[93F], HD-311, assay, fibroblast growth factor receptor activity, l(3)00844, HER2falseena-DATASET-DUKE-NUS-28-03-2016-04:29:04:072-192 - samplesCholangiocarcinoma whole genome sequencing data2018-01-24 10:50:54EGAD00001001988960628667006EGAC00001000010EGAS00001001653