{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000154"],"host":["EGA"],"description":["EGA study EGAS00001000154"],"dataset_title":["Merged analysis-ready bam files: HiSeq sequencing of matched tumour/normal DNA samples from Pancreatic Ductal Adenocarcinoma cases","Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826","Pancreatic adenocarcinoma QCMG 20120201","HiSeq sequencing data for PDAC cell lines generated by QCMG","Sequencing data for Australian Pancreatic Cancer study submitted 20130102","RNASeq on HiSeq platform of 95 pancreatic adenocarcinoma cases","Pancreatic adenocarcinoma QCMG 20110901"],"repository":["EGA"],"category":["restricted"],"pubmed_abstract":["Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis."],"pubmed_title":["Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes."],"pubmed_authors":["Biankin Andrew V AV, Waddell Nicola N, Kassahn Karin S KS, Gingras Marie-Claude MC, Muthuswamy Lakshmi B LB, Johns Amber L AL, Miller David K DK, Wilson Peter J PJ, Patch Ann-Marie AM, Wu Jianmin J, Chang David K DK, Cowley Mark J MJ, Gardiner Brooke B BB, Song Sarah S, Harliwong Ivon I, Idrisoglu Senel S, Nourse Craig C, Nourbakhsh Ehsan E, Manning Suzanne S, Wani Shivangi S, Gongora Milena M, Pajic Marina M, Scarlett Christopher J CJ, Gill Anthony J AJ, Pinho Andreia V AV, Rooman Ilse I, Anderson Matthew M, Holmes Oliver O, Leonard Conrad C, Taylor Darrin D, Wood Scott S, Xu Qinying Q, Nones Katia K, Fink J Lynn JL, Christ Angelika A, Bruxner Tim T, Cloonan Nicole N, Kolle Gabriel G, Newell Felicity F, Pinese Mark M, Mead R Scott RS, Humphris Jeremy L JL, Kaplan Warren W, Jones Marc D MD, Colvin Emily K EK, Nagrial Adnan M AM, Humphrey Emily S ES, Chou Angela A, Chin Venessa T VT, Chantrill Lorraine A LA, Mawson Amanda A, Samra Jaswinder S JS, Kench James G JG, Lovell Jessica A JA, Daly Roger J RJ, Merrett Neil D ND, Toon Christopher C, Epari Krishna K, Nguyen Nam Q NQ, Barbour Andrew A, Zeps Nikolajs N, Kakkar Nipun N, Zhao Fengmei F, Wu Yuan Qing YQ, Wang Min M, Muzny Donna M DM, Fisher William E WE, Brunicardi F Charles FC, Hodges Sally E SE, Reid Jeffrey G JG, Drummond Jennifer J, Chang Kyle K, Han Yi Y, Lewis Lora R LR, Dinh Huyen H, Buhay Christian J CJ, Beck Timothy T, Timms Lee L, Sam Michelle M, Begley Kimberly K, Brown Andrew A, Pai Deepa D, Panchal Ami A, Buchner Nicholas N, De Borja Richard R, Denroche Robert E RE, Yung Christina K CK, Serra Stefano S, Onetto Nicole N, Mukhopadhyay Debabrata D, Tsao Ming-Sound MS, Shaw Patricia A PA, Petersen Gloria M GM, Gallinger Steven S, Hruban Ralph H RH, Maitra Anirban A, Iacobuzio-Donahue Christine A CA, Schulick Richard D RD, Wolfgang Christopher L CL, Morgan Richard A RA, Lawlor Rita T RT, Capelli Paola P, Corbo Vincenzo V, Scardoni Maria M, Tortora Giampaolo G, Tempero Margaret A MA, Mann Karen M KM, Jenkins Nancy A NA, Perez-Mancera Pedro A PA, Adams David J DJ, Largaespada David A DA, Wessels Lodewyk F A LF, Rust Alistair G AG, Stein Lincoln D LD, Tuveson David A DA, Copeland Neal G NG, Musgrove Elizabeth A EA, Scarpa Aldo A, Eshleman James R JR, Hudson Thomas J TJ, Sutherland Robert L RL, Wheeler David A DA, Pearson John V JV, McPherson John D JD, Gibbs Richard A RA, Grimmond Sean M SM"],"name_synonyms":["pancreatic duct adenocarcinoma, pancreas tubular adenocarcinoma, pancreatic duct cancer, pancreatic ductal carcinoma, whole genome, ductal adenocarcinoma of the pancreas, pancreatic tubular adenocarcinoma, pancreas ductal adenocarcinoma., Genomes, malignant neoplasm of duct of Wirsung, pancreatic ductal adenocarcinoma, ductal adenocarcinoma of pancreas"],"description_synonyms":["whole exome, NEOPL PANCREATIC, Materials, single-organism developmental process, Activity, Transcriptome Profile, acetylglucosaminyltransferase-like protein, Neoplasms, postnatal development, number, Pancreas Cancer, Mbp1, Gene Expression Profile, Gene, pancreas, growth and development, Profiles, Pancreas Cancers, LARGE1, presence, Pancreatic Neoplasm, froggy, Gyltl1a, Mutations, Ca tail of pancreas, Ca head of pancreas, adenocarcinoma of the pancreas, Pancreatic Cancer, Pancreatic Acinar, increased risk of pancreatic cancer, myd, Pancreatic Carcinomas, PANCREAS NEOPL, average, study, Complete, Whole Genome, intestinum duodenum, Genetic, like-acetylglucosaminyltransferase, Genomes, Pancreatic Carcinoma, MDDGB6, Acinar Carcinoma, Profile, Tissue, Complete Genome Sequencing, Mbp-1, LARGE, Pancreatic Cancers, Signatures, Sequencing, Duodenums, BPFD#36, anterior intestine, Expression Signature, Clients, Whole, Transcriptomes, Pancreatic Acinar Carcinomas, pancreatic tumour, pancreas neoplasm, Cancer, Carcinoma, upper intestine, Transcriptome, gyltl1b-b, malignant neoplasm of body of pancreas, pancreatic neoplasm, Expression Profiles, familial, Genome Sequencing, pancreas adenocarcinoma, Cistrons, Client, Pancreas Neoplasm, development, Gene Expression, count in organism, Complete Genome, dodecadactylon, MDDGA6, mKIAA0609, Expression Signatures, Gene Expression Signatures, Neoplasm, Genetic Materials, pancreatic carcinoma, simple tissue, Gene Expression Signature, PANCREATIC NEOPL, proximal intestine, Pancreatic, Cancer of the Pancreas, KIAA0609, Expression Profile, acetylglucosaminyltransferase-like 1A, Transcriptome Profiles, Carcinomas, fg, malignant neoplasm of tail of pancreas, pancreatic tumor, Cancer of Pancreas, gyltl1b, malignant neoplasm of head of pancreas, postnatal growth, mdc1d, pancreatic cancer, Exomes, initiation, common, patient, INSDC_feature:gene, Cancers, whole genome, LARGE_HUMAN, Pancreas, Pancreatic Neoplasms, Pancreatic Acinar Carcinoma, MDC1D, like-glycosyltransferase, enr, Ca body of pancreas, Patient, Material, Gene Expression Profiles, cardinality, PAAD, Cistron, Signature, Genetic Material., PNCA, other neoplasm, Pancreas Neoplasms, growth, General activity, Acinar Carcinomas, glycosyltransferase-like protein LARGE1"],"pubmed_title_synonyms":["Axonal Pathfinding, Carcinoma, Axon Pathfinding, NEOPL PANCREATIC, Materials, Neural Guidance, Neoplasms, malignant neoplasm of body of pancreas, pancreatic neoplasm, familial, Pancreas Cancer, Gene, pancreas, Cistrons, Pancreas Cancers, Pangenome, Pancreas Neoplasm, Pancreatic Neoplasm, Ca tail of pancreas, Ca head of pancreas, Neural Pathfinding, Pancreatic Cancer, Core Genome, Neoplasm, Genetic Materials, Pancreatic Acinar, pancreatic carcinoma, increased risk of pancreatic cancer, Neurite Guidance, PANCREATIC NEOPL, Pancreatic, Cancer of the Pancreas, Pancreatic Carcinomas, PANCREAS NEOPL, Carcinomas, malignant neoplasm of tail of pancreas, pancreatic tumor, Cancer of Pancreas, Genetic, Pathfinding, Genomes, Pancreatic Carcinoma, malignant neoplasm of head of pancreas, Acinar Carcinoma, Accessory Genome, Neuronal Pathfinding, pancreatic cancer, axon growth cone guidance, Cancers, Pancreatic Cancers, Pancreas, Pancreatic Neoplasms, Pancreatic Acinar Carcinoma, Neuronal Guidance, Pan-genome, Ca body of pancreas, Axon, Material, Cistron, Genetic Material., PNCA, Pancreas Neoplasms, Pancreatic Acinar Carcinomas, axon chemotaxis, Acinar Carcinomas, pancreatic tumour, pancreas neoplasm, Cancer"],"pubmed_abstract_synonyms":["SMAD family member 4, 145kDa, MAPKK 4, Materials, p19<ARF>, TGF beta Type II Receptor, tef, Tyro1, Tumor, DNA replication-independent chromatin organization, HALR, P270, Mutations, atm/tefu, ras, bbl, madh4, ARF-INK4a, Whole Transcriptome, Transcriptome Sequencing, Kinase, 1700124K17Rik, Sek, Fs(3)Hor, C-K-RAS, p16(INK4a), BAF200, TbetaR II Kinase, Animalia, Type II TGF beta Receptors, BCC7, cell process disease, tumor disease, TGFbeta-RII, Neuronal Pathfinding, Pancreatic Cancers, NTef2, RIIDN, high frequency, Axon, telo1, CT1.3, stage, Pancreatic Acinar Carcinomas, MAGE3B, ELD, single organism signaling, Tumors, Tgfbr2T, CT1.6, hOSA1, Neural Guidance, mutagenesis, animalia, malignant neoplasm of body of pancreas, Exome, familial, tumours, Fs(3)Sz11, Sap155, Benign, ductal adenocarcinoma of the pancreas, pancreatic carcinoma, pancreatic duct cancer, bfy, 155kDa, PANCREATIC NEOPL, Pancreatic, Carcinomas, Transforming Growth Factor-beta Type II Receptor, TGF-beta 2, Complete Transcriptome, MEK4, Cancer of Pancreas, whole organism, malignant neoplasm of head of pancreas, Osa1, OSA1, Benign Neoplasms, Pancreas, Malignant Neoplasms, AW743858, DNA replication-independent chromatin assembly, C-JUN N-terminal kinase kinase 1, zipzap|p200, Ca body of pancreas, RASK2, Material, Koerper, Whole Exome Sequencing, CG2684, bhy, TBR-II, Type II TGF-beta Receptors, DNA, other neoplasm, MAGE-3b, INK4A, Transforming Growth Factor-beta Type II Receptors, axon chemotaxis, Acinar Carcinomas, SF3b1, CDKN2, TA-8, LDS1B, NEOPL PANCREATIC, INK4, Neoplasms, developmental stage, number, Pancreas Cancer, pancreas, chromatin assembly/disassembly, LFS1, Pancreas Cancers, KIAA1506, NEOPL, 2400007E14Rik, LDS2B, DmelCG6535, Pancreatic Cancer, SMAD 4, Transforming Growth Factor beta Type II Receptors, Cek8, Kras-2, SERK1, neoplasm, Type II TGF-beta Receptor, pancreas tubular adenocarcinoma, Complete, Injury, Exome Sequencings, medea, Pathfinding, Pancreatic Carcinoma, Acinar Carcinoma, K-RAS4B, K-RAS4A, smad4, BAF250, tumour, MEK 4, MAGE3, E(zen)3, Sequencing, MAGE6, Neoplasias, Stress-activated protein kinase kinase 1, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Whole Exome, pancreatic ductal carcinoma, Whole, p19ARF, constitutitional genetic, ZNF656, Neoplastic Growth, Cancer, Axonal Pathfinding, TP16, JNKK, SMARCF1, Malignant Neoplasm, Complete Exome Sequencings, BM029, DNIIR, body, K-RAS2B, K-RAS2A, pancreatic ductal adenocarcinoma, pancreatic neoplasm, dpc4, CG6535, LDS2, whole body, Madh4, c-Ki-ras, p19-lt-ARF-gt-, Pancreas Neoplasm, p16INK4a, MDS, ductal adenocarcinoma of pancreas, pancreas ductal adenocarcinoma, PRP10, Exome Sequencing, neoplastic growth, MT, Serk1, P14ARF, MED, 1110030E03Rik, chemical analysis, Neoplasm, Mutageneses, Prp10, Neurite Guidance, Hsh155, RIIC, SKK1, MFS2, P16INK4A, AA409119, Embryonic, MRD14, malignant neoplasm of tail of pancreas, Genotoxic Stress, AI256621, pancreatic tumor, NS, malignant neoplasm of duct of Wirsung, med, Carcinogeneses, pancreatic cancer, Cancers, Lds, TGF beta Type II Receptors, disease of cellular proliferation, signalling, INK4a-ARF, TbetaR-II Kinase, signalling process, Stress, Receptor, Pancreas Neoplasms, l(3)XIIm137, hereditary, TGF-beta Type II Receptor, Neoplasia, NEOPLASMS BENIGN, DPC4, MTS1, JNKK 1, SF3b145, PRKMK4, determination, neoplasia, Cus1, Smarcf1, Pctr1, Tp53, MAGEA6, Pancreatic Neoplasm, BAF250a, Tumorigenesis., Tier, Ca tail of pancreas, Ca head of pancreas, SAP145, FAA3, 2610311M13Rik, rb, Arf, ARF, SF3B145, A930032N02Rik, k-ras, SF3b155, TELO1, SF3b150, rask2, Targ4, hSMAD4, DmelCG2684, DNA replication-independent nuclesome assembly, MADH4, XSmad4alpha, Complete Exome Sequencing, Whole Transcriptome Sequencing, neoplasm (disease), TbetaR-II, MTS-1, Oncogeneses, TAAD2, AT1, at1, genetic, AAT3, anon-EST:Posey121, Mothers against DPP homolog 4, signaling process, ATA, Deletion target in pancreatic carcinoma 4 homolog, ATC, ATD, P14, ATE, Malignancies, P16, tumor, P19, ATM, P16-INK4A, Atm, pancreatic tumour, pancreas neoplasm, l(3)12m-137, Carcinoma, JNK kinase 1, SAPK kinase 1, HIP8, Ki-ras, MLM, Mage-a6, p16, SAPKK1, neoplastic disease, atm, DNA replication-independent nucleosome organisation, Neural Pathfinding, p21, Genetic Materials, B120, Cancer of the Pancreas, dSmad4, PRPF10, Genetic Material, chromatin assembly, TbetaRII, DNA Injury, pancreatic duct adenocarcinoma, DNA Injuries, Xsmad4, 1110020H15Rik, SAP155, axon growth cone guidance, ATATM, early, Pancreatic Acinar Carcinoma, TGF-beta Type II Receptors, 2810441F20Rik, Genotoxic, HYPD, c-Jun N-terminal kinase kinase 1, Oncogenesis, Horka, P53, JIP, Fs(3)Horka, p44, Cistron, inherited genetic, PNCA, Transcriptome Sequencings, KI-RAS, TGFR-2, chromatin modification, biological signaling, MAPKK4, MAP kinase kinase 4, Tumorigeneses, Tefu, DmelCG1775, Complete Exome, ARABIDOPSIS THALIANA ATAXIA-TELANGIECTASIA MUTATED, Kras2, NS3, p53, jip, Benign Neoplasm, Gene, Malignant, presence, hELD, Hek8, C030026E19Rik, l(3)SG36, Pancreatic Acinar, increased risk of pancreatic cancer, DmF2, Animal, JNKK1, MYHRS, KRAS2, SEK1, KRAS1, Sek1, Pancreatic Carcinomas, PANCREAS NEOPL, lod, p21B, tel1, MKK4, WES, Genetic, Malignancy, 5730566F07Rik, metazoa, SMAD4, MLL3, Neuronal Guidance, Trp53, Ink4a|Arf, MAD homolog 4, AU042018, chromatin assembly or disassembly, Xatm, JNK-activating kinase 1, heterogeneity, CMM2, Epl1, p200, Smad4, TRP53, Axon Pathfinding, P16INK4, Transforming Growth Factor beta Type II Receptor, 2810001M05Rik, TGF-beta receptor type II, Type II TGF beta Receptor, l(3)11m-254, K-ras, D18Wsu70e, Tumorigenesis, Cistrons, Xp53, AI385584, count in organism, Metazoa, TGFBR2, Ink4a/Arf, TEL1, core, xsmad4a, transcription-coupled nucleosome assembly, AI929937, dATM, CG1775, MAPK|ERK kinase 4, C1orf4, Complete Transcriptome Sequencing, SAPK|ERK kinase 1, frequent, 2900005C20Rik, CDK4I, B230398H18Rik, DNA Lesion, TGF-beta type II receptor, l(3)SG70, ataxia-telangiectasia mutated, Pancreatic Neoplasms, SAPKK-1, Transforming Growth Factor beta Type II, atdc, DNA Lesions, Deletion target in pancreatic carcinoma 4, pancreatic tubular adenocarcinoma, kras, 2.7.12.2, P19ARF, ATDC, CFC2, cardinality, 4432409D24Rik, assay, transforming growth factor-beta receptor type II"],"additional_accession":[]},"is_claimable":false,"name":"Genome Landscape of Primary Pancreatic Ductal Adenocarcinoma","description":"The purpose of the Australian ICGC Pancreatic Cancer Genome Sequencing Initiative\nstudy is to identify the common driving mutations underlying the initiation and\ndevelopment of Pancreatic Adenocarcinoma in a large cohort of pancreatic cancer\npatients (n=350). Matched genome sequences will be generated from normal tissue\n(duodenum) and resected primary tumour tissue in each patient using exome and\nwhole genome sequencing. The complete repertoire of somatic mutations will be\ndetermined (substitutions, indels, copy number changes and structural changes).\nWhere possible, matched transcriptome sequencing will also be carried out to\ndetermine locus activity, which mutations are actively expressed and which\nrearrangements give rise to gene-fusion transcripts.","dates":{"updated":"2017-07-26 15:39:29"},"accession":"EGAS00001000154","cross_references":{"TAXONOMY":["9606"],"pubmed":["23103869"],"EGA":["EGAD00001000049","EGAD00001000660","EGAD00001000371","EGAD00001000096","EGAD00001003298","EGAD00001000323","EGAD00001002192","EGAC00001000010"]}}