{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000660"],"sample_count":["353"],"description":["EGA dataset EGAD00001000660"],"repository":["EGA"],"title":["Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826"],"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"],"additional_accession":[]},"is_claimable":false,"name":"QCMG_20130826 - samples","description":"Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAD00001000660","cross_references":{"TAXONOMY":["9606"],"pubmed":["23103869"],"EGA":["EGAC00001000010","EGAS00001000154"]}}