{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T04:12:55Z","timestamp":1775189575482,"version":"3.50.1"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2019,1,10]],"date-time":"2019-01-10T00:00:00Z","timestamp":1547078400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006596","type":"journal-article","created":{"date-parts":[[2019,1,10]],"date-time":"2019-01-10T13:28:37Z","timestamp":1547126917000},"page":"e1006596","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":57,"title":["Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8891-4138","authenticated-orcid":true,"given":"Deena M. A.","family":"Gendoo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2197-7083","authenticated-orcid":true,"given":"Robert E.","family":"Denroche","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolina","family":"Radulovich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gun Ho","family":"Jang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathieu","family":"Lemire","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dianne","family":"Chadwick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9996-5771","authenticated-orcid":true,"given":"Ilinca M.","family":"Lungu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emin","family":"Ibrahimov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ping-Jiang","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lincoln D.","family":"Stein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie M.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John M. S.","family":"Bartlett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming-Sound","family":"Tsao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neesha","family":"Dhani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Hedley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Gallinger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Haibe-Kains","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,1,10]]},"reference":[{"issue":"7424","key":"ref1","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature11547","article-title":"Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes","volume":"491","author":"AV Biankin","year":"2012","journal-title":"Nature"},{"issue":"7540","key":"ref2","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nature14169","article-title":"Whole genomes redefine the mutational landscape of pancreatic cancer","volume":"518","author":"N Waddell","year":"2015","journal-title":"Nature"},{"key":"ref3","article-title":"Personalized <em>In Vitro<\/em> and <em>In Vivo<\/em> Cancer Models to Guide Precision Medicine","author":"C Pauli","year":"2017","journal-title":"Cancer Discovery"},{"key":"ref4","article-title":"Pancreatic cancer cell lines as patient-derived avatars: genetic characterisation and functional utility","author":"ES Knudsen","year":"2017","journal-title":"Gut"},{"issue":"8","key":"ref5","doi-asserted-by":"crossref","first-page":"e103873","DOI":"10.1371\/journal.pone.0103873","article-title":"Generation and Characterisation of Novel Pancreatic Adenocarcinoma Xenograft Models and Corresponding Primary Cell Lines","volume":"9","author":"AB Wennerstr\u00f6m","year":"2014","journal-title":"PLOS ONE"},{"key":"ref6","article-title":"Ductal pancreatic cancer modeling and drug screening using human pluripotent stem cell- and patient-derived tumor organoids","author":"L Huang","year":"2015","journal-title":"Nat Med"},{"issue":"11","key":"ref7","doi-asserted-by":"crossref","first-page":"e0142631","DOI":"10.1371\/journal.pone.0142631","article-title":"Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression","volume":"10","author":"T Xie","year":"2015","journal-title":"PLOS ONE"},{"issue":"7","key":"ref8","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1016\/j.celrep.2016.07.023","article-title":"Integrated Patient-Derived Models Delineate Individualized Therapeutic Vulnerabilities of Pancreatic Cancer","volume":"16","author":"K Witkiewicz Agnieszka","journal-title":"Cell Reports"},{"issue":"7592","key":"ref9","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nature16965","article-title":"Genomic analyses identify molecular subtypes of pancreatic cancer","volume":"531","author":"P Bailey","year":"2016","journal-title":"Nature"},{"issue":"4","key":"ref10","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/nm.2344","article-title":"Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy","volume":"17","author":"EA Collisson","year":"2011","journal-title":"Nat Med"},{"issue":"6","key":"ref11","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1001\/jamaoncol.2016.3916","article-title":"Association of distinct mutational signatures with correlates of increased immune activity in pancreatic ductal adenocarcinoma","volume":"3","author":"AA Connor","year":"2017","journal-title":"JAMA Oncology"},{"issue":"7625","key":"ref12","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/nature19823","article-title":"A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns","volume":"538","author":"F Notta","year":"2016","journal-title":"Nature"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrg1767","article-title":"Structural variation in the human genome","volume":"7","author":"L Feuk","year":"2006","journal-title":"Nat Rev Genet"},{"issue":"5","key":"ref14","doi-asserted-by":"crossref","first-page":"487","DOI":"10.2174\/138920011795495321","article-title":"Clinically Relevant Genetic Variations in Drug Metabolizing Enzymes","volume":"12","author":"N Pinto","year":"2011","journal-title":"Current drug metabolism"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nm0315-206","article-title":"Copy number variations\u2019 effect on drug response still overlooked","volume":"21","author":"C Willyard","year":"2015","journal-title":"Nat Med"},{"issue":"1","key":"ref16","first-page":"324","article-title":"Organoid Models of Human and Mouse Ductal Pancreatic Cancer","volume":"160","author":"F Boj Sylvia","journal-title":"Cell"},{"issue":"3","key":"ref17","doi-asserted-by":"crossref","first-page":"25","DOI":"10.21037\/cco.2017.06.15","article-title":"Preclinical models of pancreatic ductal adenocarcinoma","volume":"6","author":"BD Krempley","year":"2017","journal-title":"Chinese clinical oncology"},{"issue":"21","key":"ref18","doi-asserted-by":"crossref","first-page":"4452","DOI":"10.1242\/dev.096628","article-title":"Artificial three-dimensional niches deconstruct pancreas development in vitro","volume":"140","author":"C Greggio","year":"2013","journal-title":"Development (Cambridge, England)"},{"issue":"1","key":"ref19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1399-0004.2009.01230.x","article-title":"Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications","volume":"76","author":"HT Lynch","year":"2009","journal-title":"Clinical genetics"},{"key":"ref20","article-title":"Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research","author":"M Hidalgo","year":"2014","journal-title":"Cancer Discovery"},{"issue":"2","key":"ref21","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.ccell.2017.07.007","article-title":"Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma","volume":"32","author":"BJ Raphael","year":"2017","journal-title":"Cancer Cell"},{"issue":"8","key":"ref22","doi-asserted-by":"crossref","first-page":"e0182855","DOI":"10.1371\/journal.pone.0182855","article-title":"Tumor engraftment in patient-derived xenografts of pancreatic ductal adenocarcinoma is associated with adverse clinicopathological features and poor survival","volume":"12","author":"I Pergolini","year":"2017","journal-title":"PLoS One"},{"key":"ref23","article-title":"Patient-derived xenografts undergo mouse-specific tumor evolution","author":"U Ben-David","year":"2017","journal-title":"Nat Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"620601","DOI":"10.4061\/2011\/620601","article-title":"Molecular Characteristics of Pancreatic Ductal Adenocarcinoma","volume":"2011","author":"NA Ottenhof","year":"2011","journal-title":"Pathology Research International"},{"key":"ref25","article-title":"Clinical and genetic implications of dna mismatch repair deficiency in patients with pancreatic ductal adenocarcinoma","author":"JM Cloyd","year":"2017","journal-title":"JAMA Surgery"},{"key":"ref26","unstructured":"!! INVALID CITATION !!! {Ben-David, 2018 #73;Ben-David, 2018 #73}."},{"issue":"8","key":"ref27","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1158\/0008-5472.CAN-10-4049","article-title":"Hypoxia Predicts Aggressive Growth and Spontaneous Metastasis Formation from Orthotopically Grown Primary Xenografts of Human Pancreatic Cancer","volume":"71","author":"Q Chang","year":"2011","journal-title":"Cancer Research"},{"issue":"12","key":"ref28","doi-asserted-by":"crossref","first-page":"i172","DOI":"10.1093\/bioinformatics\/bts236","article-title":"Xenome\u2014a tool for classifying reads from xenograft samples","volume":"28","author":"T Conway","year":"2012","journal-title":"Bioinformatics"},{"issue":"14","key":"ref29","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"5","key":"ref30","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nat Genet"},{"issue":"9","key":"ref31","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Research"},{"issue":"14","key":"ref32","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1093\/bioinformatics\/bts271","article-title":"Strelka: accurate somatic small-variant calling from sequenced tumor\u2013normal sample pairs","volume":"28","author":"CT Saunders","year":"2012","journal-title":"Bioinformatics"},{"issue":"3","key":"ref33","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"K Cibulskis","year":"2013","journal-title":"Nat Biotech"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"ST Sherry","year":"2001","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"ref35","doi-asserted-by":"crossref","first-page":"D805","DOI":"10.1093\/nar\/gku1075","article-title":"COSMIC: exploring the world\u2019s knowledge of somatic mutations in human cancer","volume":"43","author":"SA Forbes","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"16","key":"ref36","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"K Wang","year":"2010","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"ref37","doi-asserted-by":"crossref","first-page":"E2423","DOI":"10.1002\/humu.22771","article-title":"Oncotator: Cancer Variant Annotation Tool","volume":"36","author":"AH Ramos","year":"2015","journal-title":"Human Mutation"},{"issue":"1","key":"ref38","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/1755-0998.12549","article-title":"vcfr: a package to manipulate and visualize variant call format data in R","volume":"17","author":"BJ Knaus","year":"2017","journal-title":"Molecular Ecology Resources"},{"issue":"14","key":"ref39","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/btu168","article-title":"VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants","volume":"30","author":"V Obenchain","year":"2014","journal-title":"Bioinformatics"},{"issue":"19","key":"ref40","doi-asserted-by":"crossref","first-page":"3012","DOI":"10.1093\/bioinformatics\/btw325","article-title":"GenVisR: Genomic Visualizations in R","volume":"32","author":"ZL Skidmore","year":"2016","journal-title":"Bioinformatics"},{"issue":"8","key":"ref41","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/nmeth.1628","article-title":"CREST maps somatic structural variation in cancer genomes with base-pair resolution","volume":"8","author":"J Wang","year":"2011","journal-title":"Nat Meth"},{"issue":"18","key":"ref42","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"T Rausch","year":"2012","journal-title":"Bioinformatics"},{"issue":"1","key":"ref43","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/1471-2105-14-244","article-title":"RCircos: an R package for Circos 2D track plots","volume":"14","author":"H Zhang","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"ref44","doi-asserted-by":"crossref","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for Computing and Annotating Genomic Ranges","volume":"9","author":"M Lawrence","year":"2013","journal-title":"PLOS Computational Biology"},{"issue":"14","key":"ref45","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"M Lawrence","year":"2009","journal-title":"Bioinformatics"},{"issue":"8","key":"ref46","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1093\/bioinformatics\/btv723","article-title":"PharmacoGx: an R package for analysis of large pharmacogenomic datasets","volume":"32","author":"P Smirnov","year":"2016","journal-title":"Bioinformatics"},{"issue":"6","key":"ref47","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1186\/1471-2164-13-591","article-title":"Copynumber: Efficient algorithms for single- and multi-track copy number segmentation","volume":"13","author":"G Nilsen","year":"2012","journal-title":"BMC Genomics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/nmeth.2883","article-title":"PyClone: statistical inference of clonal population structure in cancer","volume":"11","author":"A Roth","year":"2014","journal-title":"Nature Methods"},{"key":"ref50","article-title":"R: A Language and Environment for Statistical Computing","year":"2017"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006596","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T02:11:42Z","timestamp":1588990302000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006596"}},"subtitle":[],"editor":[{"given":"Amos","family":"Tanay","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,1,10]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,1,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006596","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/209692","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,10]]}}}