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dc.contributor.authorContino, Gianmarco
dc.contributor.authorEldridge, Matthew D.
dc.contributor.authorSecrier, Maria
dc.contributor.authorBower, Lawrence
dc.contributor.authorElliott, Rachael Fels
dc.contributor.authorWeaver, Jamie
dc.contributor.authorLynch, Andy G.
dc.contributor.authorEdwards, Paul A.W.
dc.contributor.authorFitzgerald, Rebecca C.
dc.date.accessioned2017-08-15T15:30:08Z
dc.date.available2017-08-15T15:30:08Z
dc.date.issued2016-06-10
dc.identifier.citationContino , G , Eldridge , M D , Secrier , M , Bower , L , Elliott , R F , Weaver , J , Lynch , A G , Edwards , P A W & Fitzgerald , R C 2016 , ' Whole-genome sequencing of nine esophageal adenocarcinoma cell lines ' , F1000Research , vol. 5 , 1336 . https://doi.org/10.12688/F1000RESEARCH.7033.1en
dc.identifier.issn2046-1402
dc.identifier.otherPURE: 250827920
dc.identifier.otherPURE UUID: 07fb2eb9-443f-428d-82e7-69ac4d64064d
dc.identifier.otherScopus: 85010840102
dc.identifier.otherORCID: /0000-0002-7876-7338/work/36106405
dc.identifier.urihttp://hdl.handle.net/10023/11480
dc.descriptionThis work was funded by an MRC Programme Grant to R.C.F. and a Cancer Research UK grant to PAWE. The pipeline for mutation calling is funded by Cancer Research UK as part of the International Cancer Genome Consortium. G.C. is a National Institute for Health Research Lecturer as part of a NIHR professorship grant to R.C.F. AGL is supported by a Cancer Research UK programme grant (C14303/A20406) to Simon Tavaré and the European Commission through the Horizon 2020 project SOUND (Grant Agreement no. 633974).en
dc.description.abstractEsophageal adenocarcinoma (EAC) is highly mutated and molecularly heterogeneous. The number of cell lines available for study is limited and their genome has been only partially characterized. The availability of an accurate annotation of their mutational landscape is crucial for accurate experimental design and correct interpretation of genotype-phenotype findings. We performed high coverage, paired end whole genome sequencing on eight EAC cell lines-ESO26, ESO51, FLO-1, JH-EsoAd1, OACM5.1 C, OACP4 C, OE33, SK-GT-4-all verified against original patient material, and one esophageal high grade dysplasia cell line, CP-D. We have made available the aligned sequence data and report single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number alterations, identified by comparison with the human reference genome and known single nucleotide polymorphisms (SNPs). We compare these putative mutations to mutations found in primary tissue EAC samples, to inform the use of these cell lines as a model of EAC.
dc.language.isoeng
dc.relation.ispartofF1000Researchen
dc.rights© 2016 Contino G et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectR Medicineen
dc.subjectQH301 Biologyen
dc.subjectQR180 Immunologyen
dc.subjectMedicine(all)en
dc.subjectImmunology and Microbiology(all)en
dc.subjectBiochemistry, Genetics and Molecular Biology(all)en
dc.subjectPharmacology, Toxicology and Pharmaceutics(all)en
dc.subjectDASen
dc.subject.lccRen
dc.subject.lccQH301en
dc.subject.lccQR180en
dc.titleWhole-genome sequencing of nine esophageal adenocarcinoma cell linesen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.contributor.institutionUniversity of St Andrews.Statisticsen
dc.identifier.doihttps://doi.org/10.12688/F1000RESEARCH.7033.1
dc.description.statusPeer revieweden


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