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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.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 .
dc.identifier.otherORCID: /0000-0002-7876-7338/work/36106405
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.subjectR Medicineen
dc.subjectQH301 Biologyen
dc.subjectQR180 Immunologyen
dc.subjectImmunology and Microbiology(all)en
dc.subjectBiochemistry, Genetics and Molecular Biology(all)en
dc.subjectPharmacology, Toxicology and Pharmaceutics(all)en
dc.titleWhole-genome sequencing of nine esophageal adenocarcinoma cell linesen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.contributor.institutionUniversity of St Andrews. Statisticsen
dc.description.statusPeer revieweden

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