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Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.

Published version
Peer-reviewed

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Article

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Authors

Contino, Gianmarco 
Eldridge, Matthew D 
Secrier, Maria 
Bower, Lawrence 
Fels Elliott, Rachael 

Abstract

Esophageal 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.

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Keywords

Esophageal adenocarcinoma, cancer genome, cell line, copy number alteration, high-grade dysplasia, single nucleotide variant, whole genome sequencing

Journal Title

F1000Res

Conference Name

Journal ISSN

2046-1402
2046-1402

Volume Title

5

Publisher

F1000 Research
Sponsorship
Medical Research Council (MC_UU_12022/2)
European Commission Horizon 2020 (H2020) Societal Challenges (633974)
Cancer Research UK (14545)
Cancer Research Uk (None)
Cancer Research UK (20406)
This 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).