Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.
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.
Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK.
Gianmarco
G
Contino
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Matthew D
MD
Eldridge
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Maria
M
Secrier
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Lawrence
L
Bower
Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK.
Rachael
R
Fels Elliott
Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK.
Jamie
J
Weaver
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Andy G
AG
Lynch
Department of Pathology, University of Cambridge, Cambridge, UK.
Paul A W
PA
Edwards
Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK.
Rebecca C
RC
Fitzgerald
Esophageal adenocarcinoma; cancer genome; cell line; copy number alteration; high-grade dysplasia; single nucleotide variant; whole genome sequencing