Whole-genome sequencing of nine esophageal adenocarcinoma cell lines

Gianmarco Contino, Matthew D. Eldridge, Maria Secrier, Lawrence Bower, Rachael Fels Elliott, Jamie Weaver, Andy G. Lynch, Paul A.W. Edwards, Rebecca C. Fitzgerald

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)
66 Downloads (Pure)

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.

Original languageEnglish
Article number1336
JournalF1000Research
Volume5
DOIs
Publication statusPublished - 10 Jun 2016

Bibliographical note

Open Peer Review, this version: version 1; peer review: 3 approved.

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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