Contino, G;
Eldridge, MD;
Secrier, M;
Bower, L;
Fels Elliott, R;
Weaver, J;
Lynch, AG;
... Fitzgerald, RC; + view all
(2016)
Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.
F1000Research
, 5
, Article 1336. 10.12688/f1000research.7033.1.
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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.
| Type: | Article |
|---|---|
| Title: | Whole-genome sequencing of nine esophageal adenocarcinoma cell lines |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.12688/f1000research.7033.1 |
| Publisher version: | http://doi.org/10.12688/f1000research.7033.1 |
| Language: | English |
| Additional information: | © 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. |
| Keywords: | Esophageal adenocarcinoma, cancer genome, cell line, copy number alteration, high-grade dysplasia, single nucleotide variant, whole genome sequencing |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10037720 |
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