Whole-genome sequencing of nine esophageal adenocarcinoma cell lines

Research output: Contribution to journalArticlepeer-review

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Whole-genome sequencing of nine esophageal adenocarcinoma cell lines. / Contino, Gianmarco; Eldridge, Matthew D.; Secrier, Maria; Bower, Lawrence; Elliott, Rachael Fels; Weaver, Jamie; Lynch, Andy G.; Edwards, Paul A.W.; Fitzgerald, Rebecca C.

In: F1000Research, Vol. 5, 1336, 10.06.2016.

Research output: Contribution to journalArticlepeer-review

Harvard

Contino, G, Eldridge, MD, Secrier, M, Bower, L, Elliott, RF, Weaver, J, Lynch, AG, Edwards, PAW & Fitzgerald, RC 2016, 'Whole-genome sequencing of nine esophageal adenocarcinoma cell lines', F1000Research, vol. 5, 1336. https://doi.org/10.12688/F1000RESEARCH.7033.1

APA

Contino, 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, 5, [1336]. https://doi.org/10.12688/F1000RESEARCH.7033.1

Vancouver

Author

Contino, Gianmarco ; Eldridge, Matthew D. ; Secrier, Maria ; Bower, Lawrence ; Elliott, Rachael Fels ; Weaver, Jamie ; Lynch, Andy G. ; Edwards, Paul A.W. ; Fitzgerald, Rebecca C. / Whole-genome sequencing of nine esophageal adenocarcinoma cell lines. In: F1000Research. 2016 ; Vol. 5.

Bibtex

@article{f9b5552b5a5b442a9f5ad1ea1bb02755,
title = "Whole-genome sequencing of nine esophageal adenocarcinoma cell lines",
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.",
keywords = "Esophageal adenocarcinoma, whole genome sequencing, cell line, high-grade dysplasia, cancer genome, copy number alteration, single nucleotide variant",
author = "Gianmarco Contino and Eldridge, {Matthew D.} and Maria Secrier and Lawrence Bower and Elliott, {Rachael Fels} and Jamie Weaver and Lynch, {Andy G.} and Edwards, {Paul A.W.} and Fitzgerald, {Rebecca C.}",
note = "Open Peer Review, this version: version 1; peer review: 3 approved.",
year = "2016",
month = jun,
day = "10",
doi = "10.12688/F1000RESEARCH.7033.1",
language = "English",
volume = "5",
journal = "F1000Research",
issn = "2046-1402",
publisher = "Faculty of 1000 Ltd",

}

RIS

TY - JOUR

T1 - Whole-genome sequencing of nine esophageal adenocarcinoma cell lines

AU - Contino, Gianmarco

AU - Eldridge, Matthew D.

AU - Secrier, Maria

AU - Bower, Lawrence

AU - Elliott, Rachael Fels

AU - Weaver, Jamie

AU - Lynch, Andy G.

AU - Edwards, Paul A.W.

AU - Fitzgerald, Rebecca C.

N1 - Open Peer Review, this version: version 1; peer review: 3 approved.

PY - 2016/6/10

Y1 - 2016/6/10

N2 - 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.

AB - 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.

KW - Esophageal adenocarcinoma

KW - whole genome sequencing

KW - cell line

KW - high-grade dysplasia

KW - cancer genome

KW - copy number alteration

KW - single nucleotide variant

UR - http://www.scopus.com/inward/record.url?scp=85010840102&partnerID=8YFLogxK

UR - https://www.repository.cam.ac.uk/handle/1810/288830

U2 - 10.12688/F1000RESEARCH.7033.1

DO - 10.12688/F1000RESEARCH.7033.1

M3 - Article

AN - SCOPUS:85010840102

VL - 5

JO - F1000Research

JF - F1000Research

SN - 2046-1402

M1 - 1336

ER -