A somatic reference standard for cancer genome sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-07

AUTHORS

David W Craig, Sara Nasser, Richard Corbett, Simon K Chan, Lisa Murray, Christophe Legendre, Waibhav Tembe, Jonathan Adkins, Nancy Kim, Shukmei Wong, Angela Baker, Daniel Enriquez, Stephanie Pond, Erin Pleasance, Andrew J Mungall, Richard A Moore, Timothy McDaniel, Yussanne Ma, Steven J M Jones, Marco A Marra, John D Carpten, Winnie S Liang

ABSTRACT

Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Results were combined with previously generated data allowing for comparison to a fourth lineage on earlier NGS technology. Aggregate variant detection led to the identification of consensus variants, including key events that represent hallmark mutation types including amplified BRAF V600E, a CDK2NA small deletion, a 12 kb PTEN deletion, and a dinucleotide TERT promoter substitution. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions. More... »

PAGES

24607

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep24607

DOI

http://dx.doi.org/10.1038/srep24607

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1040391884

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27094764


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