Ontology type: schema:ScholarlyArticle Open Access: True
2016-07
AUTHORSDavid 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
ABSTRACTLarge-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... »
PAGES24607
http://scigraph.springernature.com/pub.10.1038/srep24607
DOIhttp://dx.doi.org/10.1038/srep24607
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PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/27094764
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JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/srep24607'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/srep24607'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep24607'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep24607'
This table displays all metadata directly associated to this object as RDF triples.
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19 BLANK NODES