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A somatic reference standard for cancer genome sequencing

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 sequen...

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Autores principales: Craig, David W., Nasser, Sara, Corbett, Richard, Chan, Simon K., Murray, Lisa, Legendre, Christophe, Tembe, Waibhav, Adkins, Jonathan, Kim, Nancy, Wong, Shukmei, Baker, Angela, Enriquez, Daniel, Pond, Stephanie, Pleasance, Erin, Mungall, Andrew J., Moore, Richard A., McDaniel, Timothy, Ma, Yussanne, Jones, Steven J. M., Marra, Marco A., Carpten, John D., Liang, Winnie S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837349/
https://www.ncbi.nlm.nih.gov/pubmed/27094764
http://dx.doi.org/10.1038/srep24607
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author Craig, David W.
Nasser, Sara
Corbett, Richard
Chan, Simon K.
Murray, Lisa
Legendre, Christophe
Tembe, Waibhav
Adkins, Jonathan
Kim, Nancy
Wong, Shukmei
Baker, Angela
Enriquez, Daniel
Pond, Stephanie
Pleasance, Erin
Mungall, Andrew J.
Moore, Richard A.
McDaniel, Timothy
Ma, Yussanne
Jones, Steven J. M.
Marra, Marco A.
Carpten, John D.
Liang, Winnie S.
author_facet Craig, David W.
Nasser, Sara
Corbett, Richard
Chan, Simon K.
Murray, Lisa
Legendre, Christophe
Tembe, Waibhav
Adkins, Jonathan
Kim, Nancy
Wong, Shukmei
Baker, Angela
Enriquez, Daniel
Pond, Stephanie
Pleasance, Erin
Mungall, Andrew J.
Moore, Richard A.
McDaniel, Timothy
Ma, Yussanne
Jones, Steven J. M.
Marra, Marco A.
Carpten, John D.
Liang, Winnie S.
author_sort Craig, David W.
collection PubMed
description 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.
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spelling pubmed-48373492016-04-27 A somatic reference standard for cancer genome sequencing Craig, David W. Nasser, Sara Corbett, Richard Chan, Simon K. Murray, Lisa Legendre, Christophe Tembe, Waibhav Adkins, Jonathan Kim, Nancy Wong, Shukmei Baker, Angela Enriquez, Daniel Pond, Stephanie Pleasance, Erin Mungall, Andrew J. Moore, Richard A. McDaniel, Timothy Ma, Yussanne Jones, Steven J. M. Marra, Marco A. Carpten, John D. Liang, Winnie S. Sci Rep Article 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. Nature Publishing Group 2016-04-20 /pmc/articles/PMC4837349/ /pubmed/27094764 http://dx.doi.org/10.1038/srep24607 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Craig, David W.
Nasser, Sara
Corbett, Richard
Chan, Simon K.
Murray, Lisa
Legendre, Christophe
Tembe, Waibhav
Adkins, Jonathan
Kim, Nancy
Wong, Shukmei
Baker, Angela
Enriquez, Daniel
Pond, Stephanie
Pleasance, Erin
Mungall, Andrew J.
Moore, Richard A.
McDaniel, Timothy
Ma, Yussanne
Jones, Steven J. M.
Marra, Marco A.
Carpten, John D.
Liang, Winnie S.
A somatic reference standard for cancer genome sequencing
title A somatic reference standard for cancer genome sequencing
title_full A somatic reference standard for cancer genome sequencing
title_fullStr A somatic reference standard for cancer genome sequencing
title_full_unstemmed A somatic reference standard for cancer genome sequencing
title_short A somatic reference standard for cancer genome sequencing
title_sort somatic reference standard for cancer genome sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837349/
https://www.ncbi.nlm.nih.gov/pubmed/27094764
http://dx.doi.org/10.1038/srep24607
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