A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis

Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth...

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Autores principales: Shand, Megan, Soto, Jose, Lichtenstein, Lee, Benjamin, David, Farjoun, Yossi, Brody, Yehuda, Maruvka, Yosef, Blainey, Paul C., Banks, Eric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7722876/
https://www.ncbi.nlm.nih.gov/pubmed/33293579
http://dx.doi.org/10.1038/s42003-020-01460-9
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author Shand, Megan
Soto, Jose
Lichtenstein, Lee
Benjamin, David
Farjoun, Yossi
Brody, Yehuda
Maruvka, Yosef
Blainey, Paul C.
Banks, Eric
author_facet Shand, Megan
Soto, Jose
Lichtenstein, Lee
Benjamin, David
Farjoun, Yossi
Brody, Yehuda
Maruvka, Yosef
Blainey, Paul C.
Banks, Eric
author_sort Shand, Megan
collection PubMed
description Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth (LinST), of short somatic mutations in the HT115 colon cancer cell-line, that are validated using a known cell lineage that includes thousands of mutations and a high confidence region covering 2.7 gigabases per sample.
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spelling pubmed-77228762020-12-11 A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis Shand, Megan Soto, Jose Lichtenstein, Lee Benjamin, David Farjoun, Yossi Brody, Yehuda Maruvka, Yosef Blainey, Paul C. Banks, Eric Commun Biol Article Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth (LinST), of short somatic mutations in the HT115 colon cancer cell-line, that are validated using a known cell lineage that includes thousands of mutations and a high confidence region covering 2.7 gigabases per sample. Nature Publishing Group UK 2020-12-08 /pmc/articles/PMC7722876/ /pubmed/33293579 http://dx.doi.org/10.1038/s42003-020-01460-9 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Shand, Megan
Soto, Jose
Lichtenstein, Lee
Benjamin, David
Farjoun, Yossi
Brody, Yehuda
Maruvka, Yosef
Blainey, Paul C.
Banks, Eric
A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title_full A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title_fullStr A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title_full_unstemmed A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title_short A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
title_sort validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7722876/
https://www.ncbi.nlm.nih.gov/pubmed/33293579
http://dx.doi.org/10.1038/s42003-020-01460-9
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