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

Megan Shand; Jose Soto; Lee Lichtenstein; David Benjamin; Yossi Farjoun; Yehuda Brody; Yosef Maruvka; Paul C. Blainey; Eric Banks

doi:10.1038/s42003-020-01460-9

Communications Biology (Dec 2020)

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

Megan Shand,
Jose Soto,
Lee Lichtenstein,
David Benjamin,
Yossi Farjoun,
Yehuda Brody,
Yosef Maruvka,
Paul C. Blainey,
Eric Banks

Affiliations

Megan Shand: Broad Institute of Harvard and MIT
Jose Soto: Broad Institute of Harvard and MIT
Lee Lichtenstein: Broad Institute of Harvard and MIT
David Benjamin: Broad Institute of Harvard and MIT
Yossi Farjoun: Broad Institute of Harvard and MIT
Yehuda Brody: Broad Institute of Harvard and MIT
Yosef Maruvka: Broad Institute of Harvard and MIT
Paul C. Blainey: Broad Institute of Harvard and MIT
Eric Banks: Broad Institute of Harvard and MIT

DOI: https://doi.org/10.1038/s42003-020-01460-9
Journal volume & issue: Vol. 3, no. 1
pp. 1 – 8

Abstract

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Megan Shand et al. present Lineage derived Somatic Truth (LinST), a validated data set of somatic mutations from a colon cancer cell line with a known lineage tree structure. They show that LinST can be used to benchmark true-positive and false-positive rates in somatic variant-calling pipelines applied to cancer genomic data.

Published in Communications Biology

ISSN: 2399-3642 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/commsbio/

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