Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15110%2F21%3A73610437" target="_blank" >RIV/61989592:15110/21:73610437 - isvavai.cz</a>

Result on the web

<a href="https://www.nature.com/articles/s41587-021-00994-5" target="_blank" >https://www.nature.com/articles/s41587-021-00994-5</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s41587-021-00994-5" target="_blank" >10.1038/s41587-021-00994-5</a>

Result language

angličtina

Original language name

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Original language description

Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G &gt; T/C &gt; A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10606 - Microbiology

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

NATURE BIOTECHNOLOGY

ISSN

1087-0156

e-ISSN

—

Volume of the periodical

39

Issue of the periodical within the volume

9

Country of publishing house

US - UNITED STATES

Number of pages

27

Pages from-to

1141-1167

UT code for WoS article

000694844000025

EID of the result in the Scopus database

2-s2.0-85114706613