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Article

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples.

Genetics in medicine : official journal of the American College of Medical Genetics - 1 Apr 2019

Barnell Erica K, Ronning Peter, Campbell Katie M, Krysiak Kilannin, Ainscough Benjamin J, Sheta Lana M, Pema Shahil P, Schmidt Alina D, Richters Megan, Cotto Kelsy C, Danos Arpad M, Ramirez Cody, Skidmore Zachary L, Spies Nicholas C, Hundal Jasreet, Sediqzad Malik S, Kunisaki Jason, Gomez Felicia, Trani Lee, Matlock Matthew, Wagner Alex H, Swamidass S Joshua, Griffith Malachi, Griffith Obi L

Abstract excerpt

PURPOSE: Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. METHODS: This manual review standard operating procedure (SOP) consists of methods to annotate...

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Identifiers

PMID: 30287923
DOI: 10.1038/s41436-018-0278-z
PMCID: PMC6450397

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