An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing.

ABSTRACT:

Background

Multi-sample comparison is commonly used in cancer genomics studies. By using next-generation sequencing (NGS), a mutation's status in a specific sample can be measured by the number of reads supporting mutant or wildtype alleles. When no mutant reads are detected, it could represent either a true negative mutation status or a false negative due to an insufficient number of reads, so-called "coverage". To minimize the chance of false-negative, we should consider the mutation status as "unknown" instead of "negative" when the coverage is inadequately low. There is no established method for determining the coverage threshold between negative and unknown statuses. A common solution is to apply a universal minimum coverage (UMC). However, this method relies on an arbitrarily

SUBMITTER: Hutson N 

PROVIDER: S-EPMC8638096 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature