Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing.

ABSTRACT: Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequen

SUBMITTER: Samson CA 

PROVIDER: S-EPMC7648094 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature