AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples

Abstract

The detection of somatic DNA variants in tumor samples with low tumor purity or sequencing depth remains a daunting challenge despite numerous attempts to address this problem. In this study, we constructed a substantially extended set of actual positive variants originating from a wide range of tumor purities and sequencing depths, as well as actual negative variants derived from sequencer-specific sequencing errors. A deep learning model named AIVariant, trained on this extended dataset, outperforms previously reported methods when tested under various tumor purities and sequencing depths, especially low tumor purity and sequencing depth.