Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach

Background The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remains challenging. Results Here, we present a method for Position-Based Variant Identification (PBVI) that uses empirically-derived distributions of alternate nucleotides from a control dataset. We modeled this approach on 11 segmental overgrowth genes. We show that this method improves detection of single nucleotide mosaic variants of 0.01-0.05 variant allele fraction compared to other low-level variant callers. At depths of 600 x and 1200 x, we observed > 85% and > 95% sensitivity, respectively. In a cohort of 26 individuals with somatic overgrowth disorders PBVI showed improved signal to noise, identifying pathogenic variants in 17 individuals. Conclusion PBVI can facilitate identification of low-level mosaic variants thus increasing the utility of next-generation sequencing data for research and diagnostic purposes.

Automated summary

PBVI is a method for Position-Based Variant Identification that improves the detection of low-level mosaic variants by using empirically-derived distributions of alternate nucleotides from a control dataset. Modeled on 11 segmental overgrowth genes, this method shows superior detection of single nucleotide mosaic variants of 0.01-0.05 variant allele fraction. Sensitivity of over 85% and 95% was observed at depths of 600 x and 1200 x, respectively, demonstrating its utility in identifying pathogenic variants in individuals with somatic overgrowth disorders.