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Updated: Nov 9, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
Jeffrey N Dudley1, Celine S Hong2, Marwan A Hawari1
1National Human Genome Research Institute, National Institutes of Health, 50 South Drive Room 5140, Bethesda, MD, 20892, USA.
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 × and 1200 ×, 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.
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