A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

ABSTRACT: Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data. These candidate mosaic variants were subsequently evaluated using >100x BGI, Element, and PacBio HiFi data. High confidence candidate SNV

SUBMITTER: Daniels CA 

PROVIDER: S-EPMC11642750 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature