Work

Detecting non-allelic homologous recombination from high-throughput sequencing data

Year: 2015

Type: article

Abstract: Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge. We present a probabilistic model of NAHR and demonstrate its ability to find NAHR in low-coverage sequencing data from 44 individuals. We identify NAHR-mediated deletions or duplications in 109 of 324 potential NAHR loci in at least one of the individuals. These calls segregate by ancestry, are more common in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA and CYP2E1.

Source: Genome biology

DOI: 10.1186/s13059-015-0633-1

Authors: Matthew M Parks, Charles E Lawrence, Benjamin J Raphael

Institution: Brown University

Language: English

Topic: Genomic variations and chromosomal abnormalities

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $5,490