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

Matthew M. Parks; Charles E. Lawrence; Benjamin J. Raphael

doi:10.1186/s13059-015-0633-1

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

Matthew M. Parks, Charles E. Lawrence, Benjamin J. Raphael

Research output: Contribution to journal › Article › peer-review

36 Scopus citations

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.

Original language	English (US)
Article number	72
Journal	Genome biology
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s13059-015-0633-1
State	Published - Apr 8 2015
Externally published	Yes

All Science Journal Classification (ASJC) codes

Genetics
Ecology, Evolution, Behavior and Systematics
Cell Biology

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10.1186/s13059-015-0633-1

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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.",

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AB - 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.

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

Abstract

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