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

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

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


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 languageEnglish (US)
Article number72
JournalGenome biology
Issue number1
StatePublished - Apr 8 2015
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology


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