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Genome Res. 2011 Jun;21(6):840-9. doi: 10.1101/gr.115956.110. Epub 2010 Dec 3.

Alu repeat discovery and characterization within human genomes.

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1
School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

Abstract

Human genomes are now being rapidly sequenced, but not all forms of genetic variation are routinely characterized. In this study, we focus on Alu retrotransposition events and seek to characterize differences in the pattern of mobile insertion between individuals based on the analysis of eight human genomes sequenced using next-generation sequencing. Applying a rapid read-pair analysis algorithm, we discover 4342 Alu insertions not found in the human reference genome and show that 98% of a selected subset (63/64) experimentally validate. Of these new insertions, 89% correspond to AluY elements, suggesting that they arose by retrotransposition. Eighty percent of the Alu insertions have not been previously reported and more novel events were detected in Africans when compared with non-African samples (76% vs. 69%). Using these data, we develop an experimental and computational screen to identify ancestry informative Alu retrotransposition events among different human populations.

PMID:
21131385
PMCID:
PMC3106317
DOI:
10.1101/gr.115956.110
[Indexed for MEDLINE]
Free PMC Article
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