<i>Alu</i> repeat discovery and characterization within human genomes

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<jats:p>Human genomes are now being rapidly sequenced, but not all forms of genetic variation are routinely characterized. In this study, we focus on <jats:italic>Alu</jats:italic> 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 <jats:italic>Alu</jats:italic> 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 <jats:italic>Alu</jats:italic>Y elements, suggesting that they arose by retrotransposition. Eighty percent of the <jats:italic>Alu</jats:italic> 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 <jats:italic>Alu</jats:italic> retrotransposition events among different human populations.</jats:p>

Journal

  • Genome Research

    Genome Research 21 (6), 840-849, 2010-12-03

    Cold Spring Harbor Laboratory

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