Alu repeat discovery and characterization within human genomes
- Fereydoun Hormozdiari1,2,5,
- Can Alkan2,3,5,
- Mario Ventura2,4,5,
- Iman Hajirasouliha1,
- Maika Malig2,
- Faraz Hach1,
- Deniz Yorukoglu1,
- Phuong Dao1,
- Marzieh Bakhshi1,
- S. Cenk Sahinalp1 and
- Evan E. Eichler2,3,6
- 1School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada;
- 2Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA;
- 3Howard Hughes Medical Institute, Seattle, Washington 98195, USA;
- 4Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
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↵5 These authors contributed equally to this work.
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.
Footnotes
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↵6 Corresponding author.
E-mail eee{at}gs.washington.edu.
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.115956.110.
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[Supplemental material is available for this article.]
- Received September 27, 2010.
- Accepted December 2, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
