Alu repeat discovery and characterization within human genomes
- Fereydoun Hormozdiari1,
- Can Alkan2,
- Mario ventura3,
- Iman Hajirasouliha1,
- Maika Malig2,
- Faraz Hach1,
- Deniz Yorukoglu1,
- Phuong Dao1,
- Marzieh Bakhshi1,
- S. Cenk Sahinalp1 and
- Evan E. Eichler2,4
- * Corresponding author; email: eee{at}gs.washington.edu
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 4,342 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 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 to 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.
- Received September 27, 2010.
- Accepted December 2, 2010.
- Copyright © 2010, Cold Spring Harbor Laboratory Press
