TY  - JOUR
A1  - Hormozdiari, Fereydoun
A1  - Alkan, Can
A1  - Ventura, Mario
A1  - Hajirasouliha, Iman
A1  - Malig, Maika
A1  - Hach, Faraz
A1  - Yorukoglu, Deniz
A1  - Dao, Phuong
A1  - Bakhshi, Marzieh
A1  - Sahinalp, S. Cenk
A1  - Eichler, Evan E.
T1  - Alu repeat discovery and characterization within human genomes
Y1  - 2011/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 840 
EP  - 849 
DO  - 10.1101/gr.115956.110 
VL  - 21 
IS  - 6 
UR  - http://genome.cshlp.org/content/21/6/840.abstract 
N2  - 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. 
ER  -