Alu repeat discovery and characterization within human genomes.
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.
School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
Fereydoun
F
Hormozdiari
Can
C
Alkan
Mario
M
Ventura
Iman
I
Hajirasouliha
Maika
M
Malig
Faraz
F
Hach
Deniz
D
Yorukoglu
Phuong
P
Dao
Marzieh
M
Bakhshi
S Cenk
SC
Sahinalp
Evan E
EE
Eichler
D020087:Alu Elements / Q000235:genetics*; D001483:Base Sequence; D044383:Black People / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods