Shurjo K. Sen,*
Jianxin Wang, Jungnam Lee,
Hui Wang, Pauline A. Callinan, Matthew Dyer, Richard Cordaux, Ping Liang, and
Mark A. Batzer
From the Department of Biological Sciences, Biological
Computation and Visualization
Center, Center for BioModular
Multi-Scale Systems, Louisiana State
University, Baton Rouge (S.K.S.;
K.H.; J.L.; H.W.; P.A.C.;
M.D.; R.C.; M.A.B.); and
Department of Cancer Genetics,
Roswell Park Cancer Institute,
Buffalo (J.W.; P.L.)
Received February 6, 2006; accepted for publication March 22, 2006; electronically published May 3, 2006.
Recombination between Alu elements results in genomic deletions associated with many human genetic disorders. Here, we compare the reference human and chimpanzee genomes to determine the magnitude of this recombination process in the human lineage since the human-chimpanzee divergence ~6 million years ago. Combining computational data mining and wet-bench experimental verification, we identified 492 human-specific deletions(for a total of ~400 kb) attributable to this process, a significant component of the insertion/deletion spectrum of the human genome. The majority of the deletions (295 of 492) coincide with known or predicted genes (including 3 that deleted functional exons, as compared with orthologous chimpanzee genes), which implicates this process increating a substantial portion of the genomic differences between humans and chimpanzees. Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome.* These two authors contributed equally to this work.