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Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection

Omer Gokcumen12, Paul L Babb3, Rebecca C Iskow12, Qihui Zhu12, Xinghua Shi12, Ryan E Mills12, Iuliana Ionita-Laza4, Eric J Vallender25, Andrew G Clark6, Welkin E Johnson25* and Charles Lee12*

Author Affiliations

1 Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA

2 Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA

3 Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA 19104, USA

4 Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA

5 New England Primate Research Center, One Pine Hill Drive, Southborough, MA 01772, USA

6 Department of Molecular Biology and Genetics, Cornell University, 107 Biotechnology Building, Ithaca, NY 14853, USA

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Genome Biology 2011, 12:R52  doi:10.1186/gb-2011-12-5-r52

Published: 31 May 2011



Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation.


In this study, we identified over 2,000 human CNVs that overlap with orthologous chimpanzee or orthologous macaque CNVs. Of these, 170 CNVs overlap with both chimpanzee and macaque CNVs, and these were collapsed into 34 hotspot regions of CNV formation. Many of these hotspot regions of CNV formation are functionally relevant, with a bias toward genes involved in immune function, some of which were previously shown to evolve under balancing selection in humans. The genes in these primate CNV formation hotspots have significant differential expression levels between species and show evidence for positive selection, indicating that they have evolved under species-specific, directional selection.


These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions.