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Human Molecular Genetics Advance Access originally published online on January 7, 2008
Human Molecular Genetics 2008 17(8):1127-1136; doi:10.1093/hmg/ddn002
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

Arthur S. Lee1,2, María Gutiérrez-Arcelus1,3, George H. Perry1,4, Eric J. Vallender5, Welkin E. Johnson5, Gregory M. Miller5, Jan O. Korbel6,7 and Charles Lee1,8,*

1 Department of Pathology, Brigham and Women’s Hospital, 221 Longwood Ave., Boston, MA 02115, USA 2 Harvard University, Cambridge, MA 02138, USA 3 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico 4 School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA 5 New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA 6 Molecular Biophysics and Biochemistry Department, Yale University School of Medicine, New Haven, CT 06520, USA 7 European Molecular Biology Laboratory, Heidelberg 69117, Germany 8 Harvard Medical School, Boston, MA 02115, USA

* To whom correspondence should be addressed. Tel: +1 6172780031; Fax: +1 6172646861; Email: clee{at}rics.bwh.harvard.edu

Received September 27, 2007; Accepted January 3, 2008

Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385 000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of ~50 million years of primate evolution (~25 million years in each lineage). Furthermore, for eight of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate outbred model organism with which hypotheses concerning the specific functions of phenotypically relevant human CNVs can be tested.


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