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Human Molecular Genetics Advance Access published online on July 31, 2007
Human Molecular Genetics, doi:10.1093/hmg/ddm208
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases

Adam J de Smith1,*, Anya Tsalenko2,*, Nick Sampas2, Alicia Scheffer2, N Alice Yamada2, Peter Tsang2, Amir Ben-Dor2, Zohar Yakhini2, Richard J Ellis3, Laurakay Bruhn2, Stephen Laderman2, Philippe Froguel1,4 and Alexandra IF Blakemore1,**

1 Genomic Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK 2 Agilent Laboratories, Santa Clara, CA, USA 3 North West London Hospitals NHS Trust Regional Genetics Service, Northwick Park Hospital, Harrow, UK 4 CNRS 8090-Institute of Biology, Pasteur Institute, Lille, FR

** Correspondence to Dr Alexandra IF Blakemore: Email - a.blakemore{at}imperial.ac.uk; Tel. - (+44) 208 383 2366; Address - Hammersmith Hospital Campus, Imperial College London, Du Cane Road, London W12 0NN

Received June 14, 2007; Revised July 23, 2007; Accepted July 23, 2007

The discovery of copy number variation in healthy individuals is far from complete, and due to the resolution of detection systems used, the majority of loci reported so far are relatively large (~65% > 10kb). Applying a two-stage high-resolution array CGH approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants (CNVs) detected by more than one consecutive probe. These clustered into 1469 copy number variant regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of end-points in those observed in multiple samples. Only 6% of the CNVRs analysed showed evidence of both copy number losses and gains at the same site. A further 6089 variants were detected by single probes: 48% of these were observed in more than one individual.

In total, 2570 genes were seen to intersect variants: 1284 in novel loci. Genes involved in differentiation and development were significantly overrepresented, and approximately half the genes identified feature in the OMIM database. The biological importance of many of the genes affected, along with the well-conserved nature of the majority of the copy number variants, suggests they could have important implications for phenotype and, thus, be useful for association studies of complex diseases.

* These two authors contributed equally to this work.


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