Human Molecular Genetics Advance Access originally published online on July 31, 2007
Human Molecular Genetics 2007 16(23):2783-2794; doi:10.1093/hmg/ddm208
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Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases
1 Genomic Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, 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, France
* To whom correspondence should be addressed. Tel: +44-2083832366; Email: a.blakemore{at}imperial.ac.uk
Received June 14, 2007; Accepted July 23, 2007
The discovery of copy number variation in healthy individuals is far from complete, and owing to the resolution of detection systems used, the majority of loci reported so far are relatively large (
65%>10 kb). Applying a two-stage high-resolution array comparative genomic hybridization 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 CNV regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4 kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of endpoints 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 over-represented and approximately half of the genes identified feature in the Online Mendelian Inheritance in Man database. The biological importance of many genes affected, along with the well-conserved nature of the majority of the CNVs, suggests that they could have important implications for phenotype and, thus, be useful for association studies of complex diseases.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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