The Copy Number Variation (CNV) project
There are an increasing number of evidences that Copy Number Variations (CNVs) significantly contribute to the nucleotide diversity of human genome, besides single nucleotide polymorphisms (SNPs). Additionally, CNVs seems to contribute more to human disease susceptibility than previously expected, although a complete picture of the phenotypic consequences of CNVs has not yet been revealed.
As the part of the Structural Variation Consortium project, we have reported the first generation human CNV Map among 270 HapMap samples (Nature 2006). Especially, we have developed a novel CNV detection algorithm GEMCA (Genotyping Microarray based CNV Analysis), using Affymetrix high density 500K Mapping Arrays (Genome Research 2006).
Figure1: Whole genome profile of Affymetrix 500K signal intensity ratio of male(NA15510) to female(NA10851) sample. Red dot represents probes at the CNV loci. [Click on image for enlargement]
Figure2: Magnified view from figure1 showing 1072Kbp CNV at 3p24.3 [Click on image for enlargement]
Figure3: The chromosomal distribution of the 1,447 CNV is shown. The blue bars on the right-hand represents the actual physical position of the CNVs, and the length of red bars on the left-hand side indicates the frequency with which the associated CNV region is called. [Click on image for enlargement]
Finished CNV call database and browser
Database of Genomic Variant (Toronto University)
Affymetrix 500KEA(early access) and commercial 500K set raw data
Gene Expression Omnibus, with accession numbers GSE5013 and GSE5173
The Wellcome Trust Sanger Institute WGTP (Whole Genome Tiling Path) array raw data
ArrayExpress, with accession number E-TABM-107