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Interim description of properties of WTCCC/GSV CNV typing array

The CNV typing array being used by the WTCCC+ project comprises ~104,000 probes targeted to ~11,000 loci, the majority of which (~90%) were identified in a preliminary analysis of a CNV discovery project conducted by the Genome Structural Variation consortium in 20 individuals of European ancestry and 20 individuals of West African ancestry. Over 95% of the polymorphic CNVs genotyped in the CEU population by McCarroll et al using the Affymetrix 6.0 platform are covered by the array (in the sense that they overlap with loci on the array). Our preliminary estimate is that approximately 20-30% of the loci on the array are both polymorphic in our British study population and provide sufficient data quality to assign integer copy numbers to individuals. This estimate could change, and in particular could decrease, with further analyses. In addition, ~15% of loci on the array comprise Variable Numbers of Tandem Repeat (VNTR) loci, which are likely polymorphic but for which integer copy numbers cannot be reliably determined for individuals. This description of the properties of the data resulting from the array is preliminary and will change as analyses mature.