We designed an experimental strategy to discover CNVs greater than ~500 base pairs (bp) in individuals with European or West African ancestry (Fig. 1). Using a set of 20 NimbleGen arrays, each comprising ~2.1-million long oligonucleotide probes covering the assayable portion of the genome (median spacing of 56 bp), we performed 800 comparative genome hybridization (CGH) experiments with female lymphoblastoid cell-line DNA competed against a common male European reference sample (NA10851). The female test DNAs comprised 19 CEU (Utah residents with ancestry from northern and western Europe)-European HapMap individuals, 20 YRI (Yoruba from Ibadan, Nigeria)-West Africans, and a Polymorphism Discovery Resource individual (NA15510). It was estimated that 40 samples would provide 95% power to sample variants with minor allele frequencies of 5% in either population.
