Fig. 1

Landscape of human copy number variation. (A) CNV heatmap of a 734-kbp duplicated region flanking the 17q21.31 MAPT locus in 13 individuals (11 sequenced to high coverage). Read depth–based copy number (CN) estimations (3-kbp windows) are indicated by color (scale provided to the right). FISH at two separate loci validates these absolute CN predictions across five individuals (9). (B) Copy number landscape of the 17q21.31 locus across three different populations showing marked population stratification (159 genomes analyzed). A European-enriched duplication overlaps the gene KIAA1267 and is present on two haplotypes—along form (205 kbp) and a short form (155 kbp). A 210-kbp duplication of the NSF gene ranges from two to six copies with increased copy number in Asians. For validation with array CGH, see fig. S31. (C) Copy number frequency histograms of the KIAA1267 and NSF duplications based on median read depth predict discrete copies. Duplications of the KIAA1267 locus are specific to Europeans at a frequency of 72%. 25% of Asians have six copies of NSF.