Figure 2

Size distribution of candidate CNVs detected. The five plots show numbers of candidate copy number gains and losses identified using Xba and Hind arrays, arranged according to the numbers of SNPs within the aberrations: A) all CNVs (>= 4 SNPs); B) CNVs >= 11 SNPs; C) CNVs >= 21 SNPs; D) CNVs >= 41 SNPs and E) CNVs >= 101 SNPs. The y-axis value of each horizontal line represents the total number of CNVs detected by a given method: 1 – CNAG Ref2; 2 – CNAG Ref50; 3 – CNAG-GLAD Ref2; 4 – CNAG-GLAD Ref50; 5 – dChip Ref50; 6 – dChip Ref214; 7 – dChip-GLAD Ref50; 8 – dChip-GLAD Ref214; 9 – CNAT-GLAD Ref50; 10 – CNAT-GLAD Ref106; 11 – CNAT-GLAD Ref214 (the reference sets are described in Figure 1 and in the Methods.) The left and right side of each panel correspond to the fraction of deletions and duplications, respectively. The orange bars within the black lines show the fraction of CNVs that passed the following confidence thresholds: p <= 0.05 (t-test) and copy number < 1.25 for deletions (left); or p <= 0.05 (t-test) and copy number > 2.75 for duplications (right). The fractions of false positive deletion calls, calculated based on SNP heterozygosity, are indicated by the red vertical bars on the left side of each panel. For example, the y-axis value of the top line (5) in plot 'A' indicates the total number of candidate CNVs (52,478) including at least 4 consecutive SNPs identified by dChip Ref50 (from Xba and Hind data). 30% of the 52,478 putative CNVs were deletions (left) and 70% were duplications (right). 99% of the deletions (orange fraction of the line, left) and 22% of the duplications (orange fraction of the line, right) passed our p-value <= 0.05 and copy number (<1.25 or >2.75) thresholds described above. 34% of the candidate deletions were considered to be false positives, indicated by the red bar (left).