PAGE 5 OF 14 Nucleic Acids Research, 2010, Vol. 38, No. 9 e105 Figure 1. Positions of simulated copy number variants with University of California Santa Clara genome browser (http://genome.ucsc .edu/cgi-bin/hgGateway) tracks on chromosome 1. The copy number (sim1 copy, sim2 copy), the size of copy number variant (sim1 size, sim2 size) and the frequency of copy number variant detection method (sim2 mm) were designated at each location for simulations 1 and 2. Table 2. Number of CNV SNPs and ROC curve residuals for each DNA type in the pilot dataset Method CBS CNVFinder cnvPartition GLAD Nexus Rank Nexus SNPRank PennCNV QuantiSNP Parametera 1 SD 4 SD 6,4,4,2 SDe 7,5,4,2 SDe Conﬁdence >0 Conﬁdence >5 All calls Smoothed m > |0.3| Threshold = 1E–2 Threshold = 1E–4 Threshold = 1E–2 Threshold = 1E–4 SNPs 1 SNPs 2 Conﬁdence >2 L = 2M L = 2M; LBF >0 Measureb CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual CNV SNPs ROC residual ROC residual ROC residual CNV SNPs ROC residual ROC residual Buccal 391 0.0024 0.0024 336 0.0007 0.0005 329 0.0018 0.0018 135 0.0011 0.0011 29 843 0.0057 0.0026 592 0.0016 0.0011 278 0.0016 0.0016 0.0016 468 0.0026 0.0025 Saliva 209 0.0009 0.0009 371 0.0007 0.0005 212 0.0012 0.0012 157 0.0010 0.0010 54 662 0.0098 0.0029 1528 0.0008 0.0008 411 0.0016 0.0016 0.0016 739 0.0022 0.0021 Blood 688 8.3E–5 5.9E–5 218 0.0008 0.0007 410 0.0013 0.0013 646 0.0009 0.0011 57 186 0.0573 0.0014 2717 0.0003 0.0003 382 0.002 0.0019 0.0019 568 0.0029 0.0023 Ampliﬁed Buccal 51 404 0.0217 0.0217 2032 0.0063 0.0038 4900 0.0166 0.0167 7667 0.0121 0.0122 285 812 0.0096 0.0170 85 646 0.0217 0.0216 6 663 0.0201 0.0142 0.0144 36 200 0.0267 0.0235 aBold text designates NSR optimal parameter results for each method. bCNV SNPs are given as number per sample.