Table 1 Summary statistics of stringent CNVs found in ASD and PDx control data sets
Unrelated ASD CasesPDx Controls
No. samples6761000
No. males/females560/116502/498
No. stringent CNVsa23,49349,524
Mean no. CNVs/ sample ± SDb34.75 ± 6.4049.52 ± 5.95
Median no. CNVs/sample3449
Mean CNV size, kb ± SD97.75 ± 229.41287.50 ± 198.59
Median CNV size, kb3030
% gain /% loss42.36/57.6448.24/51.76
No. CNVs of size >1 Mb (%)471 (2)942 (1.90)
No. CNVs of size from 100 Kb to 1 Mb (%)3715 (15.81)7982 (16.12)
No. CNVs of size from <100 Kb (%)19,307 (82.18)40,600 (81.98)
  • ASD, autism spectrum disorder; CNV, copy number variations; PDx, control cohort DNA samples.

  • a CNVs detected in the same individual using two algorithms, DNA Analytics and DNAcopy, were merged with the outside probes used as boundaries and defined as stringent CNV dataset containing at least five consecutive probes. Samples containing CNVs larger than 5 Mb were excluded (Table S1).

  • b We observed a significant difference in average number of CNVs per sample in PDx controls than in ASD cases (One-tailed exact Wilcoxon test p value < 2.2e-16) possibly due to reference bias.