Table 3 Details of platform comparison
ArraysNo. SamplesNo. Stringent CNVsAverage CNVs/SampleAverage CNV Size, kbNo. Overlapping calls% Overlap/ Validationa% CNVs With Insufficient Probes in Other ArrayNovel CNVs/Sample
1Agilent 1M82274733.5 ± 6.11107183667.531.27 ± 5.38
Affy 500K822893.52 ± 2.285201896562.17 ± 1.22
2Agilent 1M262897134.24 ± 6.45972725303823.84 ± 5.30
Ilmn 1M single262477918.24 ± 4.6911027295759.127.82 ± 3.11
3Agilent 1M1141337.55 ± 6.7683992439.7028.55 ± 5.13
Ilmn 1M duo1116914.36 ± 4.32841086467.215.54 ± 1.81
4Agilent 1M234827035.49 ± 6.23984439535.616.44 ± 4.27
Affy 6.023415,31565.45 ± 8.878047013477.4645.35 ± 7.39
5Agilent 1M2694536.35 ± 6.27108328353323.73 ± 4.63
Ilmn Omni 2.5M26123047.31 ± 9.77613803181.432.69 ± 8.57
  • ASD, autism spectrum disorder; CNV, copy number variations; PDx, control cohort DNA samples.

  • a % overlap/validation- refers to the percentage of CNVs that were also detected by the other array. For example, for the first platform comparison between Agilent 1M and Affy500K arrays, only 6% of the CNVs detected by Agilent 1M were also detected by Affy500K while 65% of the CNVs detected by Affy500K were also detected or validated by Agilent 1M array.