Table 1.
Summary of CNV in ASD and Controls
| Popgen Controls |
Autism Probands |
|||||
|---|---|---|---|---|---|---|
| All CNVs |
All CNVs |
Autism Specifica |
||||
| Full | Stringentb | Full | Stringentb | Full | Stringentb | |
| # Samples | 500 | 500 | 427 | 427 | 427 | 427 |
| # CNVs | 3695 | 1558 | 3396 | 1315 | 889 | 277 |
| CNV/Genomec | 7.4 | 3.1 | 8.0 | 3.1 | 2.1 | 0.65 |
| Mean/Median Size (kb) | 315/151 | 470/224 | 390/162 | 603/219 | 518/121 | 1082/194 |
| % Gain/Loss | 59/41% | 70/30% | 58/42% | 62/38% | 61/39% | 57/43% |
| Overlapping CNV/Loci (%)d | 3005/333 (81%) | 1226/142 (78%) | 2734/277 (80%) | 983/94 (74%) | 398/122 (44%) | 31/13 (11%) |
| >1 Mb CNV(%) | 343 (9%) | 250 (16%) | 339 (10%) | 212 (16%) | 63 (7%) | 32 (12%) |
Not seen in the initial 500 controls. There were 50 probands run in a previous study with the Affymetrix 10K array.4 The 10K array detected five different CNVs in five individuals. Of these putative CNVs, three were confirmed by the current 500K experiments, one was a false positive, and one had no probe coverage on the 500K platform so its status is unknown.
Stringent data set as called by >1 algorithms or arrays. Analysis with dChip was performed in batches of ∼100 probands. For CNAG version 2.0, we set the reference pool to include all samples and performed an automatic batch pair-wise analysis with sex-matched controls. For GEMCA, we used two designated DNA samples (NA10851 and NA15510) as references for pair-wise comparison to all proband experiments. We further filtered these results by including only those CNVs that were common to both pair-wise experiments. In all instances, CNVs were merged if they were detected in the same individual by more than one algorithm with the outside probe boundaries.
CNV/genome breakdown by algorithm: dChip Merged (3.0/genome), CNAG Merged (5.6/genome), GEMCA (5.5/genome). Validation experiments with q-PCR and FISH are described in the text. Another form of validation comes from examining the trios where we can demonstrate inheritance in 48 (maternal is 25, paternal is 23) of the autism-specific stringent data set. Also from the trios, 148 confirmed regions (inheritance assignment) in the stringent data set that overlap with controls (maternal is 65, paternal is 83).
Represents the total number of overlapping and/or recurrent CNVs, the number of overlapping/CNV loci, and the percentage of overlapping CNVs, out of the total data set.