Table 1  Genome-wide Burden of Genes Intersected by Rare CNVs in a Combined Sample of 2,147 European ASD Affected Subjects and 2,640 European Control Subjects
Type   Group Size   No. of Rare Genic CNVs   No. of Genes Intersected by Rare CNVs   Baseline Gene Rate (Control) a   Case-Control Gene Ratio   p  corr  b
All  all  6,859  6,745  3.55  1.41  0.00001∗
Deletions  all  2,946  2,804  1.23  1.40  0.00049∗
Duplications  all  3,913  5,217  2.32  1.41  0.00001∗
All  30–500 kb  6,307  5,163  2.89  1.07  0.03628∗
>500 kb  552  2,491  0.66  2.88  0.00001∗
>1 Mb  187  1,337  0.26  4.48  0.00001∗
Deletions  30–500 kb  2,795  2,014  1.07  1.07  0.20110
>500 kb  151  947  0.16  3.60  0.00051∗
>1 Mb  63  647  0.08  4.58  0.02289∗
Duplications  30–500 kb  3,512  3,934  1.83  1.08  0.03750∗
>500 kb  401  1,896  0.50  2.64  0.00026∗
>1 Mb  124  890  0.18  4.43  0.00036∗
Rare CNVs in samples of European ancestry were defined as ≥30 kb in size and present in the total sample set at a frequency < 1%. Gene coordinates were defined by the RefSeq boundaries plus a 10 kb region on either side. All genomic analyses used UCSC Genome Browser hg18. ∗Significant differences (p ≤ 0.05) are indicated.
a  The baseline gene rate (control) is defined as the average number of genes intersected by CNVs per control subject.
b  Genome-wide p values were estimated in 100,000 permutations (one sided) and additionally corrected (pcorr) for global case-control differences in CNV rate and size. Analyses were further stratified according to CNV type (deletions or duplications) and size.