. 2014 May 1;94(5):677–694. doi: 10.1016/j.ajhg.2014.03.018

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.

The baseline gene rate (control) is defined as the average number of genes intersected by CNVs per control subject.

Genome-wide p values were estimated in 100,000 permutations (one sided) and additionally corrected (p_corr) for global case-control differences in CNV rate and size. Analyses were further stratified according to CNV type (deletions or duplications) and size.