Table 1. Significant CNV regions in the stage I discovery sample.

Cytoband	Start position (bp)	Type	Allele frequency	Avg. CN	Length (bps)	Gene	DGV	P-value
1q12	141,622,815	Loss	0.21	1.58390	395,766	ANKRD20A12P	+	3.09E−07
1p36.13	17,546,966	Loss	0.24	1.52439	4,858	PADI4	+	2.94E−06
1p36.21	13,306,366	Loss	0.23	1.57085	192,072	PRAMEF14	−	1.73E−06
1p36.21	13,167,437	Loss	0.22	1.56805	130,829	PRAMEF3	+	1.12E−07
1p36.32	2,573,413	Loss	0.22	1.55573	108,341	TTC34	+	1.03E−05
2p16.1	56,378,184	Loss	0.23	1.54534	120,493	CCDC85A	+	5.83E−07
2p22.3	33,077,316	Loss	0.23	1.54556	3,928	LTBP1	+	1.02E−03
2p25.3	1,506,306	Loss	0.23	1.59170	16,162	TPO	+	2.61E−07
3q29	199,289,792	Loss	0.25	1.51397	142,634	ANKRD18DP	+	6.27E−08
5q35.1	170,061,229	Gain	0.29	2.57862	4,470	KCNIP1	+	1.57E−06
6p21.32	33,140,517	Loss	0.22	1.56019	8,849	HLA-DPA1	+	1.88E−06
6p21.32	33,133,423	Loss	0.22	1.56438	7,095	HLA-DPA1	+	1.00E−06
6p21.32	33,158,459	Loss	0.21	1.57858	4,840	HLA-DPB1	+	7.36E−07
6p22.3	22,156,930	Loss	0.30	1.43742	4,981	LINC00340	−	3.94E−05
7q34	142,107,052	Loss	0.21	1.57438	69,930	PRSS1	+	1.58E−06
7q34	142,107,052	Loss	0.21	1.57438	69,930	PRSS3P2	+	1.58E−06
8q24.3	144,785,898	Loss	0.24	1.52527	27,257	ZNF623	+	3.63E−05
14q32.33	105,491,658	Gain	0.55	3.10113	19,535	ADAM6	+	5.23E−07
14q32.33	105,807,945	Gain	0.33	2.51647	37,608	LINC00226	+	3.38E−08
17p13.3	670,214	Loss	0.26	1.47994	2,402	NXN	+	1.79E−08
21q22.3	46,142,957	Loss	0.30	1.39238	27,264	PCBP3	+	1.56E−07
21q22.3	43,780,913	Loss	0.23	1.53278	23,647	HSF2BP	+	2.12E−04
21q22.3	46,171,463	Loss	0.31	1.37456	29,943	PCBP3	+	2.48E−07
21q22.3	43,728,391	Loss	0.23	1.54411	52,523	HSF2BP	+	7.05E−04
22q11.22	21,430,797	Gain	0.30	2.44319	139,593	MIR650	+	9.66E−08
22q11.22	21,430,797	Gain	0.30	2.44319	139,593	IGLL5	+	9.66E−08
22q11.23	22,694,904	Loss	0.39	1.22954	33,941	GSTT1	+	3.90E−08
22q11.23	22,629,805	Loss	0.37	1.25476	40,795	GSTT2	+	6.34E−07

Avg. CN, average copy number; bp, base pair; CNV, copy number variation; DGV, Database of Genomic Variants (http://projects.tcag.ca/variation/). Allele frequencies are inferred from the averaged CN based on a diallelic assumption for each variant.

The statistical significance level was set at P<10⁻³ in the genome-wide CNV discovery stage; NCBI RefSeq (hg18; build 36) was used to annotate the location and coding region of each CNV region in the genome.