Table 1.

Exome versus GWAS array calls for CNVs of known importance in schizophrenia.

Large CNVs from the literature				Exome array probe coverage			GWAS	Exome array
Ref.	CNV	Location (Mb)	Kbp	Probes	%length	Kbp per probe	Total CNVs	Total CNVs	True discovery	False discovery
(2, 16, 21)	DEL 1q21.1-q21.2	chr1:145.8-147.8	1, 945	108	47%	18.01	8	8	8	0
(2)	DEL 3q29	chr3:195.7-197.3	1, 630	253	91%	6.44	4	4	4	0
(2, 16)	DEL 15q13.2-q13.3	chr15:30.9-32.5	1, 600	161	97%	18.63	5	5	5	0
(2, 22)	DUP 16p11.2	chr16:29.5-30.3	460	163	77%	3.68	11	10	10	0
(2, 16)	DEL 22q11.2	chr22:18.7-21.8	3, 150	498	92%	6.33	8	8	8	0

Note: A total of 9 loci were examined. Four loci are not included in Table 1:17q12, and 22q12.2 (no CNV was detected from either GWAS or exome arrays (100% agreement));2p16.3 and 7q36.3 (insufficient exome array coverage).