Table 1.

Genome-wide SCZ and ASD Risk Variant Datasets Tested for BrainSpan Module Enrichment.

Dataset	Reference	Variant Type	Description	Patient N	Control N	Analysis
SCZ
SCZ PGC-deCODE*	12	Common	PGC + deCODE meta-analysis	36,989	113,075	MAGMA
SCZ CLOZUK-PGC*	9	Common	CLOZUK + PGC meta-analysis	40,675	64,643	MAGMA
SCZ Richards	24	Rare	Rare variants (MAF<1%)	5,585	8,103	MAGMA
SCZ Genovese	11	Ultra-rare	43 genes enriched for deleterious ultra-rare variants (p<0.01)	4,877	6,242	Fisher’s Exact Test
SCZ DNM	10, 26–33	De novo	Compilation of DNMs	1,139	NA	DenovolyzeR
SCZ CNV	4	CNV	13 unique loci (FDR<0.05)	21,094	20,227	Logistic Regression
ASD
ASD iPSYCH-PGC	23	Common	iPSYCH + PGC meta-analysis	18,381	27,969	MAGMA
ASD SFARI	www.sfari.org	Gene list	80 literature-curated genes (score 1 or 2)	NA	NA	Fisher’s Exact Test
ASD Sanders	15	Rare	65 genes (FDR<0.1)	3,982	1,911	Fisher’s Exact Test
ASD DNM	34, 35	De novo	Compilation of DNMs	4,424	NA	DenovolyzeR
ASD CNV	15	CNV	9 unique loci, +3 nested loci, in SSC and AGP cohorts (FDR<0.05)	4,687	2,100	Logistic Regression

^*The PGC-deCODE meta-analysis includes 1,513 SCZ cases and 36,989 controls from the deCODE study not in the CLOZUK-PGC study and the SCZ CLOZUK-PGC meta-analysis includes 5,220 SCZ cases and 18,823 controls not in the SCZ PGC-deCODE study.