Table 4.

Set-based TDT test in autism SNP data sets

Data set	Sourcea	P-valueb
		eQTLs	eQTL2s
Primary
With rs10513025	AGRE-NIMH	3.8 × 10−1	2.0 × 10−2
Exclude rs10513025	AGRE-NIMH	4.4 × 10−1
Replication	AGP-1M	4.4 × 10−1	1.3 × 10−1
	SSC-V1	9.3 × 10−1	9.3 × 10−1
Meta-analysis	Imputed	2.0 × 10−1	4.0 × 10−1
		6.0 × 10−2
Control	NHGRI-VU	7.2 × 10−1	2.6 × 10−1

The result from a set-based TDT test of our SEMA5A eQTL and eQTL² regions is shown here for our primary (with and without the original GWAS associated SNP), replication and control data sets. The combined eQTL and eQTL² regions were used to perform a set-based TDT test in the meta-analysis data set.

^aAGRE-NIMH: combined data sets from AGRE (Autism Genetic Resource Exchange, www.agre.org) and NIMH (National Institute for Mental Health, collections of DNA from multiplex and simplex families with ASD by the NIMH Autism Genetics Initiative) (17). AGP-1M: Autism Genome Project (http://www.autismgenome.org/) (20). SSC-V1: Simons Simplex Collection V1 Public Cohort (https://sfari.org/simons-simplex-collection) (83). Imputed: imputed data sets based on AGRE-NIMH, AGP, SSC-V1 and AGRE-CHOP. Both the P-values for separate test (above) and combined tests (below) are shown in the table. NHGRI-VU: Vanderbilt University NUgene Project type 2 diabetes SNP data set (dbGap: phs000237.v1.p1)) (89).

^bPermutation-based P-value from set-based association tests of SEMA5A eQTLs and eQTL²s. P-values < 0.05 are bolded.