Table 2.

Comparison of Family-Based versus Published Case-Control GWA Findings for the Signals Identified in the NIMH 500K Screen

SNP	Model	NIMH (500K)		TGEN8		GSK10
		p (two-tailed)	Fams	p (one-tailed)	n (AD + CTRL)	p (one-tailed)	n (AD + CTRL)
rs11159647, with affection status	add	0.05	128	0.04	1384	0.9∗	1315
rs179943, with affection status	add	0.007	55	0.8∗	1376	0.5∗	1368
rs3826656, with affection status	dom	0.02	90	N.A.	N.A.	N.A.	N.A.
rs2049161, with affection status	add	0.04	78	0.2	1407	0.045	1386

Family-based (NIMH) p values are two sided and identical to those of Table 1. Case-control (TGEN⁷ and GSK¹⁰) p values are one sided, on the basis of an allelic chi-square test (1 d.f.) with the genotype frequencies of the original publications (note that the FBAT-GEE and age of onset statistics could not be computed here because of the lack of onset-age data in the original reports). The results presented in this table are based on the complete data sets made available by the authors of the respective studies. Fams, informative families. The asterisks represent association with opposite allele as compared to 500K analyses (see identity of associated alleles in legend to Table 1). “N.A.” represents no data provided for this marker. Significant p values are represented in bold.