Two-stage family-based designs for sequencing studies

BMC Proceedings

Table 1 Mean score tests for the complete pedigrees.

Phenotype	Parameter	Mean score test			Proportion of variants (%)
					Prioritized		Replicated		1-Stage QTDT_M
	Simulated	-	Null	+	Null	+/-	Null	+/-	Null	+/-
DBP	Baseline	-1.42	-0.25	+0.42	10.2	14.7	1.8	5.3	1.7	9.3
	Intercept	-1.36	-0.32	+0.24	10.1	17.3	1.4	4.0	3.5	8.0
	Slope	+0.70	+0.14	-0.12	10.2	13.3	1.7	0.0	3.3	4.0
SBP	Baseline	-1.40	-0.35	+0.20	10.2	16.0	0.3	2.7	1.7	9.3
	Intercept	-1.34	-0.31	+0.37	10.1	17.3	0.0	4.0	2.0	13.3
	Slope	+0.85	+0.21	+0.11	10.2	12.0	0.5	0.0	2.3	0.0

Mean score tests for the complete pedigrees for protective, null, and deleterious variants, along with the proportion of the top 100 variants prioritized using only the related members and replicated at α= 0.05/100 using only the unrelated members, and the proportion of variants significant at α= 0.05/1000 in a single-stage QTDT_M test. The "+" and "−" represent variants with positive and negative association with the phenotypes respectively. If higher blood pressure is assumed to have more risk, "+" would correspond to deleterious variants and "−" would correspond to protective variants. In total, there are 6 deleterious variants, 9 protective variants, and 961 noncausal variants being discovered and tested.

ISSN: 1753-6561