A multistep approach to single nucleotide polymorphism–set analysis: an evaluation of power and type I error of gene-based tests of association after pathway-based association tests

Table 2 Comparison of power for genes showing at least a 10 percentage point increase in power for multistep pathway analysis

Gene name	Pathway description		Single-step power		Multi-step power
Gene name	Number of genes	Percent Causal	VC_test	Burden _test	Burden _test-Burdentest	Burden _test-VC_test	VC_test-VC_test	VC_test-Burden _test
EPS8L1	5	60 %	0.010	0.170	0.560	0.015	0.010	0.005
FLNB	5	60 %	0.000	0.140	0.480	0.035	0.035	0.040
COL5A3	10	60 %	0.000	0.095	0.405	0.050	0.020	0.005
CASP5	10	60 %	0.090	0.000	0.000	0.000	0.255	0.000
SNAPC3	10	60 %	0.005	0.000	0.000	0.000	0.130	0.005
C21orf33	10	60 %	0.025	0.010	0.105	0.135	0.010	0.000
TNN	5	100 %	0.035	0.010	0.055	0.140	0.085	0.005

Power for genes, as well as characteristics of the pathway they are contained in. Bolded entries represent the largest power achieved by each of the methods (single-step and multistep). In each of these scenarios, the multistep approach offers anywhere from a 10 to 40 % increase in power over the conventional single-step approaches

ISSN: 1753-6561