Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data

Table 1 Family-wise error rate (FWER) and average power of weighted-sum method I using different permutation procedures

Permutation procedure^a	FWER	Power			Computing time (approximate)^b
	D ₄	D ₁	D ₂	Disease
Normal 10³	0.1600	0.1200	0.0123	0.0069	36 minutes
Normal 10⁶	0.1200	0.1200	0.0085	0.0074	16 days
Standard permutation	0.0650	0.1183	0.0065	0.0069	16 days
Fast permutation	0.0550	0.1172	0.0065	0.0065	4.5 days

Data used here are the 200 data sets from GAW17 with all nonsynonymous SNPs.
^aNormal 10³ is the normal approximation with 1,000 permutations; normal 10⁶ is the normal approximation with 10⁶ permutations; standard permutation is the standard permutation procedure with 10⁶ permutations; and fast permutation is the fast permutation procedure with the maximum number of permutations, 10⁶.
^bAll studies are performed in Matlab on a computer with a CPU of 2.66 GHz and 32 GB memory. The computing time is the total running time for all four phenotypes.

ISSN: 1753-6561