Table II.

Estimated power^§ under a range of observed data conditions.

Interleukin 6 (IL-6)			Class-level score test (alternative specifications of ωj)▽
Data generating model*	Gene	n	(1)	(2)	(3)	minP score♯	Change‡
(a) SNPs + time	SLC6A7	150	0.489	0.440	0.105	0.377	0.140
		300	0.771	0.772	0.169	0.690	0.005
	EBF3	150	0.779	0.792	0.292	0.526	0.079
		300	0.984	0.989	0.524	0.923	0.093
(b) SNPs + poly(time, 5)	SLC6A7	150	0.640	0.606	0.175	0.545	0.208
		300	0.913	0.916	0.245	0.869	0.441
	EBF3	150	0.933	0.933	0.447	0.789	0.316
		300	1.000	1.000	0.743	0.995	0.678
(c) SNPs + time + SNPs * time	SLC6A7	150	0.430	0.349	0.115	0.297	0.021
		300	0.721	0.685	0.186	0.586	0.017
	EBF3	150	0.673	0.639	0.213	0.417	0.095
		300	0.970	0.977	0.441	0.843	0.087
C-reactive protein (CRP)			Class-level score test (alternative specifications of ωj)▽
Data generating model*	Gene	n	(1)	(2)	(3)	minP score♯	Change‡
(a) SNPs + time	MREG	150	0.300	0.358	0.146	0.258	0.13
		300	0.741	0.725	0.272	0.681	0.291
	TPRG1	150	0.380	0.386	0.222	0.183	0.105
		300	0.732	0.704	0.386	0.479	0.183
(b) SNPs + poly(time, 3)	MREG	150	0.358	0.335	0.145	0.289	0.191
		300	0.713	0.747	0.259	0.650	0.398
	TPRG1	150	0.379	0.349	0.196	0.188	0.132
		300	0.720	0.680	0.358	0.453	0.278
(c) SNPs + time + SNPs * time	MREG	150	0.958	0.965	0.538	0.872	0.502
		300	1.000	1.000	0.884	0.999	0.863
	TPRG1	150	0.949	0.930	0.442	0.823	0.159
		300	0.999	0.999	0.759	0.996	0.331

^§Power is defined as the proportion of 1000 simulations for which we correctly reject the null hypothesis.

^▽Weights are defined as follows: (1) ω_j = 1/m; (2) ${\omega }_j=\text{Beta}{({\text{MAF}}_j,0.5,0.5)}^2/{\sum }_{k=1}^m\text{Beta}{({\text{MAF}}_k,0.5,0.5)}^2$; and (3) ${\omega }_j=\text{Beta}{({\text{MAF}}_j,1,25)}^2/{\sum }_{k=1}^m\text{Beta}{({\text{MAF}}_k,1,25)}^2$, where m is the number of single nucleotide polymorphisms (SNPs) within the corresponding class.

^*Mixed effects models with person-specific intercept terms are used to generate repeated natural log biomarker response data.

^♯Power for minP score corresponds to the proportion of minimum p-values of SNP-level score tests within the class that are significant after applying a Bonferroni adjustment for the number of SNPs within the class.

^‡Power for the change analysis corresponds to the proportion of significant tests of additive association, after a Bonferroni adjustment for the number of SNPs within the class, based on a linear model of the natural log transformation of the difference in biomarker response between baseline (t = 0) and peak, corresponding to 2 h for interleukin-6 (IL-6) and 24 h for C-reactive protein (CRP).