A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants  Wei Pan, Il-Youp Kwak, Peng Wei  The American Journal of Human Genetics  Volume 97, Issue 1, Pages 86-98 (July 2015) DOI: 10.1016/j.ajhg.2015.05.018 Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 1 Empirical Power for Simulation Set-up B with a Pathway of 20 Genes One gene included one causal SNP. (A and C) Each gene contained 1–20 independent (A) or correlated (C) SNPs. (B) Each gene contained 3–100 independent SNPs. (D) Each gene contained 1–20 correlated SNPs and the causal SNP was excluded in analysis. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 2 Empirical Power for Simulation Set-up C with a Pathway of 20 Genes Five genes each included one causal SNP. (A and C) Each gene contained 1–20 independent (A) or correlated (C) SNPs. (B) Each gene contained 3–100 independent SNPs. (D) Each gene contained 1–20 correlated SNPs and the causal SNP was excluded in analysis. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 3 Empirical Power for Simulation Set-up D with a Pathway of 20 Genes Ten genes each included one to three causal SNPs. (A and C) Each gene contained 1–20 independent (A) or correlated (C) SNPs. (B) Each gene contained 3–100 independent SNPs. (D) Each gene contained 1–20 correlated SNPs and the causal SNP was excluded in analysis. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 4 Empirical Power for Simulation Set-up D′ with a Pathway Containing 20 Genes Ten genes each included one to three causal SNPs. (A and C) Each gene contained 1–20 independent (A) or correlated (C) SNPs. (B) Each gene contained 3–100 independent SNPs. (D) Each gene contained 1–20 correlated SNPs and the causal SNP was excluded in analysis. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 5 Empirical Power for Simulation Set-ups E and F with a Pathway Containing 40 and 80 Genes, Respectively Ten genes each included 1–3 causal SNPs, and each gene contained 1–20 correlated SNPs. Set-up E with a pathway of 40 genes (A) and set-up F with a pathway of 80 genes (B) are shown. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 6 Empirical Power for RVs in Simulation Set-up D2 with a Pathway Containing 20 Genes Ten genes each included one causal RV. Each gene contained 1–20 independent (A) or correlated (B) RVs. The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions

Figure 7 Distributions of the p Values from aSPUpath and GRASS and Their Comparison in the Log10 Scale for the WTCCC CD Data Shown are aSPUpath (A) and GRASS (B) and comparison (C). The American Journal of Human Genetics 2015 97, 86-98DOI: (10.1016/j.ajhg.2015.05.018) Copyright © 2015 The American Society of Human Genetics Terms and Conditions