Additional file 2 of A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies
Creators: name: Shao, Zhonghe
name: Wang, Ting
name: Qiao, Jiahao
name: Zhang, Yuchen
name: Huang, Shuiping
name: Zeng, Ping
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2. Figure S1. Estimated power for the seven SNP-set methods under the polygenic case (A) and the mixed case (B) with a significance level α of 10−5. Here, PVE = 0.3%, 0.5% or 1% at the right side, the number of causal SNPs (prop) = 0.05, 0.20 or 0.50 or the distribution of effect size including double, normal and t on the top, the number of the total analyzed SNPs = 50, 200 or 500 on the x-axis. The power was estimated across 103 replications. Figure S2. Rank of power for the seven SNP-set methods under the sparse case (A), the polygenic case (B), and the mixed case (C) with a significance level α of 10−5. The number in each cell represents − log(P). normal: SNP effect sizes followed a standard normal distribution; double: SNP effect sizes followed a standard double exponential distribution; t: SNP effect sizes followed a standard t-distribution. Figure S3. Estimated power for the seven SNP-set methods in the case of rare variant association study under the polygenic case (A) and the mixed case (B) with a significance level α of 10−5. Here, PVE = 0.3%, 0.5% or 1% at the right side, the number of causal SNPs (prop) = 0.05, 0.20 or 0.50 or the distribution of effect size including double, normal and t on the top, the number of the total analyzed SNPs = 50, 200 or 500 on the x-axis. The power was estimated across 103 replications. Figure S4. Upset plot to illustrate the number of identified genes shared across seven SNP-set methods for six psychiatric disorders. Figure S5. A Enrichment of differentially expressed pleiotropic genes associated with the six psychiatric disorders in terms of expression level across the 54 GTEx tissues. P values are shown in the y-axis with a scale of − log10. The bar in red represents significant enrichment after Bonferroni’s adjustment for multiple hypothesis tests; B Top 10 significant types of pathways in terms of the GO and KEGG enrichment analyses. BP Biological process, CC Cellular component, MF Molecular function. Figure S6. Bar plot of 531 unique genes associated with the six psychiatric disorders. The red color in the heatmap represents the rank of P values of SKAT and HMP; prop: the proportion of significant cis-SNPs (P &lt; 5 × 10−8) within each associated gene. Figure S7. A Enrichment of differentially expressed pleiotropic genes related to the four plasma lipid traits in terms of expression level across the 54 GTEx tissues. P values are shown in the y-axis with a scale of − log10. The bar in red represents significant enrichment after Bonferroni’s adjustment for multiple hypothesis tests; B Top 10 significant types of pathways in terms of the GO and KEGG enrichment analyses. BP Biological process, CC Cellular component, MF Molecular function. Figure S8. A Enrichment of differentially expressed pleiotropic genes associated with the nine immune-related diseases in terms of expression level across the 54 GTEx tissues. P values are shown in the y-axis with a scale of − log10. The bar in red represents significant enrichment after Bonferroni’s adjustment for multiple hypothesis tests; B Top 10 significant types of pathways in terms of the GO and KEGG enrichment analyses. BP Biological process, CC Cellular component, MF Molecular function. Table S1. Summary information of the six psychiatric disorders, four plasma lipid traits and nine immune-related diseases. Table S2. Ratio between the empirical type I error and the given significance level estimated over 105 simulations under rare variants. Table S3. Estimated power over 103 simulations with common variants. Table S4. Total running time of 103 simulations for the seven SNP-set methods under various simulation settings. Table S5. Identified genes associated with the six psychiatric disorders. Table S6. Identified genes associated with the four plasma lipid traits. Table S7. Identified genes associated with the nine immune-related diseases.