L-GATOR: Genetic Association Testing for a Longitudinally Measured Quantitative Trait in Samples with Related Individuals Xiaowei Wu, Mary Sara McPeek

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L-GATOR: Genetic Association Testing for a Longitudinally Measured Quantitative Trait in Samples with Related Individuals Xiaowei Wu, Mary Sara McPeek The American Journal of Human Genetics Volume 102, Issue 4, Pages 574-591 (April 2018) DOI: 10.1016/j.ajhg.2018.02.016 Copyright © 2018 American Society of Human Genetics Terms and Conditions

Figure 1 Q-Q Plots of PMALT and L-GATOR p Values for the FHS SBP Data before the Removal of Cohort 1 Genotypes Q-Q plots of genome-wide p values for association with SBP in the FHS data before the removal of genotypes for cohort 1 are shown. The p values were computed by the PMALT method (A) or the L-GATOR method (B). In each panel, p values for 369,046 genome-wide SNPs are plotted on the negative log10 scale. The American Journal of Human Genetics 2018 102, 574-591DOI: (10.1016/j.ajhg.2018.02.016) Copyright © 2018 American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots for L-GATOR p Values versus PMALT p Values from the FHS SBP Data before and after the Removal of Cohort 1 Genotypes The L-GATOR p value of each SNP in the FHS SBP data is plotted against its PMALT p value, where both p values are on the negative log10 scale. Shown are the results before (A) and after (B) removal of the genotypes for cohort 1. In each case, the red line represents perfect concordance between the PMALT and L-GATOR p values (ratio of 1 between them), whereas the blue lines represent a 10-fold difference between the PMALT and L-GATOR p values (ratio of 10:1 or 1:10). Shown in green are the SNPs with extremely significant (p value <10−10) differences in allele frequency between cohort 1 and the other cohorts. The American Journal of Human Genetics 2018 102, 574-591DOI: (10.1016/j.ajhg.2018.02.016) Copyright © 2018 American Society of Human Genetics Terms and Conditions

Figure 3 Q-Q Plots of PMALT and L-GATOR p Values for the FHS SBP Data after Removal of Cohort 1 Genotypes Q-Q plots of genome-wide p values for association with SBP in the FHS data after removal of genotypes for cohort 1 are shown. The p values were computed by the PMALT method (A) or the L-GATOR method (B). In each panel, p values for 369,046 genome-wide SNPs are plotted on the negative log10 scale. The American Journal of Human Genetics 2018 102, 574-591DOI: (10.1016/j.ajhg.2018.02.016) Copyright © 2018 American Society of Human Genetics Terms and Conditions