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MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS

Figure 3

Genome-wide significant results from standard GWAS approach and MultiPhen tested on combinations of the lipids using NFBC1966 data.

Each bar shows the number of SNPs reaching genome-wide significance for a given phenotype-combination analysis (specified by the first letters of each trait, such that CHL refers to an analysis on the CHOL, HDL and LDL), with the SNPs discovered by both the univariate approach and MultiPhen shown by the white segment of the bar, the SNPs discovered by the univariate approach only shown by the grey segment, and the SNPs discovered by MultiPhen only illustrated by the black segment. The bars labelled ALL2 and ALL3 combine results across analyses on all combinations of two and three lipid traits, respectively, while ALL combines the results across the analyses of all 2, 3 and 4 combinations of the traits. A complete breakdown of these results is presented in Tables S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15.

Figure 3