Extended Data Fig. 3: Quality control analyses for the GWAS of LF clinical outcome. | Nature Microbiology

Extended Data Fig. 3: Quality control analyses for the GWAS of LF clinical outcome.

From: Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Extended Data Fig. 3

(A) Principal component analysis (PCA) of the NG and SL cohorts, colored by clinical outcome. PCs were computed on unrelated individuals, and then all individuals were projected onto those components. (B) Quantile-quantile plots of -log10 P-values from the outcome GWAS against expected quantiles. (C) Comparison of the outcome GWAS lead variants with and without inclusion of age as a covariate. P-values in B and C are based on saddlepoint-approximated score tests (SAIGE), while meta-analysis P-values are derived from meta-analysis (METAL) of P-values generated from each cohort. Odds ratios are computed from Firth logistic regression.

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