Fig. 3: Comparison of the GWAS results obtained with different approaches with 12 DPs (when applicable).
a Original is considered as the ground truth and is obtained on a centralized cleartext dataset by relying on the PLINK36 software. Panels (c) and (e) are also obtained with PLINK (see “Methods” section and Supplementary Fig. 4). Panels (b) and (d) are the results obtained with FAMHE-GWAS and FAMHE-FastGWAS, respectively. In the original study and in our secure approach, genome-wide signals of association (log10(P) < 5 × 10−7, dotted line) were observed on chromosomes 6 and 3. The P values shown are nominal values without multiple testing correction and are obtained using standard two-sided t tests for testing whether the linear regression coefficient associated with a variant is nonzero.
