The command used for association testing with MV-PLINK [7], [23] (https://genepi.qimr.edu.au/staff/manuelF/multivariate/main.html) was: plink.multivariate —noweb —file geno —mqfam —mult-pheno pheno.phen —out output. We applied an additive model. MV-PLINK produces an F-statistic and a p-value per genetic variant analyzed. This p-value of multivariate association was extracted from the output. Note that the canonical correlation analysis (CCA) applied by MV-PLINK is similar to multivariate analysis of variance (MANOVA) as CCA is applied to a single genetic variant at a time.
