Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Fig 3
Improvement in imputation performance subsequent to the addition of add-on tags.
Mean INFO score and r2 (between imputed and sequenced ground truth) of target variants designed to be tagged by add-on tags based on three array designs: 1) H3Africa array without any add-on tags 2) The H3Africa array with random add-on tags 3) The H3Africa array with population-specific add-on tags selected based on the proposed approach. Facet grids illustrate results based on two tag SNP selection settings: coverage-guaranteeing within prioritized regions (Setting 1) and efficiency-driven in all other regions (Setting 2). Error bars represent standard error (SE) of the mean imputation quality within each MAF bin.