Fig. 3: HLA associations with vaccine responses fine-mapped to HLA variants.
Forest plots of beta effect estimates from linear mixed-model association tests (center points) for fine-mapped variants for each trait colored by population (Uganda, red; South Africa, green; Burkina Faso, blue) with 95% confidence intervals (bars), followed by corresponding distributions for the pooled linear mixed-model (‘pooled’, solid black horizontal line) and fixed-effects meta-analyses including all cohorts (‘fixed meta’). Variants were identified to be independently associated with each trait using combined manual and automated regression approaches. Dashed vertical black lines represent no effect (beta = 0), and solid vertical red lines cross the beta estimate of the ‘pooled’ model as a reference. The originating locus of association is represented by solid arrowed lines colored by trait indicating the relevant region of association on chromosome 6. Associations demonstrating significant evidence (PQ ≤ 1 × 10−3) of heterogeneity using Cochran’s Q test are highlighted with a red asterisk. No adjustments were made for multiple testing. Exact P values for the association tests are provided in Supplementary Table 12. PRN was not administered to South African infants; hence, there are no measured effects for this population. Data from 1,320 Ugandan individuals, 716 individuals from South Africa and 309 individuals from Burkina Faso, restricted by relatedness were included in the analysis.
