Extended Data Fig. 3: Complex associations of human genetic variation at the PRB locus with oral microbiome phenotypes.
From: Human and bacterial genetic variation shape oral microbiomes and health
a, Diploid copy number of PRB1 estimated for SPARK participants from WGS read-depth (n = 12,519). b, Associations of genetic variants at the PRB locus with relative abundance of Stomatobaculum SGB5266. The association of PRB1 copy number is highlighted (red point). c, Allelic series of effect sizes of PRB1 diploid copy numbers on relative abundance of Stomatobaculum SGB5266 (in s.d. units, n = 12,517). d, Partial colocalization of associations of genetic variants at the PRB locus with Stomatobaculum SGB5266 relative abundance (-log10(p), x-axis) and oral microbiome composition (-log10(p), y-axis). PRB1 copy number (red point) and a common PRB4 loss-of-function variant (blue point) appear to deviate from a generally concordant pattern of associations, likely reflecting multiple causal effects. e, Effect sizes on Stomatobaculum SGB5266 relative abundance for each additional copy of PRB1 compared to each functional copy of PRB4 (n = 12,519). Error bars, 95% CIs in all panels. P-values were computed using two-sided linear mixed models (b,d).
