Figure 3.
Genotype-phenotype association for G/C-14010, T/G-13915 and C/G-13907. (a-d) Number of individuals in various genotype and phenotype classes in major geographic regions and/or populations in which they are most prevalent. We observed a significant association for G/C-14010 in Kenya (n = 190, d.f. = 4, χ2 = 21.77, P = 0.0002) and in Tanzania (n = 231, d.f. = 4, χ2 = 21.90, P = 0.0002) We did not observe a significant association for C/G-13907 in the Afro-Asiatic Sudanese (n = 17, d.f. = 2, χ2 = 2.54, P = 0.2808) or for T/G-13915 in Afro-Asiatic Kenyans (n = 61, d.f. = 4, χ2 = 6.14, P = 0.1889). A large proportion of individuals who are homozygous for the ancestral G-14010, T-13915 and C-13907 alleles are classified as lactase persistent, indicating that there are additional unidentified variants associated with lactase persistence in these populations. (e) Linear regression-based test of association for each polymorphic SNP genotyped in this study in each of the subpopulations. Dashed line denotes significance after a conservative Bonferroni correction for the total number of SNPs tested. G/C-14010 is the most significant of all 123 genotyped SNPs in the Kenyan Nilo-Saharan (KE-NS) and Tanzanian Afro-Asiatic (TZ-AA) samples. C/G-13907 shows the strongest (though not significant) association of all other genotyped SNPs in the Kenyan Afro-Asiatic (KE-AA) samples. (f) Meta-analysis of the combined P values for each SNP over all subpopulations. G/C-14010 is highly significant, even after Bonferroni correction (P = 2.9 × 10−7). C/G-13907 and T/G-13915 are not significant after Bonferroni correction (P = 0.001 and P = 0.002, respectively). SD-AA, Sudanese Afro-Asiatic; SD-NS, Sudanese Nilo-Saharan; TZ-NS, Tanzanian Nilo-Saharan; TZ-NK, Tanzanian Niger-Kordofanian; TZ-HZ, Tanzanian Hadza; TZ-SW, Tanzanian Sandawe.