Genetics of Pigmentation Diversity Jun 20, 2017 20:08:27 GMT
Post by Admin on Jun 20, 2017 20:08:27 GMT
(a) A regression tree with two nodes based on HERC2 haplotypes and country (or region) of origin of each individual (ARM, Armenia; AZR, Azerbaijan; CRM, Crimea (peninsula of Ukraine); GEO, Georgia; KAZ, Kazakhstan; TJK, Tajikistan; UZB, Uzbekistan), most striking is the major node where we have the higher percentage of blue eyes (50.6%) in individuals carrying H1/H1. In the first node, the origin of population of the individuals carrying H1/H1 is not reported because the P-value is not significant. (b) Tree obtained from model-based recursive partitioning; East refers to populations from ESR, and West refers to those from WSR.
Given the brown versus not-brown eye trait, we performed the algorithm for model-based recursive partitioning (Figure 1b). Interestingly, a person belonging to WSR and carrying H1/H1 genotype has a higher probability of having blue or green/grey eye (94%) as compared with a person from ESR (72%).
In the attempt to combine the roles of OCA2 and HERC2 genes, we used MDR method5 (Figure 2), by using the two analysed haplotypes and rs7495174 SNP position. Our MDR analysis shows a synergistic interaction between them; the prediction accuracy of the tested model is 86.62%, with a sensitivity of 98.02%. The presence of HERC2 H1/H1 plus the A/A OCA2 genotype remarkably predicts blue eyes (ratio brown/not brown: 0.1324), whereas the presence of H2 compared with every alleles of OCA2 SNP is enough to predict brown eye (Figure 2).
MDR analysis. Representation of haplotype–SNP combinations among attributes considered in interaction model for brown versus not brown; the dark grey cells represent the genotype combinations associated with ‘high risk’ of having a specific eye colour, light grey cells are associated with ‘low risk’, and white cells mean lack of data. Each cell is a representation of the number of individuals with brown eyes (left bar) and not brown eyes (right bar).