Unexpected Relationships and Inbreeding in HapMap Phase III Populations
Figure 1
IBD estimates of previously annotated and novel relatedness in phase III HapMap.
Each circle represents a pair of individuals with estimated Cotterman coefficients of relatedness K0, K1, and K2 (percent of the genome shared IBD0, IBD1, and IBD2). (A) Previously annotated relationships given by the International HapMap Consortium [2], Pemberton et al. [19], and Kyriazopoulou-Panagiotopoulou et al. [20] were plotted by group (x-axis) and K1 values (y-axis) and labeled by their degree of relationship. Arrow 1 corresponds to identical samples NA21737/NA21344. (B) Unexpected K2 values (y-axis) in previously annotated parent-child and second-degree relatedness for each group (x-axis). Only K2 values greater than 0.001 are shown. Arrow 2 corresponds to NA21362/NA21438. (C) Estimated IBD0 (y-axis) in previously annotated parent-child relationships for each group (x-axis). Only K0 values greater than 0.001 are shown. Arrows 3–5 highlight NA12874/NA12865, NA12889/NA12877, and NA10863/NA12234, respectively. Only K2 values greater than 0.001 are shown. (D) Novel relatedness between pairs of individuals separated by group (x-axis) and estimated K1 (y-axis). Only K1 values greater than 0.025 are shown. (E) Novel relatedness between pairs of individuals previously identified in Panel B for MKK and MXL (x-axis) with unexpected K2 (y-axis). (F) Inferred degrees of relationship (including those unable to be called; x-axis) plotted as a function of K1. All 2260 pairwise comparisons inferred to be related from any study (including this one) are shown, excluding identical samples. Note the overlap between percent of genome shared IBD1 and degree of relationship. Abbreviation: NC, no relationship called; r value, relatedness value.