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Figure 3 | Journal of Translational Medicine

Figure 3

From: Congruence as a measurement of extended haplotype structure across the genome

Figure 3

Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype. A: Percent congruence of 132 extended DQ-DR-B-A haplotype groups from HLA-DRB1 to HLA-A. Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A. The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file 4: Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B: Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one SNP. Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A, seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity

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