Table 2 The minimum dissimilarity between major haplotypes in each of the six HLA genes (loci).

From: Mapping the genetic diversity of HLA haplotypes in the Japanese populations

Haplotype

HLA-A (n = 39)

HLA-B (n = 74)

HLA-C (n = 67)

HLA-DR (n = 61)

HLA-DQ (n = 70)

HLA-DP (n = 87)

H1

28.21

29.73

16.42

32.79

34.29

16.09

H2

2.56

2.70

17.91

32.79

21.43

11.49

H3

2.56

28.38

25.37

34.43

21.43

44.83

H4

28.21

32.43

28.36

32.79

24.29

25.29

H5

2.56

29.73

16.42

27.87

18.57

16.09

H6

28.21

2.70

17.91

27.87

8.57

11.49

H7

2.56

37.83

25.37

–

24.29

14.94

H8

35.90

18.92

–

–

24.29

–

H9

30.77

–

–

–

8.57

–

H10

–

–

–

–

18.57

–

H11

–

–

–

–

15.71

–

  1. Dissimilarity is defined as the percentage of SNP sites where two major haplotypes found at each locus exhibited different alleles (of the SNP sites). The minimum dissimilarity for each major haplotype is then defined as the least dissimilarity observed against all other major haplotypes, thus measuring the degree of dissimilarity between the two most similar major haplotypes. A number of haplotypes were selected at each locus as follows: the haplotype frequency ≥10% for HLA-A, -B, -C and –DR; ≥6% for HLA-DQ and –DP in any of the study populations. The number of SNPs that were assayed commonly across the 12 study populations is shown in the parenthesis at each HLA locus. For example, at HLA-A locus, the H1 haplotype shows substantial differences in alleles at ≥11 of 39 commonly-assayed SNPs ( ≥28.21%) against the other haplotypes, i.e., H2-H9 at HLA-A; H9, which is found in both Chinese and Indians but not in Japanese (see Fig. 5), is assumed to be relatively dissimilar to the other haplotypes, H1-H8, as its minimum dissimilarity is 30.77% (12 of 39SNPs).
Back to article page