Evolutionary Analysis of Classical <em>HLA</em> Class I and II Genes Suggests That Recent Positive Selection Acted on <em>DPB1*04∶01</em> in Japanese Population

<div><p>The human leukocyte antigen (<em>HLA</em>) genes exhibit the highest degree of polymorphism in the human genome. This high degree of variation at classical <em>HLA</em> class I and class II loci has been maintained by balancing selection for a long evolutionary time. However, little is known about recent positive selection acting on specific <em>HLA</em> alleles in a local population. To detect the signature of recent positive selection, we genotyped six <em>HLA</em> loci, <em>HLA-A</em>, <em>HLA-B</em>, <em>HLA-C</em>, <em>HLA-DRB1</em>, <em>HLA-DQB1</em>, and <em>HLA-DPB1</em> in 418 Japanese subjects, and then assessed the haplotype homozygosity (<em>HH</em>) of each <em>HLA</em> allele. There were 120 <em>HLA</em> alleles across the six loci. Among the 80 <em>HLA</em> alleles with frequencies of more than 1%, <em>DPB1*04∶01</em>, which had a frequency of 6.1%, showed exceptionally high <em>HH</em> (0.53). This finding raises the possibility that recent positive selection has acted on <em>DPB1*04∶01</em>. The <em>DPB1*04∶01</em> allele, which was present in the most common 6-locus <em>HLA</em> haplotype (4.4%), <em>A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01</em>, seems to have flowed from the Korean peninsula to the Japanese archipelago in the Yayoi period. A stochastic simulation approach indicated that the strong linkage disequilibrium between <em>DQB1*06∶04</em> and <em>DPB1*04∶01</em> observed in Japanese cannot be explained without positive selection favoring <em>DPB1*04∶01</em>. The selection coefficient of <em>DPB1*04∶01</em> was estimated as 0.041 (95% credible interval 0.021–0.077). Our results suggest that <em>DPB1*04∶01</em> has recently undergone strong positive selection in Japanese population.</p> </div

Schematic representation of the DigiTag2 assay.

<p>The assay has four steps: target preparation, encoding, labeling and detection. SNP genotypes are encoded into well-designed oligonucleotides, designated DNA coded numbers (DCNs: D1_i, ED-1 and ED-2). D1_i is a variable sequence assigned to each SNP. Reverse complement sequences are written by attaching the character ‘c’ before the sequence name.</p

Frequencies of <i>HLA</i> class II alleles.

a<p>Heterozygosity.</p>b<p>Hardy-Weinberg equilibrium test.</p>c<p>Ewens-Watterson test.</p

Haplotype homozygosity (<i>HH</i>) × allele frequency (AF) of each <i>HLA</i> allele.

<p>The left and right panels show <i>HH</i> values of <i>HLA</i> class I alleles and <i>HLA</i> class II alleles, respectively. The class I alleles were designated as follows: <i>HLA-A</i> (red diamond), <i>HLA-C</i> (yellow square), and <i>HLA-B</i> (green triangle); the class II alleles were designated as follows: <i>HLA</i>-<i>DRB1</i> (blue diamond), <i>HLA-DQB1</i> (purple square), and <i>HLA-DPB1</i> (pink triangle). In both panels, only <i>HH</i> values of alleles with frequencies of more than 0.01 are shown.</p

Individual heterozygosity of each subject with the most common 6-locus <i>HLA</i> haplotype.

<p>The individual heterozygosity in the genomic region on the short arm of chromosome 6 was assessed using the sliding window analysis; in this analysis, the window and step sizes were set to be 1 Mb and 200 kb, respectively. The individual heterozygosity was defined as a proportion of heterozygous SNPs to SNPs genotyped in a single subject. This analysis was performed for five Japanese subjects with the <i>A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01</i> haplotype: (A) three of these five subjects were homozygous for this haplotype (blue, red, and green) and (B) two subjects had the heterozygous genotypes of the <i>A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01</i> haplotype and the <i>A*24∶02-C*07∶02-B*07∶02-DRB1*01∶01–DQB1*05∶01-DPB1*04∶02</i> haplotype (orange) and of the <i>A*33∶03-C*14∶03-B*44∶03-DRB1*13∶02-DQB1*06∶04-DPB1*04∶01</i> haplotype and the <i>A*24∶02-C*12∶02-B*52∶01-DRB1*15∶02-DQB1*06∶01-DPB1*09∶01</i> haplotype (purple).</p

Frequencies of <i>HLA</i> class I alleles.

a<p>Heterozygosity.</p>b<p>Hardy-Weinberg equilibrium test.</p>c<p>Ewens-Watterson test.</p

Estimation of model parameters for positive selection acting on <i>DPB1*04∶01</i>.

<p>The recombination rate (<i>c</i>), initial haplotype frequency (<i>f</i>₁(0)), and selection coefficient (<i>s</i>), were estimated by comparing the four haplotype frequencies observed in our study population with the respective values predicted via simulation. (A) Posterior distributions of the three parameters that produced simulated data that resemble the observed data. (B) Frequency distribution of <i>s</i> accepted in simulation runs. The mean and 95% credible interval of <i>s</i> are 0.041 and 0.021−0.077.</p

Electropherogram of singleplex PCR products with 192 pairs of locus-specific primers.

<p>The designed amplicon size is depicted below each lane.</p

Pairwise estimates of LD parameters, |<i>D</i>’| (upper diagonal) and <i>r</i>² (lower diagonal) for every pair of <i>HLA</i> alleles.

<p>The name of each allele is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046806#pone.0046806.s001" target="_blank">Data S1</a>.</p

Extended <i>HH</i> (<i>EHH</i>) × relative locus position for12 <i>HLA-DPB1</i> alleles.

<p>Extended <i>HH</i> (<i>EHH</i>) × relative locus position for12 <i>HLA-DPB1</i> alleles.</p