HLA-DPB1 allelic frequency of the Pumi ethnic group in south-west China and evolutionary relationship of Pumi with other populations

Population Genetic Dissection of HLA-DPB1 Amino Acid Polymorphism to Infer Selection

Although allele frequency data for most HLA loci provide strong evidence for balancing selection at the allele level, the DPB1 locus is a notable exception, with allele frequencies compatible with neutral evolution (genetic drift) or directional selection in most populations. This discrepancy is especially interesting as evidence for balancing selection has been seen at the nucleotide and amino acid (AA) sequence levels for DPB1. We describe methods used to examine the global distribution of DPB1 alleles and their constituent AA sequences. These methods allow investigation of the influence of natural selection in shaping DPβ diversity in a hierarchical fashion for DPB1 alleles, all polymorphic DPB1 exon 2-encoded AA positions, as well as all pairs and trios of these AA positions. In addition, we describe how asymmetric linkage disequilibrium for all DPB1 exon 2-encoded AA pairs can be used to complement other methods. Application of these methods provides strong evidence for the operation of balancing selection on AA positions 56, 85-87, 36, 55 and 84 (listed in decreasing order of the strength of selection), but no evidence for balancing selection on DPB1 alleles.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

Sequencing-based analysis of the HLA-DPB1 polymorphism in Nu ethnic group of south-west China

In the present study, DNA typing for HLA-DPB1 was performed using polymerase chain reaction-sequencing-based typing method in 72 randomly selected Nu ethnic individuals inhabiting the Yunnan province of south-west China. Among the 12 detected DPB1 alleles, the most frequent was DPB1*1301, with the percentage of 20.83%, followed by DPB1*0501 (19.44%), DPB1*040101 (16.67%) and DPB1*2801 (9.72%). The allele DPB1*1501 was found for the first time in the Chinese population. Neighbour-joining showed that the Nu ethnic minority belonged to East Asian cluster and was most closely related to Lisu, being consistent with the historical records. In addition, the results obtained in this study will also provide useful information on organ transplantation, forensic investigations and disease association studies.

The distribution of HLA alleles revealed a founder effect in the geographically isolated Chinese population, Drung

The Drung ethnic minority is one of the smallest ethnic groups of China, geographically isolated by mountains and rivers. Before 1949, Drung society maintained many vestiges of the primitive commune system. The origin and migration of the Drung and their genetic background are still unknown because of limited records about this population. Here, we for the first time demonstrated the unique distribution of HLA alleles in the Drung by high-resolution sequence-based typing (SBT) method. Number of alleles detected is obviously less than expected and only a few alleles with a high homozygosity in each locus are predominant in this minority. The characteristics of HLA allele distribution in the Drung could reflect founder effects, suggesting the Drung probably descended from very few ancestors. The statistical analysis based on allele frequencies indicated that the Drung was an isolated ethnic group, but it also provided the clue that the Drung was genetically related to Chinese southwestern ethnic groups. Significant reduced allelic diversity and genetic isolate in the Drung make it an ideal homogeneous population and very useful model to study the evolution of HLA and the origin and migration of Chinese ethnic groups. The research paved a way to elucidate the genetic background of this mysterious minority and disease predisposition.

Polymorphism of the DPB1 locus in Hani ethnic group of south-western China

Polymorphism of HLA-DPB1 was revealed with a sequencing-based typing (SBT) method in 47 unrelated healthy individuals from Yunnan Hani ethnic minority. The alleles DPB1*5901 and DPB1*7001 were detected for the first time in Chinese populations. A dendrogram showed that the Hani ethnic group belongs to the southern group of Chinese.

Polymorphism of human leukocyte antigen-DRB1, -DQB1, and -DPB1 genes of Shandong Han population in China

In the present study, polymerase chain reaction-sequence-based typing (PCR-SBT) was used to analyze human leukocyte antigen (HLA)-DRB1, -DQB1, and -DPB1 alleles of 98 unrelated healthy Shandong Han individuals. A total of 60 alleles, in which 28 in DRB1, 15 in DQB1 and 17 in DPB1 were found. Among the 28 detected DRB1 alleles, DRB1*150101, DRB1*070101, DRB1*090102, DRB1*120201, and DRB1*080302 were commonly observed, with frequencies of 16.3%, 11.2%, 10.2%, 8.2%, and 5.6%, respectively. The most predominant DQB1 allele was DQB1*030101/0309 with the frequency of 20.4%, followed by DQB1*0201/0202 (14.8%), DQB1*0602 (14.3%), DQB1*030302 (12.2%), and DQB1*060101/060103 (10.7%). Of the 17 detected DPB1 alleles, DPB1*0501 was the most frequent allele with the frequency of 37.2%. DPB1*020102 (18.4%), DPB1*040101 (11.2%), DPB1*0402 (7.1%), and DPB1*1701 (6.6%) were also very frequent alleles. A total of 53 estimated DRB1-DQB1 two-locus haplotypes were observed in Shandong Han population, of which DRB1*150101-DQB1*0602 was the most predominant, followed by DRB1*090102-DQB1*030302, DRB1*070101-DQB1*0201/0202 DRB1*120201-DQB1*030101/0309, and DRB1*080302- DQB1*060101/060103. The distribution of the HLA class II alleles and haplotypes frequencies as well as the dendrogram showed that the Shandong Han population belongs to the northern group of Chinese. The data have implications for anthropological studies and disease associations.

HLA-DPB1 allelic frequency of the Lisu ethnic group in the Southwest China and evolutionary relationship of Lisu with other populations

A sequencing-based typing of human leukocyte antigen-DPB1 (HLA-DPB1) gene was carried out in 37 unrelated healthy individuals from the Yunnan Lisu ethnic minority. A total of 12 DPB1 alleles, in which DPB1*1301 (33.3%), DPB1*0402 (16.6%), DPB1*040101 (13.8%), and DPB1*0501 (11.1%) were highly predominant, were found, and allele DPB1*200102 was found for the first time in a Chinese population. A dendrogram constructed by neighbor-joining method showed that the Lisu ethnic group belongs to East Asian cluster.

HLA-DPA1 promoter haplotypes are differently distributed in southern Chinese ethnic groups

DPA1 gene is one of the human leukocyte antigen (HLA) class II genes and its promoter is highly polymorphic. From comparative studies among five southern Chinese populations, Jing, Li, Bai, Lahu, and Meizhou Han, we describe their single-nucleotide polymorphism (SNP)/haplotype frequency data of HLA-DPA1 gene promoter in this study. Within the 760-bp promoter region, we have identified 21 SNPs and nine possible haplotypes. Pair-wise comparisons show similar frequencies distribution of the HLA-DPA1 promoter haplotypes among Jing, Li, and Bai, whereas all pair-wise comparisons involved with Lahu or Meizhou Han and other ethnic groups show remarkable difference. The differences in frequencies of HLA-DPA1 promoter alleles may reveal different ethnic origins and demographic histories of the five populations. Our study may help distinguishing each of these populations by sequence variations of HLA-DPA1 promoter, which may be served as functional molecular markers for clinical and immunological studies involving the DPA1 locus.

HLA-DRB1, DQB1 and DPB1 polymorphism in the Naxi ethnic group of South-western China

Polymorphism of HLA-DRB1, DQB1 and DPB1 was revealed with a sequencing-based typing (SBT) method in unrelated healthy volunteers from the Naxi ethnic group. Among the 43 DRB1 alleles detected, the most common allele was DRB1*12021 with a frequency of 17%, followed by DRB1*08032, DRB1*09012 and DRB1*1404 with frequencies of 8.5%, 7.4% and 7.4%, respectively. Among 23 DQB1 alleles detected, the most frequent DQB1 allele was DQB1*03011/0309 (21.9%), followed by DQB1*0502 (16.4%) and DQB1*05031 (9.6%). For the DPB1 locus, the most common alleles were DPB1*0501 (25.5%), DPB1*0402 (14.6%) and DPB1*02012 (12.0%). The most common DRB1-DQB1-DPB1 haplotype was DRB1*1404-DQB1*05031-DPB1*0402 with a frequency of 5.26%, followed by the DRB1*08032-DQB1*06011-DPB1*1301 (3.51%). The distribution characteristics of the HLA class II alleles revealed that the Naxi ethnic group belonged to the Southern group of Chinese.