HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China

Abstract

In this study, polymerase chain reaction-sequence-specific oligonucleotide prode (SSOP) typing results for the human leukocyte antigen (HLA) class I (A, B, and C) and class II (DRB1, DQA1, DQB1, and DPB1) loci in 264 individuals of the Han ethnic group from the Canton region of southern China are presented. The data are examined at the allele, genotype, and haplotype level. Common alleles at each of the loci are in keeping with those observed in similar populations, while the high-resolution typing methods used give additional details about allele frequency distributions not shown in previous studies. Twenty distinct alleles are seen at HLA-A in this population. The locus is dominated by the A*1101 allele, which is found here at a frequency of 0.266. The next three most common alleles, A*2402, A*3303, and A*0203, are each seen at frequencies of greater than 10%, and together, these four alleles account for roughly two-thirds of the total for HLA-A in this population. Fifty alleles are observed for HLA-B, 21 of which are singleton copies. The most common HLA-B alleles are B*4001 (f= 0.144), B*4601 (f= 0.119), B*5801 (f= 0.089), B*1301 (f= 0.068), B*1502 (f= 0.073), and B*3802 (f= 0.070). At the HLA-C locus, there are a total of 20 alleles. Four alleles (Cw*0702, Cw*0102, Cw*0801, and Cw*0304) are found at frequencies of greater than 10%, and together, these alleles comprise over 60% of the total. Overall, the class II loci are somewhat less diverse than class I. Twenty-eight distinct alleles are seen at DRB1, and the most common three, DRB1*0901, *1202, and *1501, are each seen at frequencies of greater than 10%. The DR4 lineage also shows extensive expansion in this population, with seven subtypes, representing one quarter of the diversity at this locus. Eight alleles are observed at DQA1; DQA1*0301 and 0102 are the most common alleles, with frequencies over 20%. The DQB1 locus is dominated by four alleles of the 03 lineage, which make up nearly half of the total. The two most common DQB1 alleles in this population are DQB1*0301 (f= 0.242) and DQB1*0303 (f= 0.15). Eighteen alleles are observed at DPB1; DPB1*0501 is the most common allele, with a frequency of 37%. The class I allele frequency distributions, expressed in terms of Watterson's (homozygosity) F-statistic, are all within expectations under neutrality, while there is evidence for balancing selection at DRB1, DQA1, and DQB1. Departures from Hardy-Weinberg expectations are observed for HLA-C and DRB1 in this population. Strong individual haplotypic associations are seen for all pairs of loci, and many of these occur at frequencies greater than 5%. In the class I region, several examples of HLA-B and -C loci in complete or near complete linkage disequilibrium (LD) are present, and the two most common, B*4601-Cw*0102 and B*5801-Cw*0302 account for more than 20% of the B-C haplotypes. Similarly, at class II, nearly all of the most common DR-DQ haplotypes are in nearly complete LD. The most common DRB1-DQB1 haplotypes are DRB1*0901-DQB1*0303 (f= 0.144) and DR...

The Immunodominant Influenza A Virus M158–66Cytotoxic T Lymphocyte Epitope Exhibits Degenerate Class I Major Histocompatibility Complex Restriction in Humans

“…The allele frequency of HLA-C*08:01 is high among Asian populations and very low in other parts of the world. Among Singapore Chinese and Han Chinese populations, the allele frequencies are 8.6% and 13.3%, respectively (33,34), as opposed to 0.09% in Caucasians (35). In contrast, the prevalence of HLA-A*02:01 is relatively high globally; it is found in 9% to 19% of Chinese individuals and 27% to 29% of Caucasians.…”

“…In contrast, the prevalence of HLA-A*02:01 is relatively high globally; it is found in 9% to 19% of Chinese individuals and 27% to 29% of Caucasians. Micropolymorphisms of HLA-A2, such as HLA-A*02:03, -A*02:06, -A*02: 07, and -A*02:11, are more commonplace among Asians (33)(34)(35). In this study, we observed that GILGFVFTL-specific responses were present in all the HLA-A*02-positive individuals recruited and that as many as 93% and 88% of the GILGFVFTL-HLA-A*02 tetramer-positive CTLs could express CD107a and IFN-␥, respectively.…”

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

“…The EW homozygosity test of neutrality has proven to be a useful tool for detecting selection at HLA loci [3,7,209,218,219,[222][223][224][225][226][227][228][229][230][231], making it an appropriate method for these metaanalyses. This meta analysis reveals an extremely strong signal of balancing selection at DQA1, HLA-C, and DQB1.…”

In silicodesign of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

“…1A). 31,32 In this paper, we report the optimized design of a multi-epitope vaccine that takes into account all of these issues. Several elements were considered for our multiple-epitope vaccine design: epitope selection, epitope location, and linkers between epitopes.…”