HLA-B40, B18, B27, and B37 allele discrimination using group-specific amplification and SSCP method

HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of 10 918 Koreans from bone marrow donor registry in Korea

The human leucocyte antigen (HLA) system is the most polymorphic genetic system in humans, and HLA matching is crucial in organ transplantation, especially in hematopoietic stem cell transplantation. We investigated HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies at allelic level in 10 918 Koreans from bone marrow donor registry in Korea. Intermediate resolution HLA typing was performed using Luminex technology (Wakunaga, Japan), and additional allelic level typing was performed using PCR-single-strand conformation polymorphism method and/or sequence-based typing (Abbott Molecular, USA). Allele and haplotype frequencies were calculated by direct counting and maximum likelihood methods, respectively. A total of 39 HLA-A, 66 HLA-B and 47 HLA-DRB1 alleles were identified. High-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, *02:06, *11:01, *24:02, *31:01 and *33:03), 6 HLA-B (B*15:01, *35:01, *44:03, *51:01, 54:01 and *58:01) and 8 HLA-DRB1 (DRB1*01:01, *04:05, *04:06, *07:01, *08:03, *09:01, *13:02 and *15:01) alleles. At each locus, A*02, B*15 and DRB1*14 generic groups were most diverse at allelic level, consisting of 9, 12 and 11 different alleles, respectively. A total of 366, 197 and 21 different HLA-A-B-DRB1 haplotypes were estimated with frequencies of ≥0.05%, ≥0.1% and ≥0.5%, respectively. The five most common haplotypes with frequencies of ≥2.0% were A*33:03-B*44:03-DRB1*13:02 (4.97%), A*33:03-B*58:01-DRB1*13:02, A*33:03-B*44:03-DRB1*07:01, A*24:02-B*07:02-DRB1*01:01 and A*24:02-B*52:01-DRB1*15:02. Among 34 serologic HLA-A-B-DR haplotypes with frequencies of ≥0.5%, 17 haplotypes revealed allele-level diversity and majority of the allelic variation was arising from A2, A26, B61, B62, DR4 and DR14 specificities. Haplotype diversity obtained in this study is the most comprehensive data thus far reported in Koreans, and the information will be useful for unrelated stem cell transplantation as well as for disease association studies.

[Allelic and haplotypic diversity of HLA-A, -B, -C, and -DRB1 genes in Koreans defined by high-resolution DNA typing]

BACKGROUND

In this study, we used high-resolution DNA typing to investigate the distribution of HLA alleles and haplotypes in Koreans.

METHODS

HLA-A, -B, -C, and -DRB1 alleles were genotyped at the allelic (4-digit) level in 474 healthy Koreans. HLA genotyping was performed in two steps. Initially, serologic typing or generic-level DNA typing was performed using the PCR-sequence-specific oligonucleotide method, and then allelic DNA typing (exons 2 and 3 for class I, and exon 2 for DRB1) was carried out using the PCR-single-strand conformation polymorphism method or sequence-based typing. HLA allele and haplotype frequencies and linkage disequilibrium values were calculated by the maximum likelihood method using a computer program developed for the 11th International Histocompatibility Workshop.

RESULTS

A total of 21 HLA-A, 40 HLA-B, 22 HLA-C, and 29 HLA-DRB1 alleles were found in Koreans. The most frequent alleles in each locus with frequencies of ≥ 10% were, in decreasing order of frequency, as follows: A*24:02, A*02:01, A*33:03; B*51:01; C*01:02, C*03:03; and DRB1*09:01. The numbers of two- and three-locus haplotypes with frequencies of >0.5% were as follows: 44 A-C, 42 B-C, 51 A-B, 52 B-DRB1, 42 A-C-B, and 34 A-B-DRB1. Thirteen A-B-DRB1 haplotypes with frequencies of ≥ 1.0% comprised 26.0% of the total haplotypes. The six most common haplotypes were as follows: A*33:03-B*44:03-DRB1*13:02 (3.7%), A*33:03-B*44:03-DRB1*07:01 (3.0%), A*33:03-B*58:01-DRB1*13:02 (3.0%), A*24:02-B*07:02-DRB1*01:01 (2.8%), A*30:01-B*13:02-DRB1*07:01 (2.3%), and A*11:01-B*15:01-DRB1*04:06 (2.2%).

CONCLUSIONS

The information obtained in this study can be used as basic data for Koreans in the fields of organ transplantation, disease association, and anthropologic studies.

High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population

We have developed a new high-throughput, high-resolution genotyping method for the detection of alleles at the human leukocyte antigen (HLA)-A, -B, -C, and -DRB1 loci by combining polymerase chain reaction (PCR) and sequence-specific oligonucleotide probes (SSOPs) protocols with the Luminex 100 xMAP flow cytometry dual-laser system to quantitate fluorescently labeled oligonucleotides attached to color-coded microbeads. In order to detect the HLA alleles with a frequency of more than 0.1% in the Japanese population, we created 48 oligonucleotide probes for the HLA-A locus, 61 for HLA-B, 34 for HLA-C, and 51 for HLA-DRB1. The accuracy of the PCR-SSOP-Luminex method was determined by comparing it to the nucleotide sequencing method after subcloning into the plasmid vector using 150 multinational control samples obtained from the International HLA DNA Exchange University of California Los Angeles. In addition, we performed the PCR-SSOP-Luminex method for HLA allele typing on DNA samples collected from 1,018 Japanese volunteers. Overall, the genotyping method exhibited an accuracy of 85.91% for HLA-A, 85.03% for HLA-B, 97.32% for HLA-C, and 90.67% for HLA-DRB1 using 150 control samples, and 100% for HLA-A and -C, 99.90% for HLA-B, and 99.95% for HLA-DRB1 in 1,018 Japanese samples. The PCR-SSOP-Luminex method provides a simple, accurate, and rapid approach toward multiplex genotyping of HLA alleles to the four-digit or higher level of resolution in the Japanese population. It takes only approximately 5 h from DNA extraction to the definition of HLA four-digit alleles at the HLA-A, HLA-B, HLA-C, and HLA-DRB1 loci for 96 samples when handled by a single typist.

Association of transporter associated with antigen processing genes with Behçet's disease in Japanese

Contribution of transporter associated with antigen processing (TAP) genes to the pathogenesis of Behçet's disease (BD) was studied. Restriction fragment length polymorphic analysis of TAP genes was carried out in 46 Japanese patients with BD and 95 healthy subjects. There were no significant differences in allele frequencies of TAP1 and TAP2 genes between whole patients with BD and control population. No significant differences in the frequencies of TAP alleles were observed, when patients of BD with complete type or incomplete type were compared with control population, respectively. An allele frequency of TAP2C was, however, slightly but significantly high in patients with BD who had symptom of erythema nodosum (24.1%) as compared to the control group (11.6%). [p < .05, RR = 2.4]. The allele frequency of TAP2C was slightly high in HLA*B5101 positive patients with BD (28.6%) as compared to HLA*B5101 negative patients (10.9%), but the difference did not reach statistical significance. The absence of genotype TAP2B/C was observed in whole patients group, though it was present in control subjects (14.7%). [p = 0.003, RR = 0.06]. A genotype frequency of TAP2C/H was high in patients with BD who had symptom of skin lesions (7.5%) as compared to the control group (0.0%). [p = 0.03, RR = 15.4]. These results suggest the possibility that TAP molecule play some part in formation of skin lesion, such as erythema nodosum in BD in Japanese.

Rapid and simultaneous HLA class I (-A, -B and -C loci) DNA typing using the microtitre plate-reverse hybridization assay (MRHA)

We have established a precise, rapid, simple and practical HLA class I DNA typing method using the microtitre plate-reverse hybridization assay (MRHA), which enables us to perform simultaneous DNA typing of the HLA-A, -B and -C loci using the same PCR parameters and hybridization conditions. PCR-amplified products for the HLA-A, -B and -C loci were hybridized, respectively, with sequence-specific oligonucleotide (SSO) probes, which were immobilized covalently onto a microtitre plate, in hybridization buffer containing formamide at 37 degrees C. After washing at room temperature, the bound PCR products were detected by peroxidase-conjugate streptavidine followed by colour development such as enzyme immunoassay (EIA). In addition to the simple thermoregulation for hybridization and postwashing, strong positive signals, low background and high reproducibility, this DNA typing method enabled simultaneous typing of the HLA-A, -B and -C loci using a single microtitre plate as in HLA serotyping. The assignment of the HLA genotype was easily achieved by automated colorimetric reading and computer software, based on the cut-off value (threshold) established for each probe. For routine HLA class I typing, it may be possible to replace serological typing with the HLA class I DNA typing system using our MRHA method.

HLA-B*44 allele frequencies and haplotypic associations in Koreans

We have investigated the frequencies of HLA-B*44 alleles and their haplotypic associations with HLA-A, -C, and -DRB1 loci in 450 healthy unrelated Koreans, including 213 parents from 107 families. All 79 samples (17.6%) typed as B44 by serology were analyzed for B*44 alleles using polymerase chain reaction (PCR) single-strand conformation polymorphism (SSCP) method. A total of three different B*44 alleles were detected: B*44031 (allele frequency 4.7%), B*44032 (3.1%), and B*4402 (1.3%). Three characteristic haplotypes revealing strong linkage disequilibrium were A*3303-Cw*1403-B*44031-DRB1*1302 (3.6%), A*3303-Cw*07-B*44032-DRB1*0701 (2.8%), and A*3201-Cw*05-B*4402-DRB1*0405 (0.4%). In addition, a strong association was observed for B*4402 with A*0301. The B*4403-bearing haplotypes of Koreans appear to be relatively common in Asian populations, whereas the B*4402-bearing haplotypes share some similarity to those of Caucasians. HLA-B44 alleles demonstrate a limited allelic diversity and comprise distinctive extended haplotypes in the Korean population. It is suggested that the frequencies of B44 subtype mismatches among ABDRB1-matched unrelated donor-recipient pairs would be low in this population.

HLA-B*07 allele frequencies and haplotypic associations in Koreans

We have investigated the frequencies of HLA-B*07 alleles and their haplotypic associations with HLA-A, -C and -DRB1 loci in 489 healthy unrelated Koreans, including 214 parents from 107 families. All of the 45 samples (9.2%) typed as B7 by serology were analyzed for B*07 alleles using polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) method. Two different B*07 alleles were detected: B*0702 (allele frequency 0.041) and B*0705 (0.005). Two characteristic haplotypes showing strong linkage disequilibrium in Koreans were A*2402-Cw*07-B*0702-DRB1*0101 (haplotype frequency 0.028) and A*2901-B*0705-DRB1*0803 (0.005). The characteristic haplotype A*2901-B*0705-DRB1*0803, found in 100% (5/5) of B*0705-positive individuals, has not been previously described in other ethnic groups. HLA-B7 alleles comprise distinctive extended haplotypes in the Korean population. The probability of HLA-B7 allele mismatches among ABDR-matched unrelated donor-recipient pairs is expected to be low in Koreans.

Identification of dominant optimal HLA-B60- and HLA-B61-restricted cytotoxic T-lymphocyte (CTL) epitopes: rapid characterization of CTL responses by enzyme-linked immunospot assay

Human immunodeficiency virus type 1 (HIV-1)-specific cytotoxic T-lymphocyte (CTL) responses play a major role in the antiviral immune response, but the relative contribution of CTL responses restricted by different HLA class I molecules is less well defined. HLA-B60 or the related allele B61 is expressed in 10 to 20% of Caucasoid populations and is even more highly prevalent in Asian populations, but yet no CTL epitopes restricted by these alleles have been defined. Here we report the definition of five novel HLA-B60-restricted HIV-1-specific CTL epitopes, using peripheral blood mononuclear cells in enzyme-linked immunospot (Elispot) assays and using CTL clones and lines in cytolytic assays. The dominant HLA-B60-restricted epitope, Nef peptide KEKGGLEGL, was targeted by all eight subjects with B60 and also by both subjects with B61 studied. This study additionally establishes the utility of the Elispot assay as a more rapid and efficient method of defining novel CTL epitopes. This approach will help to define new CTL epitopes that may play an important role in the immune control of HIV-1.

Diversity of alleles encoding HLA-B40: relative frequencies in united states populations and description of five novel alleles

The frequency of each B*40 allele was determined by DNA sequencing in four major United States populations: Caucasians, African Americans, Asians/Pacific Islanders, and Hispanics. Thirty-two individuals from each ethnic group, who were previously described serologically as B40, B60, or B61, were randomly selected out of a pool of 82,979 unrelated individuals for allele characterization. Out of nine different B*40 alleles identified in this study, B*4001 and B*4002 were the two most frequent B*40 alleles in all the population groups. B*4001 was the primary B*40 allele seen in Caucasians (83%) and African Americans (76%), while B*4002 was found in the majority of Hispanics (62%). The distributions of both alleles were comparable in the Asian/Pacific Islander population. These two alleles were the only B*40 alleles detected in Caucasians while four to five additional B*40 alleles were seen in the other population groups. The other B*40 alleles detected in this study included: B*4003 and B*4010 in Asian/Pacific Islanders; B*4012 and B*4016 in African Americans; and B*4004, B*4006, and B*4027 in Hispanics. Analysis revealed significant differences between Hispanics and all other groups as well as between African Americans and Asian/Pacific Islanders. This report also describes five novel B*40 alleles: B*4019, B*4020, B*4024, B*4027, and B*4028.

Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descent from Upper Paleolithic populations of East Asia

The Ainu people are assumed to be the descendants of pre-agricultural native populations of northern Japan, while the majority of population of present-day Japan (Hondo-Japanese) is considered to have descended mainly from post-neolithic migrants. Sequence-level polymorphisms of the HLA-class I (HLA-A and HLA-B) genes were investigated in DNA samples of 50 Ainu living in Hidaka district, Hokkaido. HLA-A*2402, A*0201, A*0206, A*2601, A*3101, B*1501, B*5101, B*3901, and B*3501 were observed at frequencies of more than 10% and most of these have previously been found in populations of not only Asians but also North and South American Indians. A*68012, which has not so far been detected in Hondo-Japanese, was found in the Ainu (3%). On the other hand, several alleles common in Hondo-Japanese, including HLA-A*3303, A*1101, B*4403, B*5201, B*5401, B*4601, and B*0702 were infrequent in Ainu (0-1%). Correspondence and neighbor-joining analyses of various populations based on HLA-A, -B and -DRB1 gene frequencies enabled distinction between Asian, Native South American, European, and African populations. The Ainu, as well as Tlingit (Na-Dene), were placed midway between other East Asians, including Hondo Japanese, and Native South Americans (Amerindians) in the correspondence analysis. Furthermore, several HLA-A-B and HLA-B-DR-DQ haplotypes common in the Ainu, are shared with some Native American populations. These observations strongly suggest a unique place for the Ainu as descendants of some Upper Paleolithic populations of East Asia, from whom some Native Americans may have descended.

Rapid HLA class I DNA typing using microtiter plate-reverse hybridization assay (MRHA) by simple thermoregulation: high-resolution subtyping of the HLA-A2 and -B40 antigen groups

We have established a precise, rapid, simple and economical subtyping method for alleles encoding the HLA-A2 and -B40 antigens using microtiter plate-reverse hybridization assay (MRHA), which is based on the general principle of HLA oligotyping by reverse dot blot hybridization. Amino-modified sequence-specific oligonucleotide (SSO) probes were immobilized covalently onto a carboxylate-modified microtiter plate. In order to perform high-resolution subtyping of the HLA-A2 and -B40 antigen groups, the alpha1 and alpha2 domain regions were amplified using a pair of group-specific primers composed of an unlabeled sense primer and a biotinylated antisense primer. PCR-amplified products were hybridized with SSO probes in hybridization buffer containing formamide for 1 hour at 37 degrees C. After washing with 2 X SSC at room temperature, the bound PCR products were detected by alkaline phosphatase-conjugated streptavidine followed by color development. All of 8 HLA-B40 suballeles, all of 2 HLA-B47 suballeles (B40 group-specific primers used in this study allowed also B47 amplification) and 17 out of 21 HLA-A2 suballeles were discriminated. The remaining four HLA-A2 suballeles were determined by analysis after exon 4 amplification. HLA-DNA typing by this method was easily and exactly performed regardless of sample number. The greatest advantages of this technique are strong positive signals obtained, reproducibility and the ease of thermoregulation for hybridization and washing as compared to previously reported microtiter plate hybridization methods.

Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies

The distribution of HLA-B61 alleles and their association with HLA-C and DRB1 alleles were investigated in six East Asian populations (South Korean, Chinese Korean, Man (Manchu), Northern Han, Mongolian and Buryat) and Spanish Gypsies and compared to our previous report on the Japanese population. The alleles were identified using a group-specific polymerase chain reaction (PCR) and genomic DNA followed by hybridization with sequence-specific oligonucleotide probes (SSOP). Both HLA-B*4002 and B*4006 were commonly detected in the South Korean, Chinese Korean, Man, Northern Han and Japanese populations, while HLA-B*4002 was predominant in the Mongolian and Buryat populations. Strong associations of B*4002 with Cw*0304 and of B*4006 with Cw*0801 were commonly observed in these East Asian populations. In contrast, in Spanish Gypsies, only HLA-B*4006 was found and the allele exhibited a strong association with Cw*1502. HLA-B*4003 was also identified in the South Korean, Chinese Korean, Northern Han, Mongolian and Japanese populations at relatively low frequencies, and exhibited an association with Cw*0304. Moreover, the association of these B61 alleles with the DRB1 alleles revealed considerable diversity among the different populations. HLA-B*4004 and B*4009 were not observed in these populations. Consequently, the frequencies of the B61 alleles varied among the different East Asian populations, but the individual B61 alleles were carried by specific haplotypes often regardless of the ethnic differences.

Dissimilar evolution of B-locus versus A-locus and class II loci of the HLA region in South American Indian tribes

Native American populations have a limited HLA polymorphism compared with other ethnic groups. In spite of this, many novel HLA-B locus alleles, not observed in other populations, have been identified in South American tribes, and rapid evolution of this locus has been suggested. We have studied unrelated subjects of the Toba (TOB n = 116), Wichi (WIC n = 46) and Pilaga (PIL n = 14) tribes from northeastern Argentina to investigate the extent of the HLA polymorphism and obtain clues of selective forces that may have acted in these populations. In these tribes the number of HLA alleles is small at all loci except HLA-B, which presents 22 alleles. Seven novel alleles were characterized including 5 of HLA-B (B*35092, B*3518, B*3519, B*4009, B*4803) 1 at HLA-A (A*0219) and 1 at DRB1 (DRB1*0417). All these variants may have arisen by gene conversion events. Some of the novel variants represent the most frequent alleles of these populations (B*4803 in TOB and PIL; B*3519 in WIC) or are the most frequent subtypes in their lineages. HLA-A, B, DRB1,DQA1 and DQB1, but not DPB1, display relatively similar gene frequencies. This results in high heterozygosity in all the tribes for all the loci studied except HLA-DPB1. The larger polymorphism and the generation and maintenance of novel alleles at the HLA-B locus suggests a more specialized response of this locus to evolutionary forces. These effects may be related to the nature of the polymorphism, to the number of founder alleles and to the functional characteristics of the individual alleles.

Five HLA-B22 group alleles in Japanese

HLA-B22-group alleles in Japanese were identified using PCR-single-strand conformation polymorphism (SSCP) and sequence analyses. We analyzed genomic DNAs obtained from Japanese individuals positive for HLA-B22 group antigens (HLA-B54, B55, B56) including two locally proposed splits (B55.2, and B22N). In the SSCP analysis of both exons 2 and 3, we discriminated five different B22-group alleles. Each allelic pattern corresponded to each serological split antigen. Direct sequencing analysis of exon 2 and exon 3 showed that alleles encoding B54, B55.1 and B56 antigens in Japanese are encoded by B*5401, B*5502 and B*5601, respectively, and those encoding B55.2 and B22N antigens are previously unidentified alleles, B*5504 and B*5603, respectively. Full-length cDNA sequencing showed that the B*5603 sequence is identical to those of B*5501, B*5502, B*5601, and B*5602 in exons 1 to 2 except for a synonymous substitution at nucleotide position 165 in exon 2. On the other hand, the sequence of exons 3 to 7 was identical to those of some B15 and B46 alleles, suggesting that B*5603 was generated by a recombination event between one of the B55 and B56 alleles and one of the B15 and B46 alleles in intron 2. As for B*5504, the entire exon 1 to 7 sequence is identical to that of B*5502 except that the 5'-half of the exon 3 sequence is identical to those of some B7, B27, B40 and B48 alleles, suggesting that an event such as gene conversion, segmental exchange, or double recombination occurred in this region.

Serologic ambiguity and allelic frequency of the HLA-B40 family in the Korean population

The most frequently identified HLA-B type in Koreans is HLA-B40 (13.4%). Due to the lack of mono-specific alloantisera and cross reactivity of sera used as typing reagents, discrimination between the serologic splits of B40, B60 and B61, has been a problem in tissue typing laboratories. In this study, an efficient PCR-SSP typing system was established to distinguish B60 and B61 and to assess the difficulty in serologic assignment for these types. The SSP system was also used to elucidate the frequency of B40 alleles (B*4001-B*4008) encoding B40 molecules in the Korean population. Eighty eight unrelated individuals identified serologically as B40 positive were selected from 358 consecutive volunteers from the unrelated bone marrow registry. Seven sets of PCR that amplify exons 2 and 3 of the HLA-B gene using 10 sequence specific primers (SSP) were used for discrimination between B60 and B61, and for B40 allelic typing. A clear discrimination of B60 and B61 was possible in all samples including 48 serologically ambiguous samples (B60-14/48; B61-34/48) and 5 potentially B40 homozygous samples (B60/ B61 heterozygotes-4/5; B60 homozygote-1/5). Therefore, the use of a focused SSP approach enhances serologic definition of HLA types in routine clinical testing. In allelic typing, all B60 samples (26) appeared to be B*4001, but B61 samples revealed more heterogeneity (B*4002-36/58, B*4003-4/ 58, B*4006-18/58). In addition, B*4003 seemed to be closely associated with the A24-Cw3-DRB1*02 haplotype (3/4). The characterization of allele frequency as well as haplotypic association will be helpful in determination of the optimal size of the volunteer marrow donor pool in the Korean population.

Japanese population does not manifest significant association between low NK activity and HLA-B(C) locus homozygosity

It was reported previously that natural killer (NK) activity is controlled by the HLA-B(C) region and that individuals homozygous for HLA-B(C) or homozygous for the NKB complementation groups, which are mapped to the HLA-B(C) region, have fewer circulating NK cells and lower NK activity than do individuals heterozygous for these alleles. Those studies had used subjects in the United States. In the present study, we investigated the NK activity, NK subpopulation, and HLA types of 65 healthy Japanese individuals in Japan, most of whom have a quite different HLA-B(C) type than did subjects in the earlier study. Among 13 individuals having low NK activity, only two were HLA-B(C) homozygous and the rest were heterozygous. No obvious relation between low NK activity and specific HLA-B(C) allele was found. Seven of the nine HLA-B(C) homozygotes had medium or high NK activity. No significant differences were detected in either the NK activity or in the NK subset frequencies (circulating NK cell number) between HLA-B(C) homozygous and heterozygous individuals. These results indicate that HLA-B(C) homozygosity does not always induce low NK activity and that other factors also may influence NK activities.