A novel HLA-A24 (A*2420) allele identified in the Atayal tribe of Taiwan

Association of HLA-C*07:359 with HLA-A, -B, and -DRB1 alleles in Taiwanese

Objectives

It is thought that Taiwanese indigenous people were the "first people" to populate Taiwan (Formosa) having been there for over 5000 years, preceding the Dutch colonization (from 1624 to 1662) and Spanish colonization (from 1626 to 1642). Taiwan's indigenes, represented by Austronesian language speakers, currently constitute approximately 2% of the total population in Taiwan. It is unknown whether they evolved from Taiwan's Paleolithic or Neolithic cultures, arrived during or after the Neolithic period from China or Southeast Asia or both. HLA studies on the Taiwanese indigenous population have found several intriguing genetic information showing one or two relatively frequently observed alleles and a small number of relatively less frequently observed ones. We report here a relatively frequently observed HLA-C*07:359 allele in the Taiwanese indigenous population, its linkage with HLA-B*39:01, and its probable associated HLA haplotype in two Taiwanese indigenous families. HLA-C*07:359 is a rarely observed allele in the HLA-C locus in the world populations. The objective of this study is to report the allele HLA-C*07:359 that is more frequently found in the Taiwanese population, especially in the Taiwanese indigenous people, to demonstrate that it has a close linkage with HLA-B*39:01 allele in the HLA-B locus and to show the plausible deduced HLA-A-C-B-DRB1-DQB1 haplotypes in association with HLA-C*07:359 in two families of Taiwanese indigenous unrelated individuals.

Materials and Methods

The samples were peripheral whole blood, with dipotassium ethylenediaminetetraacetic acid and/or acid citrate dextrose anticoagulation additives. The sequence-based typing method was employed to confirm the low incidence of the allele of HLA-C*07:359 observed in Taiwanese. Polymerase chain reaction was carried out to amplify exons 2, 3, and 4 of the HLA-A,-B,-C,-DRB1 and-DQB1 loci with group-specific primer sets. Amplicons were sequenced using the BigDye Terminator Cycle Sequencing Ready Reaction Kit in both directions according to the manufacturer's protocol.

Results

C*07:359 is an uncommon allele in the HLA-C locus in the world general population, according to our literature review. However, in this study, it is observed in the general Taiwanese population (frequency 0.41%), especially in the Taiwanese indigenous people at a frequency of 0.23%. In addition, we deduced two probable HLA haplotypes in association with C*07:359 in two indigenous families: A*24:02-C*07:359-B*39:01-DRB1*04:36 and A*24:02-C*07:359-B*39:01-DRB1*04:04.

Conclusion

The two deduced HLA haplotypes associated with the uncommon C*07:359 allele that we report here are valuable for HLA tissue typing laboratories for reference purposes and for stem cell transplantation donor search coordinators to determine the likelihood of finding compatible donors in unrelated bone marrow donor registries for patients bearing the uncommon HLA allele. Since C*07:359 was found mostly in the Taiwanese indigenous population, we think the allele and its haplotypes we report here are important in population and anthropological studies.

High-resolution human leukocyte antigen (HLA) haplotypes and linkage disequilibrium of HLA-B and -C and HLA-DRB1 and -DQB1 alleles in a Taiwanese population

Using the maximum-likelihood method with the expectation-maximization (EM) algorithm of PYPOP, high-resolution human leukocyte antigen (HLA) three-locus haplotypes (HLA-A, -B, and -C; HLA-A, -B, and -DRB1) and four-locus haplotypes (HLA-A, -B, -C, and -DRB1) were determined. Linkage disequilibrium of high-resolution HLA-B and -C alleles and HLA-DRB1 and -DQB1 alleles was also calculated. Comparison of the Taiwanese haplotypes and haplotypes from donors in the Chinese Han population, the Asia Pacific Islander ethnic category of the NMDP (National Marrow Donor Program), and the Taiwanese cord blood units demonstrated similarities and dissimilarities among the four populations. HLA allele frequencies of our study suggested that the Taiwanese have a relative population relationship with the southern Han Chinese with regard to HLA. Our results also indicated that the Taiwanese population exhibits genetic proximity with Asian Americans with regard to HLA-A and -DRB1 but not HLA-B.

Polymorphism of HLA class I genes in Meizhou Han population of Guangdong, China

Human leukocyte antigen (HLA) is an invaluable marker for anthropological studies because of its extreme polymorphism. Most of the studies carried out in Chinese populations are about HLA class II genes, but few about class I genes. In the present study, we investigated HLA class I polymorphism using polymerase chain reaction-sequencing-based typing (PCR-SBT) method in 104 unrelated Han individuals in Meizhou of Guangdong, southern China. Twenty-three HLA-A, 43 HLA-B and 27 HLA-C alleles were identified and allele frequencies and two-locus (C/B) and three-locus (A/C/B) haplotypes were statistically analysed. The most frequent HLA-A allele is A*110101 with a frequency of 30.3%, followed by A*24020101 (22.2%) and A*2420 (11.6%). Among the 43 detected HLA-B alleles, B*5801 (17.0%), B*400101 (15.5%) and B*4601 (10.0%) were frequently observed. Among the 27 detected C alleles, the most predominant one is Cw*07020101 (25.8%), followed by Cw*0717 (14.7%). The most frequent HLA-C/B two-locus haplotype is Cw*07020101/B*400101 (10.1%). The most common HLA-A/C/B three-locus haplotype in Meizhou Han is A*110101/Cw*07020101/B*400101 (3.4%). Phylogenetic tree based on HLA class I allele frequencies genetically suggested that Meizhou Han has an affinity to southern Asian populations. The result may also reflect an admixture of Han and ethnic minorities of southern China.

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.

Point mutation in the beta sheet of the HLA-C alpha2 domain generates a novel HLA-C allele, HLA-Cw*08012, in a Puyuma Aboriginal individual in Taiwan

We report herein the identification of a new HLA-C allele using sequence-based typing (SBT). This novel allele, HLA-Cw*08012, was found in an Aboriginal individual from the Puyuma tribe in the southern part of Taiwan. This individual was typed by the SBT method as having an HLA genotype of HLA-A*2402/2402, HLA-B*1502/4801, HLA-Cw*08011/08012, HLA-DRB1*15011/08032, HLA-DRB5*01011, and DPB1*0501/1401. This new allele differs from HLA-Cw*08011 in one of the nucleotides of the polymorphic exon 3 at codon 99 [TAT-->TAC; both code for tyrosine]. This residue is located in the beta sheet of the HLA-C alpha2 domain. This new allele was detected in a few individuals of the Puyuma tribe in Taiwan, but has not yet been observed in other populations in Taiwan.

Point mutation in the alpha helix of the HLA-C alpha2 domain generates a novel HLA-C allele,HLA-Cw*0106, in a Han Chinese individual in Taiwan

We report herein the identification of a new HLA-C allele using sequence-based typing (SBT). This novel allele, HLA-Cw*0106, was found in a Han Chinese individual from Taiwan. This individual was typed using SBT as having a class I HLA genotype of HLA-A*0206/0207, HLA-B*4601/5601, and HLA-Cw*0102/0106. This new allele differs from HLA-Cw*0102 in one of the nucleotides of the polymorphic exon 3 at codon 152 (GAG-->GTG; E152V). This residue is located in the alpha helix of the HLA-C alpha2 domain and may have the potential to affect the binding of HLA-C molecules with antigenic peptides and/or the interactions with the T cell receptor. This new allele was detected in a few individuals of Han Chinese in Taiwan, but has not yet been observed in the aboriginal populations in Taiwan.

New DR5 sequences: a novel DRB1*11122 allele identified in Paiwan tribe members of Taiwan and a corrected sequence for the DRB1*1201 allele

We report herein the identification of a new DRB1 allele using sequence-based typing (SBT). This novel allele, HLA-DRB1*11122, was found in an aboriginal individual (SWP71) from the Paiwan tribe in the southern part of Taiwan. This individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4001/4002, HLA-DRB1*11122/15011, HLA-DRB3*0202, and HLA-DRB5*01011. This new allele differs from DRB1*1112 in the polymorphic exon 2 only at codon 34 (CAA-->CAG; both specify glutamine) and from DRB1*1110 in the exon 2 sequence only at codon 32 (CAT-->TAT; H32T). The most likely candidate allele which is found in the aboriginal populations of Taiwan and which may mutate into this new allele is DRB1*11011. DRB1*11122 allele differs from DRB1*11011 allele in the polymorphic exon 2 at both codon 34 (CAA-->CAG) and codon 37 (TAC-->TTC; T37F). This novel HLA-DRB1*11122 allele was also found in another aboriginal individual (SWP90) from the same Paiwan tribe. This SWP90 individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4002/5502, HLA-DRB1*11122/1201, and HLA-DRB3*01011/0202. However, the original DRB1*1201 sequence from HERLUFF was found to be erroneously reported and the corrected sequence from SWP90 is now presented herein.

Diversity of HLA among Taiwan's indigenous tribes and the Ivatans in the Philippines

Taiwan's indigenous tribes, especially the east coast tribes are not only closely related to Oceania but also with the Australian aborigines. The Ivatans of the Batan Islands in the Philippines are closely related to the Yami tribe of Taiwan as cultural and anthropological studies have shown. Many DRB1 alleles (*15021, *16021, *0404, *04051, *11011, *12021, *1401, *08032) have high allele frequencies (>20%) in certain tribes, suggesting Taiwan's indigenous tribes are homogeneous populations. These high frequency DRB1 alleles and also some HLA-A-B-DR haplotypes found in Taiwan's indigenous tribes are also found in Oceania, Australian aborigines, south and north east Asians and American Indians, lending further support to our previous findings that Taiwan's indigenous tribes are more or less genetically related to both northern and southern Asians, possibly as well as Amerindians. HLA-A*2402 with a remarkably high frequency among Taiwan's indigenous tribes (52.1% approximately 86.3%), especially the central mountain tribes, possibly represents not only founder effects and population bottlenecks, but also positive selection of the allele. Although the Ami tribe has the highest ever reported frequencies of the DRB1*0404 and DRB1*0405, these alleles have not been found to be associated with rheumatoid arthritis as previously described for Caucasians. In addition, DRB1*1401 has a high frequency in most tribes but is not associated with psoriasis as previously indicated in some studies, suggesting the involvement of some additional genetic and/or environmental factors mechanism in the development of these diseases.

Polymorphism of human HLA-DRB1 antigens generated by genetic exchange between DR2 (DRB1*15011) and DR6 (DRB1*1405) alleles: a novel DRB1 allele (DRB1*1437) identified in a Paiwan tribe member of Taiwan

We report herein the identification of a new DRB1 allele using sequence-based typing (SBT). This novel allele, HLA-DRB1*1437, was found in an aboriginal individual from the Paiwan tribe in the southern part of Taiwan. This individual was typed by SBT method as having an HLA genotype of HLA-A*02011/0203, HLA-B*15011/3901, HLA-DRB1*11011/1437, HLA-DRB3*0202/0202, and HLA-DPB1*0501/1301. This new allele differs from DRB1*1309 in the 5'-end nucleotide sequence of polymorphic exon 2 at codon 16 (CAT-->CAA; H16Q), codon 37 (AAC-->TTC; R37F), codon 47 (TTC-->TAC; F47Y), and codon 58 (GCC-->GCT; both specify alanine). By sequence comparison, it was found that this new allele has a 5'-end sequence (from amino acid residues 7 to 66) identical to that found in the DRB1*1405 allele and a 3'-end sequence (from amino acid residues 58 to 94) identical to that found in the DRB1*15011 allele. Both DRB1*1405 and DRB1*15011 alleles have been identified among the Paiwan members (Note).