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.

Recognition of the HLA-C*07:359 allele in Taiwanese individuals

One nucleotide substitution in codon 264 of HLA-C*07:02:01:01 results in a novel allele, HLA-C*07:359.

Detection of the HLA-B*40:01:35 allele in a Taiwanese individual

Nucleotide substitutions in codons -1 and 84 of HLA-B*40:01:01 result in a novel allele, HLA-B*40:01:35.

Recognition of the HLA-B*15:01:17 allele in a Taiwanese individual

Nucleotide substitution in codon 129 of HLA-B*15:01:01:01 results in a novel allele, HLA-B*15:01:17.

Discovery of the novel HLA-C*03:649 allele in a Taiwanese individual

One nucleotide substitution in codon 214 of HLA-C*03:04:01:01 results in a novel allele, HLA-C*03:649.

Recognition of the HLA-A*02:840 allele, a variant of A*02:07:01:01, in a Taiwanese individual

Two nucleotide substitutions in exon 3 of HLA-A*02:07:01:01 result in the novel allele, HLA-A*02:840.

Detection of the novel HLA-C*03:04:89, a variant of HLA-C*03:04:01:01, in a Taiwanese individual

One nucleotide substitution in codon 131 of HLA-C*03:04:01:01 results in a novel allele, HLA-C*03:04:89.

Discovery of the novel HLA-DRB1*09:01:15 allele in a Taiwanese individual

One nucleotide substitution in codon 217 of HLA-DRB1*09:01:02:01 results in a novel allele HLA-DRB1*09:01:15.

Recognition of the HLA-A*02:570:01 allele in Taiwanese individuals

Two nucleotide substitutions in codon 24 of HLA-A*02:01:01:01 result in a novel allele HLA-A*02:570:01.

Discovery of the novel HLA-B*57:164 allele, a variant of HLA-B*57:01:01:01, in a Taiwanese individual

One nucleotide substitution in codon 317 of HLA-B*57:01:01:01 results in the novel allele, HLA-B*57:164.

Discovery of a novel HLA-C*04 null allele, HLA-C*04:279N, in a Singaporean individual

A nucleotide mutation in codon 75 of HLA-C*04:01:01:01 results in a novel allele HLA-C*04:279N.

Discovery of the novel HLA-DRB1*04:358 allele, a variant of HLA-DRB1*04, in a Taiwanese individual

One nucleotide substitution in codon 140 of HLA-DRB1*04:05:01:01 results in a novel allele, HLA-DRB1*04:358.

Detection of the HLA-DQB1*03:151 allele in a Taiwanese umbilical cord blood unit

One nucleotide substitution in codon 25 of HLA-DQB1*03:01:01:01 results in a novel allele HLA-DQB1*03:151.

Recognition of the HLA-C*14:24:02 allele in a Singaporean individual

One nucleotide substitution in codon 112 of HLA-C*14:24:01 results in a novel allele, HLA-C*14:24:02.

Detection of the HLA-B*40:02:03 allele, a variant of HLA-B*40:02:01:01, in a Taiwanese individual

One nucleotide substitution in codon 67 of HLA-B*40:02:01:01 results in a novel allele, HLA-B*40:02:03.

Recognition of the HLA-C*03:04:20 allele, a variant of HLA-C*03:04:01:01, in a Taiwanese individual

One nucleotide substitution in codon 227 of HLA-C*03:04:01:01 results in a novel allele, HLA-C*03:04:20.

HLA-A*24:244, a variant of HLA-A*24:02:01:01, detected in a Taiwanese individual

One nucleotide substitution in codon 51 of HLA-A*24:02:01:01 results in the novel allele, HLA-A*24:244.

Recognition of the HLA-A*02:07:19 allele, a variant of HLA-A*02:07:01:01, in a Taiwanese individual

One nucleotide substitution at codon 310 of HLA-A*02:07:01:01 results in the novel allele, HLA*02*07:19.

Detection of the HLA-A*02:759 allele, a variant of A*02:06:01:01, in a Taiwanese individual

A nucleotide mutation in exon 1 of HLA-A*02:06:01:01 results in the novel allele, HLA-A*02:759.

Discovery of the novel HLA-B*13:173 allele in a Taiwanese individual

A nucleotide mutation in exon 1 of HLA-B*13:01:01:01 results in the novel allele HLA-B*13:173. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-C*08:03:05 allele in a Taiwanese individual

One nucleotide substitution in codon 182 of HLA-C*08:03:01:01 results in a novel allele HLA-C*08:03:05. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-DRB1*07:136 allele in a Taiwanese patient

One nucleotide substitution in codon 107 of HLA-DRB1*07:01:01:01 results in a novel allele HLA-DRB1*07:136. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-DRB1*08:113 allele in a Taiwanese bone marrow donor

Nucleotide substitutions in exon 2 of DRB1*08:34 result in the novel DRB1*08:113 allele. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-DRB1*09:31:02 allele in a College of American Pathologists HLA Survey specimen

One nucleotide substitution in codon 217 of HLA-DRB1*09:31:01 results in a novel allele HLA-DRB1*09:31:02. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-C*08:22:02 allele in a Taiwanese individual

One nucleotide substitution in codon 182 of HLA-C*08:22:01:01 results in a novel allele HLA-C*08:22:02.

HLA-A*26:35, a variant of HLA-A*26, detected in a Taiwanese individual

Nucleotide substitutions in codons 11 and 12 of HLA-A*26:01:01:01 result in a novel allele, HLA-A*26:35.

Detection of an HLA-A*02 variant, HLA-A*02:99:01, in a Taiwanese individual

One nucleotide substitution in codon 152 of HLA-A*02:06:01:01 results in a novel allele HLA-A*02:99:01. This article is protected by copyright. All rights reserved.

HLA-B*40:36, a variant of HLA-B*40, recognized in a Taiwanese individual

One nucleotide substitution in codon 116 of HLA-B*40:01:01 results in a novel allele, HLA-B*40:36. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-A*11:417 N allele in a Taiwanese individual

One nucleotide deletion at position 61 of HLA-A*11:01:01:01 results in the novel allele HLA-A*11:417 N. This article is protected by copyright. All rights reserved.

HLA-A*32:34, a variant of HLA-A*32, detected in a Taiwanese individual

One nucleotide substitution in codon 128 of HLA-A*32:01:01:01 results in a novel allele, HLA-A*32:34. This article is protected by copyright. All rights reserved.

Detection of an HLA-A*24 variant, HLA-A*24:255, in a Taiwanese individual

One nucleotide substitution in codon 82 of HLA-A*24:02:01:01 results in a novel allele HLA-A*24:255. This article is protected by copyright. All rights reserved.

Discovery of the novel HLA-B*40:483N Allele in a Taiwanese individual

Nucleotide mutations in exons 1 and 4 of HLA-B*40:01:01 result in the novel allele HLA-B*40:483N.

Detection of the novel HLA-B*55:123 allele in a Taiwanese bone marrow donor

One nucleotide substitution in exon 3 of HLA-B*55:02:01:01 results in a novel allele, HLA-B*55:123. This article is protected by copyright. All rights reserved.

A single nucleotide mutation in exon 3 produces the novel HLA-DPB1*700:01N allele

A nucleotide mutation in codon 135 of HLA-DPB1*02:01:02:01 results in the novel allele HLA-DPB1*700:01N.

Detection of the HLA-B*15:360 allele in a Taiwanese bone marrow donor

Four nucleotide substitutions in exon 3 of HLA-B*15:01:01:01 result in a novel allele, HLA-B*15:360.

Detection of the HLA-A*02:56:02 allele in a Taiwanese individual

One nucleotide substitution in codon 56 of HLA-A*02:56:01 results in a novel allele, HLA-A*02:56:02.

Recognition of the HLA-B*39:36 allele in a Taiwanese bone marrow donor

Four nucleotide substitutions in exon 3 of HLA-B*39:01:01:01 result in a novel allele, HLA-B*39:36.

Detection of the HLA-B*15:404 allele in a Singaporean bone marrow donor

Nucleotide substitutions in codons 67 and 119 of HLA-B*15:02:01:01 result in a novel allele, HLA-B*15:404.

Recognition of the HLA-A*11:85 allele in a Taiwanese bone marrow donor

One nucleotide substitution in codon 47 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:85.

Recognition of the HLA-DRB1*14:119 allele in a Singaporean bone marrow donor

Nucleotide substitutions in exon 2 of DRB1*14:54:01:01 result in the novel DRB1*14:119 allele.

A single nucleotide mutation in exon 2 produces a novel HLA-DRB1*07 null allele, HLA-DRB1*07:129N

A nucleotide mutation in codon 34 of HLA-DRB1*07:01:01:01 results in a novel allele HLA-DRB1*07:129N.

HLA-A*02:294, a variant of HLA-A*02:01:01:01, detected in a Taiwanese individual

One nucleotide substitution in codon 253 of HLA-A*02:01:01:01 results in a novel allele, HLA-A*02:294.

Detection of the HLA-A*11:32:01 allele in a Taiwanese bone marrow donor

One nucleotide substitution in codon 182 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:32:01.

Recognition of the HLA-B*51:185 allele in a Taiwanese individual

One nucleotide substitution in codon 77 of HLA-B*51:01:01:01 results in a novel allele, HLA-B*51:185.

Recognition of the HLA-A*24:141 allele in a Taiwanese individual

One nucleotide substitution in codon 178 of HLA-A*24:02:01:01 results in a novel allele, HLA-A*24:141.

Detection of the HLA-DRB1*04:80 allele, a variant of HLA-DRB1*04, in a Taiwanese individual

One nucleotide substitution in codon 67 of HLA-DRB1*04:05:01:01 results in a novel allele, HLA-DRB1*04:80.

Recognition of the HLA-C*07:199:01 allele in a Singaporean unrelated hematopoietic stem cell donor

One nucleotide substitution in codon 95 of HLA-C*07:04:01:01 results in a novel allele, HLA-C*07:199:01.

Detection of the HLA-A*11:01:06 allele in a Taiwanese individual

One nucleotide substitution in codon 105 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:01:06.

Detection of the HLA-DRB1*14:22 allele in a Taiwanese individual

DNA recombination between DRB1*14:25:01 and DRB1*14:54:01:01 produced the novel DRB1*14:22 allele.

Discovery of the novel HLA-B*35:518 allele in a Taiwanese individual

One nucleotide substitution in codon 146 of HLA-B*35:01:01:01 results in a novel allele, HLA-B*35:518.