Discovery of the novel HLA-DRB1*03:77 allele in a Taiwanese unrelated hematopoietic stem cell donor by a sequence-based typing method and identification of the probable HLA haplotype in association with DRB1*03:77

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

HLA-A*29:01-B*07:05-C*15:29*DRB1*10:01-DQB1*05:01, a deduced probable human leukocyte antigen haplotype in association with a human leukocyte antigen-C low-incidence allele C*15:29 in Taiwanese individuals

Objective:

HLA-C*15:29 is a low-frequency allele in the human leukocyte antigen (HLA)-C locus. The aim of this study is to confirm the ethnicity of C*15:29 and to deduce a probable HLA haplotype in association with C*15:29 in Taiwanese population.

Materials and Methods:

A total of 12,534 healthy unrelated Taiwanese individuals were tested for HLA using a sequence-based typing method. The DNA material was subjected to HLA genotyping for the HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 loci using a commercial polymerase chain reaction–sequencing-based typing kit as per the manufacturer's protocols.

Results:

The DNA sequence of C*15:29 is identical to C*15:02:01:01 in exons 1, 2, 3, 4, 5, and 6 except for residues 420 and 1034 where A and G of C*15:02:01:01 are substituted by C and A in C*15:29, respectively. The nucleotide substitutions introduce two amino acid replacements at residues 116 and 321 where leucine (L) and cysteine (C) of C*15:02:01:01 are replaced by phenylalanine (F) and tyrosine (Y) in C*15:29, respectively. A probable HLA haplotype associated with C*15:29 in Taiwanese was deduced as A*29:01-B*07:05-C*15:29-DRB1*10:01-DQB1*05:01. The frequency of C*15:29 is estimated at about 0.064%.

Conclusion:

Information on the ethnicity and distribution of C*15:29 and its deduced probable HLA haplotype is of value for HLA testing laboratories for reference purposes and can help bone marrow donor registries find compatible donors for patients with this uncommon HLA allele.

Human leukocyte antigen-A*33:03-B*58:01-DRB1*15:140, a deduced probable human leukocyte antigen haplotype in association with a human leukocyte antigen low-incidence allele DRB1*15:140 in Taiwanese individuals: A case analysis

Objective:

Human leukocyte antigen (HLA)-DRB1*15:140 is a low-frequency allele in the HLA-DRB1 locus. The aim of this study is to confirm the ethnicity of DRB1*15:140 and to deduce a probable HLA-DRB1*15:140-associated HLA haplotype in Taiwanese individuals.

Materials and Methods:

A total of 1815 healthy unrelated Taiwanese individuals and 14,562 unrelated mainland Chinese individuals were tested for HLA using a sequence-based typing method. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exons 1 and 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions with the BigDye Terminator Cycle Sequencing Ready Reaction Kit according to the manufacturer's protocols.

Results:

The DNA sequence of HLA-DRB1*15:140 is identical to DRB1*15:02:01:01 in exons 1 and 2, except at residue 91 of DRB1*15:02:01:01 where a G in DRB1*15:02:01:01 is replaced by an A in DRB1*15:140 (codon 2; GAC->AAC). The nucleotide substitution in exon 1 introduces a one amino acid substitution at residue 2 where an aspartic acid (D) in DRB1*15:02:01:01 is replaced by an asparagine (N) in DRB1*15:140. We deduced the probable HLA haplotype associated with DRB1*15:140 in Taiwanese to be HLA-A*33:03-B*58:01-DRB1*15:140.

Conclusion:

Information on the ethnicity and distribution of DRB1*15:140 and its deduced probable HLA haplotype in association with the low-incidence allele is of value for HLA-testing laboratories for reference purposes and can help bone marrow donor registries find compatible donors for patients with this uncommon HLA allele.

Human leukocyte antigen-A*24:02-B*40:247-C*03:04-DRB1*16:02, a deduced probable human leukocyte antigen haplotype associated with a low-incidence human leukocyte antigen allele B*40:247 in Taiwanese individuals: A case analysis

Objective

HLA-B*40:247 is a low incidence allele in the HLA-B locus. The aim of this study is to confirm the ethnicity of B*40:247 and its deduced probable HLA- associated haplotype in Taiwanese individuals.

Materials and Methods

A total of 2,329 unrelated Taiwanese individuals and 66,212 unrelated mainland Chinese individuals were tested for HLA using a sequence-based typing method. We confirmed the low incidence allele B*40:247 in Taiwanese. Polymerase chain reaction was performed to amplify exons 2, 3 and 4 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions with the *BigDye Terminator Cycle Sequencing Ready Reaction Kit according to the manufacturer's protocols.

Results

The DNA sequence of B*40:247 is identical to B*40:01:01 in exons 2, 3 and 4 except for residue 853, where G of B*40:01:01 is changed to A in B*40:247 (codon 261, GTA->ATA). The nucleotide replacement causes a one amino acid change at codon 261 where V (valine) of B*40:01:01 is replaced by I (isoleucine) in B*40:247. We deduced the probable HLA haplotype associated with B*40:247 in Taiwanese to be HLA-A*24:02-B*40:247-C*03:04-DRB1*16:02.

Conclusion

Information on the ethnicity and distribution of B*40:247 and its deduced probable HLA haplotype in association with the low incidence allele is of value for HLA testing laboratories for reference purposes and can help bone marrow donor registries find compatible donors for patients with this uncommon HLA allele.

Deduced probable human leukocyte antigen haplotypes associated with human leukocyte antigen DRB1*04:36 identified by case analysis of Taiwanese individuals

Objective:

Human leukocyte antigen (HLA) DRB1*04:36 is a low-frequency HLA-DRB1 allele. The aim here is to report the ethnicity of DRB1*04:36 and its associated HLA haplotypes among Taiwanese individuals.

Materials and Methods:

A sequence-based typing method was employed to confirm this low incidence allele. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kits and the manufacturer's protocols. One group of unrelated blood donors used in this study consists of randomized individuals with Taiwanese ethnicity who participate in the Tzu Chi Bone Marrow Donor Registry and the other group are randomized unrelated individuals from mainland China. The family members in the family part of the study are volunteer blood donors.

Results:

In exon 2, the DNA sequence of DRB1*04:36 is identical to DRB1*04:03:01 except for a nucleotide segment from residue 286 to residue 308. The nucleotide segment from residue 286 to residue 308, incidentally, is identical to that of DRB1*11:01:01:01. These observations suggest that DRB1*04:36 may have been derived through a gene recombination event involving DRB1*04:03:01 and DRB1*11:01:01:01. Our family study indicated that the HLA haplotype in association with DRB1*04:36 can be deduced to be A*24:02-B*39:01-DRB1*04:36. A randomized population study using Taiwanese suggests that additional DRB1*04:36 associated HLA haplotypes seem to exist.

Conclusion:

The information on the ethnicity of the DRB1**04:36 allele, and the deduced probable HLA haplotypes associated with the low incidence DRB1*04:36 allele that we report here, is of value to HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplantation donor search coordinators to aid the creation of strategy for finding compatible donors who are part of unrelated bone marrow donor registries when a patient carries this uncommon HLA allele.

Deduced probable human leukocyte antigen haplotypes associated with HLA-A*11:256Q and HLA-A*02:621 identified by case analyses of Taiwanese individuals

Objective:

HLA-A*11:256Q and HLA-A*02:621 are two low-frequency HLA-A alleles. The aim here is to report the ethnicity of A*11:256Q and A*02:621 and associated human leukocyte antigen (HLA) haplotypes among Taiwanese individuals.

Materials and Methods:

HLA data from randomized Taiwanese registered in the Tzu Chi Stem Cells Centre and China Shanghai Tissuebank Diagnostics were analyzed. HLA typing of the donors was carried out using a sequence-based typing method to confirm the two low-incidence alleles. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kits and the manufacturer's protocols. Exon 1 and exons 4-8 of the A*11:256Q allele were also sequenced and analyzed.

Results:

The Taiwanese ethnicity for both A*11:256Q and A*02:621 alleles was confirmed in this study. Further, the DNA sequence of A* 11:256Q was confirmed to be identical to A*11:02:01from exon 1 to exon 8 except for the residues from 409 to 417 where a segment of nine nucleotides (TACCGGCAG) is deleted in A*11:256Q. The HLA haplotype associated with A*11:256Q was deduced as A*11:256Q-B*27-DRB1*12. In exons 2 and 3, the DNA sequence of A*02:621 is identical to A*02:01:01:01 except at residue 169 where T of A*02:01:01:01 is replaced by C in A*02:621 (at codon 33; TTC->CTC). The HLA haplotype in association with A*02:621 was deduced as A*02:621-B*15:18-DRB1*12:02.

Conclusion:

The information on the ethnicity of the A*11:256Q and A*02:621 alleles and the deduced probable HLA haplotypes associated with the two low-incidence alleles reported here are valuable to HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplantation donor search coordinators to aid in finding compatible donors in unrelated bone marrow donor registries when a patient carries these uncommon HLA alleles.

HLA haplotype in association with the low incidence C*07:66 allele found by case analysis of Taiwanese and mainland Chinese individuals

Objectives:

HLA-C*07:66 is a low-incidence HLA-C allele. The aim of the study is to report the Taiwanese and mainland Chinese ethnicities of individuals with C*07:66, together with its uniqueness and polymorphism.

Materials and Methods:

A sequence-based typing method was employed to confirm this low-incidence allele. Polymerase chain reaction was performed to amplify exons 2, 3, and 4 of the HLA-A, HLA-B, and HLA-C loci and exon 2 of the HLA-DRB1 and HLA-DQB1 loci using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kit. The blood donors in this study consisted of randomized Taiwanese and mainland Chinese individuals and family members with the C*07:66 allele.

Results:

The DNA sequence of C*07:66 is identical to that of C*07:02:01:01 for exons 2, 3, and 4, except for residue 688 in exon 4. This nucleotide substitution causes a single amino acid alteration to the protein sequence of C*07:02:01:01. Confirmation of the DNA and protein sequences of C*07:66 and the Taiwanese and mainland Chinese ethnicities of individuals with this allele were established in this study. One probable HLA C*07:66-associated HLA haplotype may be deduced from these individuals.

Conclusion:

The information on the ethnicity of the C*07:66 allele and the deduced probable HLA haplotype associated with the low-incidence C*07:66 allele reported in this study may aid in HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplant donor search coordinators to help create, for patients bearing this uncommon HLA allele, strategies for finding compatible donors using bone marrow donor registries comprising unrelated individuals.

Deduced probable HLA haplotypes associated with HLA-C*04:82 found by case analysis of Taiwanese individuals

Objective:

HLA-C*04:82 is a low incidence HLA-C allele. The aim here is to report the ethnicity of C*04:82 and its associated HLA haplotypes among Taiwanese individuals.

Materials and Methods:

A sequence-based typing method was used to confirm this low incidence allele. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A, HLA-B, and HLA-C loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced in both directions using Terminator Cycle Sequencing Ready Reaction kits and the manufacturer's protocols. The potential unrelated bone marrow stem cell donors in this study were randomized individuals with Taiwanese ethnicity who participated in the Tzu Chi Bone Marrow Donor Registry. The family members in the family part of the study were volunteer blood donors.

Results:

The DNA sequence of C*04:82 was identical to C*04:01:01:01 in exons 2, 3, and 4. It differed from C*04:01:01:01 in exon 5 where a segment of nucleotides (CTAGCTGTC) was inserted between residues 969 and 970 of C*04:01:01:01. The insertion of these nucleotides caused a 35 amino acid alteration to the protein sequence of C*04:01:01:01. Three probable HLA haplotypes that were associated with C*04:82 among Taiwanese individuals were deduced. Confirmation of the DNA and protein sequences of C*04:82 and its Taiwanese ethnicity were established in this study.

Conclusion:

The ethnicity of the C*04:82 allele and the deduced probable HLA haplotypes associated with the low-incidence C*04:82 allele are of value for reference purposes for HLA testing laboratories. In addition, they can be used by search coordinators to aid the creation of a strategy for finding compatible stem cell donors for patients who carry this uncommon HLA allele.

Deduced probable HLA-C*07:359-associated human leukocyte antigen haplotypes found by case analysis of Taiwanese unrelated bone marrow hematopoietic stem cell donors

Objectives:

HLA-C*07:359 is a low-incidence allele in the human leukocyte antigen (HLA)-C locus. The objective of this study is to report the ethnicity and haplotypes of HLA-C*07:359 that were found during an analysis of Taiwanese unrelated bone marrow hematopoietic stem cell donors.

Materials and methods:

A sequence-based typing method was employed to confirm low-incidence al-leles. Polymerase chain reaction was performed to amplify exon 2 and exon 3 of the HLA-A, HLA-B, and HLA-C loci, as well as exon 2 of the HLA-DRB1 locus, using group-specific primer sets. The amplicons were sequenced in both directions using BigDye Terminator Cycle Sequencing Ready Reaction kits, according to the manufacturer's protocols. The potential unrelated bone marrow stem cell donors investigated here are individuals with Taiwanese ethnicity who are participating in the Tzu Chi Bone Marrow Donor Registry.

Results:

The DNA sequence of C*07:359 is identical to that of C*07:02:01:01 in exons 2, 3, and 4 except at residue 862, where the G of C*07:02:01:01 is substituted by the A of C*07:359. The nucleotide exchange leads to an amino acid replacement at codon 264, where the glutamic acid of C*07:02:01:01 is replaced by the lysine of C*07:359. We deduced a probable HLA-B and HLA-C haplotype that is associated with C*07:359 in Taiwanese, namely B*39-C*07:359.

Conclusion:

Information on the ethnicity of the C*07:359 allele and its deduced probable HLA haplotypes that are associated with the low-incidence C*07:359 allele reported here are of value to HLA testing laboratories for reference purposes. In addition, they can be used by stem cell transplantation donor search coordinators to determine a strategy for finding compatible donors using unrelated bone marrow donor registries when patients carry this uncommon HLA allele.

A deduced probable HLA-DRB1*16:35-associated HLA haplotype (A*11-B*13-DRB1*16:35) found in a case analysis of two Taiwanese unrelated bone marrow hematopoietic stem cell donors

Objective:

HLA-DRB1*16:35 is a low incidence allele in the HLA-DRB1 locus. The objective of this study is to report the ethnicity of DRB1*16:35 and its deduced probable HLA associated haplotype in two Taiwanese unrelated bone marrow hematopoietic stem cell donors and to determine its variation from DRB1*16:02:01 and DRB1*16:01:01.

Materials and Methods:

A sequence-based typing method was employed to confirm the low incidence allele DRB1*16:35. Polymerase chain reaction was performed to amplify exon 2 and exon 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced employing BigDye Terminator Cycle Sequencing Ready Reaction kits in both directions according to the manufacturer's protocols.

Results:

The DNA sequence of DRB1*16:35 is identical to DRB1*16:02:01 in exons 2, except for residue 364 where the C of DRB1*16:02:01 is replaced by the T of DRB1*16:35 (codon 93, CGG->TGG). The nucleotide exchange leads to an amino acid alteration to the protein sequence of DRB1*16:02:01 at residue 93 where the arginine (R) of DRB1*16:02:01 is changed to the tryptophan (W) of DRB1*16:35. We deduced the probable HLA haplotype in association with DRB1*16:35 in Taiwanese to be A*11-B*13- DRB1*16:35.

Conclusion:

Information on the deduced probable HLA haplotype in association with the low incidence DRB1*16:35 allele that we report here is of value for HLA testing laboratories for reference purposes. In addition, it can be used by stem cell transplantation donor search coordinators to determine a strategy for finding compatible donors in unrelated bone marrow donor registries when a patient has this uncommon HLA allele.