Sequence Of DRB1 Research Articles

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.

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

ObjectiveHLA-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 MethodsA 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. ResultsThe 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. ConclusionInformation 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.

Nonsynonymous substitution rate heterogeneity in the peptide-binding region among different HLA-DRB1 lineages in humans.

An extraordinary diversity of amino acid sequences in the peptide-binding region (PBR) of human leukocyte antigen [HLA; human major histocompatibility complex (MHC)] molecules has been maintained by balancing selection. The process of accumulation of amino acid diversity in the PBR for six HLA genes (HLA-A, B, C, DRB1, DQB1, and DPB1) shows that the number of amino acid substitutions in the PBR among alleles does not linearly correlate with the divergence time of alleles at the six HLA loci. At these loci, some pairs of alleles show significantly less nonsynonymous substitutions at the PBR than expected from the divergence time. The same phenomenon was observed not only in the HLA but also in the rat MHC. To identify the cause for this, DRB1 sequences, a representative case of a typical nonlinear pattern of substitutions, were examined. When the amino acid substitutions in the PBR were placed with maximum parsimony on a maximum likelihood tree based on the non-PBR substitutions, heterogeneous rates of nonsynonymous substitutions in the PBR were observed on several branches. A computer simulation supported the hypothesis that allelic pairs with low PBR substitution rates were responsible for the stagnation of accumulation of PBR nonsynonymous substitutions. From these observations, we conclude that the nonsynonymous substitution rate at the PBR sites is not constant among the allelic lineages. The deceleration of the rate may be caused by the coexistence of certain pathogens for a substantially long time during HLA evolution.

Discovery of a novel HLA-DRB1*04:05 variant, DRB1*04:05:15, in a Taiwanese and the probable HLA haplotype in association with DRB1*04:05:15

Here, we report a novel HLA-DRB1*04 allele, DRB1*04:05:15, found in a Taiwanese unrelated volunteer bone marrow hematopoietic stem cell donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*04:05:15 is identical to the sequence of DRB1*04:05:01 in exon 2, except the nucleotide at the position 198 where C is substituted by T (TAC→TAT at codon 37). Due to the silent mutation, the nucleotide replacement generated no amino acid variation in comparison with DRB1*04:05:01. We postulate the allele DRB1*04:05:15 was probably derived from DRB1*04:05:01 via a nucleotide point mutation event. The probable HLA-A, -B, -C, -DRB1 and -DQB1 haplotype in association with DRB1*04:05:15 may be deduced as A*02:01-B*48:01-C*08:03-DRB1*04:05:15-DQB1*04:01.

Discovery of the novel HLA-DRB1*04:05:14 allele in a Taiwanese unrelated haematopoietic stem cell donor by a sequence-based typing method

We report here a de novo HLA-DRB1*04 allele, DRB1*04:05:14, discovered in a Taiwanese unrelated volunteer bone marrow stem cell donor by a sequence-based typing method. In exon 2, the DNA sequence of DRB1*04:05:14 is identical to the sequence of DRB1*04:05:01 except the nucleotide at positions 321 where C is replaced by T (at codon 78; TAC→TAT). Due to the silent mutation, the nucleotide substitution produced no amino acid variation in comparison with DRB1*04:05:01. We assume DRB1*04:05:14 was derived from DRB1*04:05:01 via a point mutation. The probable HLA-A, -B and -DRB1 haplotype in association with DRB1*04:05:14 may be deduced as A*11-B*55-DRB1*04:05:14. We here report the Taiwanese ethnicity of DRB1*04:05:14.

Discovery of HLA‐DRB1*03:20 allele in a Taiwanese volunteer hematopoietic stem cell donor and the probable HLA‐A, ‐B, ‐C and ‐DRB1 haplotype in association with DRB1*03:20

The allele HLA-DRB1*03:20, a variant of DRB1*03, was first reported to the IMGT HLA database in April 2001 without indication on the ethnicity of the blood donor (Cell ID: HC 125775). We found a Taiwanese volunteer hematopoietic stem cell donor carries DRB1*03:20 by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:20 is identical to the sequence of DRB1*03:01:01 in exon 2, except a nucleotide substitution at position 341(T→C) (GTT→GCT at codon 85). The nucleotide replacement produced an amino acid variation at residue 85 (V→A). We hypothesize that DRB1*03:20 was probably derived from DRB1*03:01:01 via a nucleotide point mutation event. The probable HLA haplotype in association with DRB1*03:20 was deduced as A*11:02-B*58:01-C*07:02-DRB1*03:20. We here report the Taiwanese/Chinese ethnicity of DRB1*03:20.

Discovery of the novel HLA‐DRB1*09:01:08 allele in a Taiwanese volunteer bone marrow donor and identification of the probable HLA‐A, HLA‐B and HLA‐DRB1 haplotype in association with DRB1*09:01:08

We report here the novel variant of HLA-DRB1*09:01, DRB1*09:01:08, discovered in a Taiwanese volunteer bone marrow donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*09:01:08 is identical to the sequence of DRB1*09:01:02 in exon 2 except a silent mutation at nucleotide position 261(C→T) (GCC→GCT at codon 58). We hypothesize DRB1*09:01:08 was probably derived from DRB1*09:01:02 via a nucleotide point mutation event. The plausible HLA-A, HLA-B and HLA-DRB1 haplotype in association with DRB1*09:01:08 was deduced as A*02:07-B*46:01-DRB1*09:01:08.

MHC class II DR allelic diversity in bighorn sheep

We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA and DRB transcripts from 24 captive BHS (Ovca-DRA and Ovca-DRB) were sequenced. Based on exon 2 (β1 domain) sequences, eight different Ovca-DRB cDNA sequences were identified in BHS. Six of them were 100% identical to previously reported Ovca-DRB genomic DNA sequences. The new alleles DRB*23 and DRB*24, were closely related to two other Ovca-DRB exon 2 genomic DNA sequences. Nineteen out of 24 BHS (79%) Ovca-DRB exon 3 (β2 domain) sequences were 100% identical to exon 3 sequence of DRB1 of DS (Ovar-DRB1). Ovca-DRA full length cDNA sequences exhibited >99% identity. Based upon exon 2 sequences, this BHS herd yielded higher Ovca-DRB allelic diversity than that reported in the previous study. Positively selected amino acid positions were identified in the peptide-binding groove of BHS and DS, but BHS showed more such sites. This highlights differing population histories, and may suggest differing needs for DR peptide-binding specificities. Presence of glutamine at position 52 (52Q) in some of the desert and captive BHS is predicted to alter the efficiency of DR dimerization, which may influence antigen presentation and Th cell activation. Functional assays with unique alleles should reveal whether the presentation of M. haemolytica leukotoxin peptides to Th cells by Ovca-DRB alleles is equivalent to that of Ovar-DRB1 alleles.

Discovery of the novel HLA‐DRB1*16:16 allele in a Taiwanese unrelated bone marrow stem cell donor by a sequence‐based typing method and the probable haplotype associated with DRB1*16:16

We report here a de novo HLA-DRB1 allele, DRB1*16:16, discovered in a Taiwanese unrelated volunteer bone marrow stem cell donor by a sequence-based typing (SBT) method. In exon 2, the DNA sequence of DRB1*16:16 is identical to the sequence of DRB1*16:02:01 except the nucleotides at positions 258 (C→T), 260 (C→A) and 261 (T→G). The nucleotide substitution produced an amino acid replacement at residue 58 (A→E). The formation of DRB1*16:16 was probably generated by a DNA sequence recombination event involving DRB1*11:01:01 and DRB1*16:02:01. The probable HLA-A, -B and -DRB1 haplotype in association with DRB1*16:16 may be deduced as A*02-B*38-DRB1*16:16.

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

Here, we report a novel human leucocyte antigen (HLA)-DRB1 allele, DRB1*03:77, discovered in a Taiwanese unrelated volunteer hematopoietic stem cell donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:77 is identical to the DNA sequence of DRB1*03:01:01 in exon 2 except one nucleotide at position 223 (G→C). The nucleotide substitution caused an amino acid replacement at residue 46 (E→Q). The formation of DRB1*03:77 was thought as the result of a nucleotide point mutation. The probable HLA-A, HLA-B and HLA-DRB1 haplotype in association with DRB1*03:77 may be deduced as A*33-B*58-DRB1*03:77. The donor was a Minna Taiwanese whose ancestors came from mainland China.

Discovery of the novel HLA‐DRB1*10:04 allele in a Taiwanese volunteer bone marrow donor and identification of the probable HLA‐A, ‐B, ‐C and ‐DRB1 haplotype in association with DRB1*10:04

We report here a novel variant of HLA-DRB1*10, DRB1*10:04, discovered in a Taiwanese volunteer bone marrow donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*10:04 differs from DRB1*10:01:01, in exon 2, at nucleotide positions 296 (G fi A) and 303 (T fi G). The nucleotide changes caused an amino acid substitution at amino acid residue 70 (R fi Q). We hypothesize that the formation of DRB1*10:04 was probably the result of a gene recombination event where DRB1*10:01:01 received a minimum length of DNA sequence from DRB1*04:05:01, as the sequence of DRB1*10:04 is identical to DRB1*10:01:01 in exon 2 except the sequence from nucleotide 296 to nucleotide 303, which is identical to DRB1*04:05:01. The plausible HLA-A, -B, -C and - DRB1 haplotypes in association with DRB1*10:04 was deduced as A*01:01-B*37:01-C*06:02-DRB1*10:04.

Three novel alleles at the HLA-DRB1 locus identified by sequence-based typing

We describe here the sequences of 3 new HLA-DRB1 variants officially named DRB1*03:05:03, DRB1*11:10:02, and DRB1*14:86. These novel alleles have been detected in 3 Caucasoid individuals by sequence-based typing. The first and second alleles are the result of a silent mutation, which does not imply any amino acid change. The sequence of DRB1*14:86 exhibits a single nucleotide difference with the allele DRB1*14:01:01 at position 239.

Analysis of DRB1 sequence feature variant type associations with systemic sclerosis autoantibodies types and racial groups (47.28)

Abstract A novel sequence feature variant type (SFVT) approach to genetic association analysis has been previously shown to identify parts of HLA proteins that are associated with the development of a variety of autoimmune diseases. Using the SFVT approach, we analyzed DRB1 typing data in a cohort of patients with Systemic Sclerosis (SSc) and demographically matched controls. We found no allele that was significant at p-value of 0.05 across all the three racial groups (African American, Caucasian and Hispanic) in the dataset. But, we found 23 SFVTs that were significant across the all three racial groups. In the analysis of SFVT association with the presence or absence of different auto-antibodies, we found a large overlap among the top significant sequence features (SFs). In spite of such overlap of SFs the top 100 SFVTs were exclusively associated with the presence of either anti-centromere or anti-topoisomerase but not both, indicating that different DRB1 sequences predispose to the development of different auto-antibody types. In addition, we found that SFVTs that differ by only a few amino acids can give rise to different autoantibodies in SSc patients (e.g. association of the antigen binding motif 67L_70Q_71R with anti-centromere, versus association of 67F_70D_71R with anti-topoisomerase). Tools for the conversion of four-digit HLA typing data into an SFVT data matrix and the calculation of chi-squared association statistics have been implemented in ImmPort (www.immport.org).

Identification of a novel HLA-DRB3*01 variant, HLA-DRB3*0114, containing a DRB1 sequence motif by micro-temperature gradient gel electrophoresis confirmed by sequence-based typing

A novel human leukocyte antigen (HLA)-DRB3*01 allele carrying a HLA-DRB1-specific sequence motive in exon 2 is described.

Sequence-based genotyping of the sheep MHC class II DRB1 locus

The immunopolymorphism database (IPD) provides a single nomenclature for alleles at the major histocompatibility complex (MHC) loci for a range of different species. The minimum requirements for inclusion of a sheep class II DRB1 sequence is a submission that includes all polymorphic sites within the second exon from at least two independent polymerase chain reactions (PCR). In order to meet these requirements, we have developed a DNA-based genotyping method for the rapid analysis of allelic diversity at the DRB1 locus in domestic sheep, Ovis aries. Using a series of primers located within introns flanking exon 2 and genomic DNA from a cohort of 214 sheep representing 15 different breeds and crossbreeds, the complete exon 2 sequences of 38 Ovar-DRB1 alleles were obtained. This sequence resource allowed the development of a generic set of locus-specific primers which amplify a fragment that includes all polymorphic sites within the second exon. Bidirectional sequence analysis of the PCR product provides a composite sequence where each polymorphic site is represented by the corresponding International Union of Biochemistry nucleotide code. A Basic Local Alignment Search Tool search of alleles held within the IPD or National Center for Biotechnology Information databases allows individual allele sequences to be identified. Low levels of homozygosity (7.48%) within the cohort and verification of previously genotyped samples confirmed the broad allelic specificity of this method. It improves on currently available methods and is broadly applicable to the analysis of MHC diversity in studies investigating linkages with resistance or susceptibility to disease.

Identification of a novel HLA‐DRB allele, HLA‐DRB1*1461

We describe the identification of a new DRB1*14 allele, DRB1*1461, found in a Chinese individual. The novel allele has been identified in routine polymerase chain reaction-sequence-specific oligonucleotide and sequence-based typing. The nucleotide sequence of DRB1*1461 is identical to DRB1*1404 except for a single substitution in codon 16 (TAT-->CAT), leading to a change from Tyr to His.

Identification of two novel HLA‐DRB1*11 alleles (DRB1*110404 and DRB1*1161) in two Italian cord blood units

We describe the isolation and characterization of two novel HLA-DRB1*11 alleles, officially named DRB1*1161 and 110404. These two new variants were both identified in two Caucasoid individuals. The exon 2 sequence of DRB1*1161 is identical to that of DRB1*110101 except at codon 41, where a nucleotide substitution (GAC>AAC) is responsible for an amino-acidic change from Asp to Asn. The exon 2 sequence of the second novel allele described here, DRB1*110404, differs from that of DRB1*110401 only at codon 34 where the nucleotidic change CAA>CAG gives rise to a silent mutation.

Characterization of a novel HLA‐DRB1*04 allele (DRB1*0460) in the Italian population

We report the identification of a novel HLA-DRB1*04, officially named DRB1*0460. It was detected during performing HLA-DRB1 high resolution typing by DNA sequencing-based method. The exon 2 nucleotide sequence of DRB1*0460 is identical to that of DRB1*040301 except at codon 63 (AGC-->AAC), changing the encoded serine to asparagine.

Characterization of a novel DRB1*14 allele (DRB1*1449) in the Han‐Chinese population

We report here a novel human leukocyte antigen (HLA) allele, DRB1*1449, in the Han-Chinese population. The nature of the new allele was confirmed by the sequencing-based typing (SBT) method. Genomic DNA and six subclones containing DNA fragment of DRB1 exon 2 were sequenced in both forward and reverse directions. The exon 2 nucleotide sequence of DRB1*1449 is closely related to DRB1*1432 allele based on sequence homology. It has four nucleotide (nt) substitutions at positions 71, 196, 244 and 245 in exon 2, which lead to changes of amino acid sequences. The serological assignment of DRB1*1449 is DR14 based on the serological HLA typing result. This novel allele might be a result of recombination between DRB1*1402 and DRB1*140101 like alleles, which are very common among Chinese population.

HLA‐DRB1 alleles and Jka immunization

In transfusion medicine, anti-Jk(a) has been implicated in hemolytic transfusion reactions. Development of anti-Jk(a) after transfusion does not always occur after Jk(a-) patients receive at least 1 unit of Jk(a+) blood unit. This study was designed to identify HLA-DRB1 alleles associated with predisposition to Jk(a) immunization after blood transfusion or pregnancy. Genotyping by polymerase chain reaction and sequence-specific oligonucleotide probe nonradioactive hybridization/sequence-specific primers was performed in 20 Jk(a)-immunized patients and 200 controls from the same southern European population. Genotyping showed that HLA-DRB1*01 was significantly more frequent in Jk(a)-immunized patients than controls: 55 percent versus 17 percent (odds ratio [OR], 5.9; confidence interval [CI], 2.3-15.5; corrected p value<0.05). Because HLA-DRB1*0101, DRB1*0102, and DRB1*1001 share a common sequence in their B1 chain, that is, F in 13, R in 71, and A in 74, HLA genetic predisposition was analyzed by comparing patients and controls with respect to the distribution of F13/R71/A74-positive and -negative alleles. Results demonstrated greater positivity of the F13/R71/A74 sequence (DRB1*0101, *0102, or *1001) in patients than in controls: 65 percent versus 19.5 percent (OR, 7.7; CI, 2.9-20.5; p<0.001). In conclusion, HLA-DRB1*0101, DRB1*0102, and DRB1*1001, which share a common DRB1 sequence, appeared to be overrepresented in Jk(a)-immunized patients.