Identification of a novel HLA-DQA1 allele (DQA1*0106) by sequence-based DQA1 typing

We report here a novel DQA1 allele (DQA1*0106) identified during sequence-based HLA-DQA1 typing. Polymerase chain reaction with proofreading pfu DNA polymerase and subsequent sequencing yielded identical results as that with Taq DNA polymerase. Molecular cloning and sequencing confirmed that the new DQA1 allele is identical to DQA1*01021/2 at exon 2 except for a single nucleotide substitution (ACT-->GCT), changing codon 44 from Thr to Ala. This is the first report of polymorphism at codon 44 of HLA-DQA1 alleles.     

Identification of a novel DRB1 allele, DRB1*1112, by sequence-based DRB typing

We report here a novel DRB1 allele (DRB1*1112) identified during sequence-based HLA-DRB typing. Polymerase chain reaction with generic DRB primers and group-specific primers and subsequent sequencing yielded identical results. Molecular cloning and sequencing confirmed that the new DRB1 allele is identical to DRB1*11011 and 1129 at exon 2 except for a single nucleotide substitution at codon 37, changing the codon from Tyr (DRB1*11011) or Ser (DRB1*1129) to Phe.     

A new HLA-DRB1*11 allele, DRB1*1144, identified by cloning and sequencing

We report here the identification of a novel DRB1*11 allele, DRB1*1144, identified during sequence-based HLA-DRB1 typing. Molecular cloning and direct sequencing confirmed that the new allele is identical to DRB1*110401 at exon 2, except for a single nucleotide substitution (GTG-->GCG) changing codon 38 from Valine to Alanine.     

Identification of two novel DQA1 alleles, DQA1*0107 and DQA1*0602, by sequence-based typing in the GoKinD population

Two novel DQA1 alleles, DQA1*0107 and DQA1*0602, were discovered using DQA1 sequence-based typing (SBT) in participants in the Genetics of Kidneys in Diabetes (GoKinD) Study. The DQA1*0107 allele, found in three unrelated Caucasian participants, contains a novel polymorphism at codon 79 of exon 2 (CGC→TGC), which results in an amino acid change from an arginine to a cysteine. The participants containing this novel polymorphism also had a 1-bp insertion in intron 2 that is common to the *01 alleles. The DQA1*0602 allele, found in one Caucasian participant, contains a novel polymorphism at codon 139 of exon 3 (AGC→CGC), which results in an amino acid change from a serine to an arginine. Additionally, the *0602 allele has a base change in intron 1 that is common to the *06 alleles. Both new alleles were isolated using single-allele amplification SBT and confirmed using sequence-specific primer amplification.     

High resolution sequence-based DPB1 typing identified two novel DPB1 alleles,DPB1*9401 and DPB1*9501, from a Kenyan population

Two novel DPB1 alleles, DPB1*9401 and DPB1*9501, were identified from a Kenyan population during sequence-based HLA-DPB1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPB1 alleles is identical to DPB1*0402 at exon 2 except for a single nucleotide substitution (CGG -->TGG), changing codon 70 from Arg to Trp. The new allele has been named DPB1*9401. This is the first report of polymorphism at codon 70 of HLA-DPB1 alleles. New codon combinations have been identified in another novel DPB1 allele named DPB1*9501. The extensive diversity at DPB1 locus of this East African population is being revealed by high resolution sequence-based DPB1 typing.     

High-resolution sequence-based DPA1 typing identified two novel DPA1 alleles, DPA1*010303 and DPA1*0303, from a Kenyan population

We report here two novel DPA1 alleles, DPA1*010303 and DPA1*0303, identified from a Kenyan population during sequence-based HLA-DPA1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPA1 alleles is identical to DPA1*010301 at exon 2, except for a single nucleotide substitution (ACG ACC) at codon 15. The new allele has been named by the WHO Nomenclature Committee as DPA1*010303. The second novel DPA1 allele is identical to DPA1*0301, except for a single nucleotide difference (GAA GAC) at codon 28 that changed the amino acid from Glu to Asp. The new allele has been named by the WHO Nomenclature Committee as DPA1*0303. Identification of the two novel DPA1 alleles reflects the genetic diversity of this East African population.     

Identification of a novel HLA-DRB1 allele,DRB1*0108, by sequence-based DRB typing in two siblings

We report here a novel DRB1 allele identified during sequence-based HLA-DRB typing. This allele was detected during routine HLA typing of a patient and his family prior to bone marrow transplantation. The new allele, DRB1*0108, was found in the patient and in a brother. Molecular cloning and sequencing confirmed that the new DRB1 allele is identical to DRB1*0101 at exon 2 except for a single nucleotide substitution at codon 37 (TauCC-->TauAlphaC), changing the encoded serine to tyrosine. This position of the beta1 domain lies in the floor of the antigen-binding groove and shows the highest polymorphism among DRB1 alleles.     

Identification of a novel DR4 allele, DRB1*0442

A new DRB1 allele encoding DR4, DRB1*0442, was identified in three Caucasian siblings by reverse in-line hybridization and defined by sequencing based typing. The DRB1*0442 allele differs from DRB1*0404 by a single nucleotide at position 227 (T-->A) of codon 47 in exon 2. At the amino acid level, this substitution results in a change from tyrosine to phenylalanine. Serologically, the new allele appears to retain the DR4 antigenicity; however, this substitution may affect peptide-binding specificity.     

Identification of a novel DPA1 allele, DPA1*010602, in an East African population

We report here a novel DPA1 allele, DPA1*010602, which was identified from an East African population during sequence-based human leukocyte antigen DPA1 typing. Through cloning and sequencing of multiple clones we confirmed that the new allele is identical to DPA1*010301 at exon 2 with the exception of two nucleotide substitutions (ATG to CAG) at codon 31. The substitutions changed the amino acid at codon 31 from methionine to glutamine. The World Health Organization nomenclature committee named the new allele DPA1*010602.     

Molecular and serological identification of the HLA-A*3404 allele

A novel HLA-A null allele, A*0253 N, has been identified in two generations of a Chinese family using combined serological and molecular cloning approaches. Full-length genomic DNA sequencing indicated that this new allele differs from HLA-A*02011 by a single C to G substitution at nucleotide position 324 in exon 2. This mutation results in an amino acid change from a tyrosine codon to a stop codon at position 108. A PCR-SSP based method was developed to distinguish A*0253 N from A*02 alleles. No further individuals of A*0253 N were found in 718 Chinese blood donors who carry the HLA-A*02 allele1.     

A novel DRB1*13 allele (DRB1*1327) on a DR17, DQ2 haplotype with a DRB1*0301 sequence motif in the 2nd hyperpolymorphic region

In a sample from a Netherlands Caucasian, we found a new DRB1*13 allele ( DRB1*1327 ). The nucleotide sequence of the second exon of the novel allele was identical to DRB1*1301 except for a single productive base substitution changing codon 26 from TTC to TAC, encoding phenylalanine and tyrosine, respectively. The new allele shares sequence with DRB1*03011 from codons 5 to 66. The haplotype carrying the new allele was, from known linkage disequilibria, deduced to be DRB1*1327, DRB3*0101, DQA1*05011, DQB1*0201 , i.e. similar to the DR17, DQ2 haplotype, which suggests that the DRB1*1327 allele has arisen by a double recombination event between a DR13 donor haplotype and a DR17, DQ2 recipient haplotype.     

Novel associations among HLA-DQA1 and -DQB1 alleles, revealed by high-resolution sequence-based typing (SBT)

Althought it is a valuable tool for the identification of HLA alleles, sequence-based typing (SBT) presents difficulties when used to determine HLA-DQA1 and -DQB1 alleles. Specifically, some HLA-DQA1 alleles have a three-base deletion at codon 56 of exon 2 that interferes with the sequencing read. Moreover, the frequently used primers for HLA-DQB1 may co-amplify the HLA-DQB2 pseudogene. To overcome these problems, we amplified DQA1 exon 2 using five group-specific polymerase chain reactions (PCRs) which allowed separation of deleted from non-deleted DQA1 alleles. DQB1 exon 2 was amplified using two group-specific amplifications. To increase typing resolution, we also analyzed DQA1 exons 1, 3 and 4 and DQB1 exon 3 by PCR using sequence-specific primers (PCR-SSP) or SBT analysis. Using this method we found some important associations between DQA1 and DQB1 alleles: DQA1*05011 and DQB1*0201, DQA1*0505 and DQB1*03011, DQA1*01021 and DQB1*06, DQA1*01022 and DQB1*0502.     

Immunogenetics of a new HLA-B null allele, HLA-B*4423N.

The second example of an HLA-B*44 null allele (B*4423N) was identified by discrepancies between serological and polymerase chain reaction-sequence-specific primer (PCR-SSP) typing in two north-western European Caucasoid unrelated stem cell donor volunteers. HLA-B*4423N was identical to B*440201 except for a single nucleotide substitution at position 493 in exon 3, resulting in a premature stop codon at bases 493-495 (TAG rather than CAG at codon 141). As expected, comprehensive serological testing using 54 antisera, directed towards B44 or Bw4, failed to identify the HLA-B44 (Bw4) specificity. The B*4423N-bearing haplotype was identified as A*0201, Cw*0501, DRB1*0408, DRB4*01, DQA1*03, DQB1*0304 and the frequency of B*4423N estimated as 0.00006 (carriage frequency 0.0121%) in 16 533 subjects resident in Wales.     

Identification of a novel human DRB1*13 allele by sequence-based DRB typing

Herein, we report on a novel DRB1 allele (DRB1*1368) identified during sequence-based HLA-DRB typing. This new DRB1 allele is identical to DRB1*1301 at exon 2 except for a single-nucleotide substitution at codon 37, changing the amino acid Asn to Asp.     

Immunogenetics of a new HLA‐B null allele,HLA‐B*4423N

The second example of an HLA‐B*44 null allele (B*4423N) was identified by discrepancies between serological and polymerase chain reaction–sequence‐specific primer (PCR‐SSP) typing in two north‐western European Caucasoid unrelated stem cell donor volunteers. HLA‐B*4423N was identical to B*440201 except for a single nucleotide substitution at position 493 in exon 3, resulting in a premature stop codon at bases 493–495 (TAG rather than CAG at codon 141). As expected, comprehensive serological testing using 54 antisera, directed towards B44 or Bw4, failed to identify the HLA‐B44 (Bw4) specificity. The B*4423N‐bearing haplotype was identified as A*0201, Cw*0501, DRB1*0408, DRB4*01, DQA1*03, DQB1*0304 and the frequency of B*4423N estimated as 0.00006 (carriage frequency 0.0121%) in 16 533 subjects resident in Wales.     

Four novel human leukocyte antigen-DQA1 alleles identified in the Korean population

Four novel human leukocyte antigen (HLA)-DQA1 alleles have been characterized by direct DNA sequencing of coding exons 1-4. All the novel alleles exhibited a single nucleotide substitution either in exon 3 or in exon 4 when compared with previously defined alleles. Thus, it is likely that alleles were generated by point mutation from pre-existing alleles in the population. Substitutions resulted in either a silent (DQA1*010203) or an amino acid change (DQA1*0506, DQA1*0507, and DQA1*0508). The substituted sites were both previously known polymorphic and conserved positions. Putative haplotypes associated with the novel alleles were deduced based on the HLA types shared by the individuals carrying a novel allele or from previously reported population data.     

Description of a new HLA-DRB1*1104, DRB1*110403

We report here the exon 2 sequence of the novel HLA-DRB1*110403 which differs from DRB1*110401 by a single synonymous nucleotide substitution at codon 78, where TAC is substituted by TAT. The variant originally identified in a Caucasoid individual was confirmed by cloning and sequencing.     

Identification of a new HLA-DRB1 allele,DRB1*0321

This communication reports the identification of a new HLA-DRB1*03 allele identified in three members of a Caucasian French family. This new allele has been officially named HLA-DRB1*0321 by the World Health Organization Nomenclature Committee. The complete exon 2 sequence of DRB1*0321 is identical to that of DRB1*0307 except for the first and second nucleotides of codon 37 (TT replacing AA), which lead to the substitution of a tyrosine for a phenylalanine (AAC-->TTC at position 37). The family study showed that this new allele was transmitted into the HLA-A*0101/09, -B*0801/14, -Cw*0701, -DRB1*0321, -DRB3*0101, -DQB1*0503 and -DPB1*0401 haplotype. The complete exon 2 sequence of this new allele has been previously deposited in the EMBL Sequence Database under accession number AF297266.     

Identification of a novel HLA-DRB1 allele, HLA-DRB1*1217, in a Korean individual

We report a new DRB1 allele, DRB1*1217, identified by direct sequencing of a bacterial artificial chromosome (BAC) clone originated from genomic DNA of a Korean donor. DRB1*1217 differs from previously reported DRB1*120201 by a single nucleotide substitution, which results in an amino acid change at codon 67 [TTC→ATC (F>I)].     

HLA-DRB1*0403 is associated with dominant protection against IDDM in the general Dutch population and subjects with high-risk DQA1*0301-DQB1*0302/DQA1*0501-DQB1*0201 genotype

Insulin-dependent (Type 1) diabetes mellitus (IDDM) is a genetically controlled T-cell mediated autoimmune disease. Recently, subtyping of HLA-DRB1*04 identified the HLA-DRB1*0403 allele to be associated with protection in Caucasoids with the highest risk heterozygous genotype DQA1*0301-DQB1*0302/DQA1*0501-DQB1*0201. Some studies confirmed this finding, but other reports were not consistent with a dominantly protective trait. We here report the frequency of HLA-DRB1*0403 in a large cohort (n=200) of Dutch patients with IDDM, their first-degree family members (n=370), and random controls (n=420) of the general population in The Netherlands. We found that HLA-DRB1*0403 is strongly associated with dominant protection against development of IDDM in unrelated subject, even in the context of the highest risk HLA-DQ phenotypes and HLA-DR4-DQB1*0302 (P < 0.0001).