Identification of new DRB1*07 (DRBl*0703), DRB1*08 (DRB1*0817) and two DRB3* (DRB3*0302 and DRB3* 01014) alleles

Abstract: We report here the identification of four novel DRB alleles using a reverse hybridization (CANTYPE) assay. Molecular cloning and sequencing confirmed the initial unusual hybridization patterns. All four new alleles were detected during routine HLA typing for the Canadian Unrelated Bone Marrow Donor Registry. DRBl*0703 is identical to DRB1*0701 except for a single nudeotide substitution (AGA→AGT), changing codon 29 from Arg to Ser, a so far undetected DRB polymorphism. DRB1*0817 differs from DRBl*0801 by a single nucleotide substitution (TAC→TTC), changing codon 47 from Tyr to Phe. This polymorphism has not, until now, been identified in DRB1*08 alleles. Compared with DRB3*0301, DRB3*0302 contains a single nucleotide substitution (TAC→CAC) at codon 30, changing the encoded Tyr to His. This polymorphism is typical for DRB3*02 alleles. DRB3*01014 is identical to DRB3*0101 except for a single silent nucleotide substitution (GGG→GGA) at codon 84. This polymorphism has previously only been described for the DRB1*15012 allele. DRB1*0817, DRB3*0302 and DRB3*01014 may have arisen from gene conversion, but DRB1*0703 most likely was generated by a point mutation event. The DRB3*0302 allele was detected in two unrelated subjects, while the other three have each only been detected once.     

Identification of three new DRB3* (DRB3*0106, DRB3*0107 and DRB3*02022) alleles

Three novel DRB3* alleles were identified using CANTYPE reverse hybridization assay. The initial unusual hybridization patterns of DRB3-specific polymerase chain reaction (PCR)-amplified DNA from each subject were confirmed by cloning and sequencing analysis. DRB3*0106 allele is identical to DRB3*0101 except for a single nucleotide substitution (CTG-->GTG) changing codon 38 from Leu to Val. This polymorphism is commonly found in DRB3*03 alleles. Compared with DRB3*0202, DRB3*02022 contains a single silent nucleotide substitution (AAT-->AAC, both encoding for Asn) at codon 77. This polymorphism is also present in DRB3*0204 allele. The new DRB3*0107 allele has a sequence unique to DRB3 alleles. From codon 5 to codon 36 the sequence is identical to that of DRB3*0101 allele. From codon 37 to codon 87 the sequence of DRB1*0107 allele is identical to that of DRB3*0202. This sequence would thus explain the CANTYPE(R) DRB3-specific unusual pattern of reactions. The new DRB3*0107 could have arisen from a gene conversion between DRB3*0101 and DRB3*0202 alleles, but the DRB3*0106 and the DRB3*02022 may have been generated by a point mutation event. The DRB3*0107 allele was identified in a Caucasoid individual. The ethnic origin of the subjects carrying the other two alleles are unknown. The three alleles presented here were only identified once, in a total population of 49,000.     

A novel DRB3 allele (DRB3*0208), a new allelic variant of DRB1*1502 (DRB1*15023) and two new DQB1 (DQBl*03012 and DQB1*0614) alleJes

Abstract: Four novel HLA Class II alleles were identified using CANTYPE reverse hybridization assay. The initial unusual SSO hybridization patterns were confirmed by cloning and sequencing analysis. DRB3*0208 allele is identical to DRB3*0202 except for three nucleotide substitutions (GAT→ AGC) changing codon 57 from Asp to Ser. This polymorphism has so far been undetected in DRB3 alleles. DRB1*15023 differs from DRB1*15021 by a single silent nucleotide substitution (AAC→AAT, both encoding for Asn) at codon 33. This polymorphism has not, until now, been identified in DRB alleles. Compared with DQB1*03011, the novel DQB1*03012 contains a single silent nucleotide substitution (GCA→GCG, both encoding for Ala) at codon 38. Finally, DQB1*0614 allele is identical to DQB1*0603 except for a single nucleotide substitution (TAC→ TTC), changing codon 9 from Tyr to Phe. Polymorphisms observed here in the DQB1*03012 and DQB1*0614 alleles are present in several of the known DQB1 alleles. DRB3*0208, DQB1*03012 and DQB1*0614 may have arisen from gene conversion, but the DRB1*15023 most likely was generated by a point mutation event. DQB1*0614 was detected in three related subjects, while each of the other three new alleles has only been detected once.     

Identification of three novel alleles: DRB3*0110, DRB1*1140, and DRB1*140102

Three novel human leukocyte antigen class II alleles (DRB3*0110, DRB1*1140, and DRB1*140102) are described here. The three novel alleles were initially detected as previously unidentified SSO hybridization patterns using CANTYPE((R)) reverse hybridization assay. Sequences were determined by cloning/sequencing. DRB3*0110 allele is identical to DRB3*010101, except for a single nucleotide substitution (CGC-->AGC) changing codon 39 from Arg to Ser. This polymorphism has not, until now, been identified in DRB allele. Thus, this is an unusual mutation as the codon 39 is a fairly conserved region. The new DRB1*1140 is identical to DRB1*1116, except for a single nucleotide substitution at codon 67 from ATC (encoding for isoleucine) to TTC (encoding for phenylalanine). This polymorphism is commonly found in DRB1*11 alleles. Compared with DRB1*140101, DRB1*140102 contains a single silent nucleotide substitution (TAT-->TAC, both encoding for tyrosine) at codon 78. This polymorphism is commonly found in DRB1*14 alleles. The three new DRB alleles may have been generated by a point mutation event. The DRB3*0110 and DRB1*140102 were identified in Caucasoid individuals. The ethnic origin of the subject carrying the DRB1*1140 allele is Egyptian. The DRB1*140102 was detected in two unrelated individuals; the DRB3*0110 and DRB1*1140 were only identified once, in a total population of 80,000.     

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.     

Novel HLA-DRB1 alleles revealed by sequencing based typing,DRB1*04053 and DRB1*1143

We report the discovery of two HLA-DRB1 alleles by sequencing based typing (SBT). DRB1*04053 differs from previously reported DRB1 alleles by a single synonymous nucleotide substitution, resulting in a unique polymorphism at codon 93. DRB1*1143 differs from previously identified DRB1 alleles by a single non-synonymous nucleotide substitution, resulting in a polymorphism observed in other DRB1 and DRB3 alleles1.     

A novel HLA-DRB1 sequence, DRB1*11272

We describe the complete exon 2 sequence of a novel HLA-DRB1 allele, DRB1*11272. This allele differs from the DRB1*11271 allele by a synonymous mutation in codon 77 where an AAT is replaced with AAC, both encode for the amino acid asparagine. The same motif at codon 77 has also been found in DRB1*1107, DRB1*1333, DRB1*0422 and in most DRB1*03 alleles. A partial exon 2 sequence of this allele has previously been deposited in the EMBL Sequence Database under the accession number AF186407.     

Identification of a novel DRB1-allele (DRB1*0106) by sequence-based typing

We report herein the identification of a new DRB1 allele using sequence-based typing. The new allele, DRB1*0106, was detected during routine HLA typing of a patient undergoing bone marrow transplantation. DRB1*0106 is identical to DRB1*0101 except for two codons, 71 (AGG-->GCG) and 86 (GGT-->GTG), changing the encoded arginine to alanine and glycine to valine. Both sequences were confirmed by polymerase chain reaction with sequence-specific primers (PCR-SSP). The polymorphism at codon 71 has not been, until now, identified in DRB1*01 alleles, although it is present in all the DRB1*15 alleles as well as DRB1*1309 and DRB1*1424.     

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.     

Description of three novel HLA-DRB3 alleles: DRB3*010105, DRB3*0112 and DRB3*0113

This communication describes three novel DRB3 alleles whose exon 2 sequences are identical to that of DRB3*010102 except for a single nucleotide substitutions. Comparing with DRB3*010102, the sequence of DRB3*010105, DRB3*0112, and DRB3*0113 differ at codon 31 (TTC -> TTT), codon 84 (GGG -> CGG; Gly -> Arg), and codon 37 (TTC -> CTC; Phe -> Leu), respectively.     

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.     

Six newly identified HLA-DRB alleles: DRB1*1121, *1419, *1420, *1421, DRB3*0203 and DRB5*0103

Seven samples with irregular PCR-SSO hybridization patterns, observed during routine HLA-DRB typing, were studied in more detail. Group-specific amplification, followed by hybridization with relevant SSOs strengthened the suggestion that these samples contained new DRB alleles. DRB exon 2 segments were amplified, cloned and sequenced and revealed: DRB1*1121 [MUL] is similar to DRB 1*1102 in which codon 85 changed from GTT(V) into GTC(A); DRB1*1419 [AKKAL] is similar to DRB1*1402 with codon 71 changed from AGG(R) into AAG(K); DRB1*1420 [OND-52971] is a DRB1*1406 with codon 37 changed from AAC(N) into TTC(F); DRB1*1421 [TGI] is similar to DRB1*1417 with codon 71 changed from AGG(R) into AAG(K); DRB3*0203 [POS] is similar to DRB3*0202 in which codons 37–38 are changed from TAC GCG(YA) into TCC GTC(SV); DRB5*0103 was found in two unrelated individuals of Oriental origin [IND-24 and IND-59] and is similar to DRB5*0102 in which codon 71 AGG(R) changed into ACG(T). This particular sequence variation at position 71 has not yet been described. The new DRB sequences were confirmed using the sequencing based typing technique. Low resolution PCR-SSP typing failed to amplify two of the DRB1*14 variants, whereas high resolution PCR-SSP resulted in aberrant patterns. Class II alloantisera identify the codon 71 changes in DRB1*1419 and *1421 with respect to the MC1('DR1+DR4') epitope.     

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.     

A novel DRB1*04 allele

Discovery of the novel DRB1*0464 allele is described. This allele contains a nucleotide substitution in codon 13 that changes the amino acid histidine coded for in all other DRB1*04 alleles to tyrosine. This allele was found in a parent and one child of a North American Caucasian family with the haplotype: A*03, B*07, DRB1*0464, DRB4*0103, DQB1*0301.     

Novel HLA-DRB1 alleles discovered during routine sequencing based typing,DRB1*03052, DRB1*04032, DRB1*1139 and DRB1*1346

We report the discovery of four HLA-DRB1 alleles during routine sequencing based typing (SBT). These alleles--DRB1*03052, DRB1*04032, DRB1*1139 and DRB1*1346--differ from previously identified DRB1 alleles by known nucleotide polymorphisms.     

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*04 allele: DRB1*0445

The novel allele DRB1*0445 differs from DRB1*04051 by a single nucleotide substitution at codon 23 (CGG-->CCG), resulting in an amino-acid change from arginine to proline. The haplotype associated with the novel allele is A*2402-B*5401-Cw*0102-DRB1*0445-DRB4*01-DQB1*0302.     

Identification of three new DRB1 alleles,DRB1*0107, *0425 and *13012 and confirmation of DRB4*01033

The characterization of three novel DRB1 alleles is described, DRB1*0107, DRB1*0425 and DRB1*13012 as well as confirmation of DRB4*01033. Two alleles, DRB1*0107 and *0425, showed amino acid differences with previously identified HLA molecules. In DRB1*0107, the glutamine at position 10 was substituted by a glutamic acid. DRB1*0425 showed one amino acid difference with DRB1*0418 (I to F) at position 67, and five amino acid differences with DRB1*04011 at positions 67 (L to F), 70 (Q to D), 71 (K to R), 74 (A to L) and 86 (G to V). The alleles DRB1*13012 and DRB4*01033 had protein sequences identical to DRB1*13011 and DRB4*01031/01032, respectively. Nucleotide differences were present at position 306 for DRB1*13012 and at position 321 for DRB4*01033.