New HLA-A allele, A*0339, identified in a Spanish patient

A novel human leukocyte antigen-A allele, officially named A*0339, was found in a patient when sequence-based typing was carried out for unrelated stem cell donor search. A*0339 differs from A*03010101 in a point mutation at codon 102 (GAC→TAC), generating an exchange of amino acid from Asp to Tyr.     

HLA-B*4413 identified in a UK Caucasoid potential bone marrow donor

We describe a novel allele belonging to the B*44 allele group. HLA-B*4413 was identified in a Caucasoid potential bone marrow donor from the Anthony Nolan Bone Marrow Trust register. Initial HLA typing of this donor revealed unusual serological reactivity. Further investigation was carried out by reference strand conformation analysis (RSCA) and sequence-based typing (SBT) using DNA extracted from an Epstein-Barr virus (EBV)-transformed B-cell line made from this donor (AMI005AN). In this individual, two B*44 alleles were revealed upon initial investigation: B*4409 and a previously unseen allele which has been named B*4413. B*4413 is identical to B*44031 except for a unique nucleotide substitution resulting in an amino acid difference at residue 61 in the alpha1 helix.     

A novel HLA-A allele: A*0257

A novel human leucocyte antigen-A*02 (HLA-A*02) allele was detected by reference strand-mediated conformation analysis (RSCA) of a DNA sample from a Tarahumara individual. Direct sequencing of HLA-A locus polymerase chain reaction products identified a mutation in one of the alleles. Cloning and sequencing confirmed the presence of a new allele, A*0257 which differed from A*0206 by two nucleotides at positions 355 and 362, inducing changes in residues 95 and 97, respectively, within the peptide-binding site. Those changes suggest that allele A*0257 may have resulted from an intralocus recombination event.     

Identification of a novel HLA-A*02 allele, A*027401*

A novel HLA-A*02 allele was detected in a Caucasian patient from central Italy, requiring a hematopoietic cell transplantation. Direct sequencing identified a variation in one nucleotide position, which was confirmed by cloning. The name A*027401 was officially assigned by the WHO Nomenclature Committee in November 2004. A*027401 differs from A*02010101 by a single G to A substitution at nucleotide position 595 in exon 3. The new variant would lead to a nonsynonymous nucleotide change (GGG to AGG) at codon 175, resulting in a basic Arg in the alpha-helix of the alpha2-domain, in place of a non-polar Gly. The presence of an uncommon variation at a highly conserved nucleotide position could have implications in unrelated hematopoietic cell transplantation.     

Identification of HLA-B*56 variant (B*560502) in the Korean population

We report here a new HLA-B*56 allele, B*560502, identified by sequencing-based typing in the Korean population. HLA-B*560502 differs from B*560501 by a single nucleotide at position 141 in exon 2 (T(r)C). This single nucleotide substitution may not result in an amino acid difference in the alpha1 domain at residue 23. The putative haplotype involving B*560502 may be A*24-DRB1*1201-DQA1*0503-DQB1*0304-DPB1*0202.     

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 novel DRBI*13 (DRB1*1333), DRB1*04(DRB1*0426) and DRB5* (DRB5*0109) alleles

Abstract: Three novel HLA class H alleles (DRB1*1333, DRB1*O426, DRB5*0109) are described here. The 3 novel alleles were initially detected as previously unidentified SSO hybridization patterns using the CANTYPE reverse hybridization assay. Sequences were determined by cloning/sequencing. DRB1*1333 is identical to DRB1*1303 except for a single nucleotide substitution (ACC→AAC), changing codon 77 from Thr to Asn. This polymorphism is typical for DRB1*03 alleles. DRB1*0426 is identical to DRB1*0401 except for a single nucleotide substitution (GCC→ACC) at codon 58, changing the encoded Ala to Thr. DRB5*0109 is identical to DRB5*0101, except for a single nucleotide substitution (GAC→AAC), changing codon 70 from Asp to Asn. Both latter polymorphisms were so far undetected in DRB alleles. DRB1*1333 could have arisen from a gene conversion event, but DRB1*0426 and DRB5*0109 most likely were generated by point mutation events. For all 3 alleles, the sequence was confirmed by the original hybridization pattern (DRB1*1333) or by hybridization to a newly designed probe (DRB1*0426 and DRB5*0109). Ethnic backgrounds were Lebanese for DRB1*1333 and Caucasian for DRB1*0426 and DRB5*0109.     

应用毛细管参考链介导的构象分析法进行HLA-DR4等位基因分型

目的应用毛细管参考链构象分析法对HLA—DR4进行等位基因分型,并与测序分型结果相比较,评价该方法的准确性及实用性。方法首先应用FAM标记的引物扩增HLA-DRBl等位基因为纯合型的样本DRB1*0803、DRB1*0901的第二外显子作为参考链,与标准样品HLA-DR1第二外显子杂交获得异源双链,借助测序仪通过毛细管电泳建立中国人HLA-DR48个高频率等位基因的标准迁移率,再对30例DR4样本进行分型,并与测序分型法检测结果进行比较。结果30例样本中28例与测序法测得的等位基因结果一致。结论毛细管参考链介导的构象分析法具有准确性高、分辨率高的优势,与测序法相比具有成本低、高通量的特点,值得在移植、相关疾病等领域的HLA分型中推广应用。     

Identification of HLA-A*0249 and confirmation of A*2615

A new HLA-A*02 allele, A*0249, and the confirmatory sequence of A*2615 are here reported. Both alleles were detected by irregular patterns during routine molecular typing. A*0249 showed two mismatches with A*02011 in exon 3 at positions 538 and 539, changing amino acid 156 from leucine to arginine. Remarkable was a mismatch in exon 4, at position 779, where the C of A*0201 was changed to A in A*0249. As A*0209 has the same substitution, A*0249 may have arisen from A*0209. The A*2615 allele was identical to A*2601 in exons 2 and 3 except for a single nucleotide difference at nucleotide position 180, changing codon 36 from phenylalanine to leucine. This is a unique amino acid change, as in all the class I alleles a phenylalanine was identified at this position.     

HLA-A*02 subtype distribution in Caucasians from northern Italy: identification of A*0220

This study describes a comprehensive, easy to perform PCR-SSOP typing approach suitable for complete genomic subtyping of HLA-A*02. A single 1.6 kb PCR–amplificate spanning exons 2,3 and 4 of the HLA-A*02 gene was used for hybridization with a panel of twenty-four SSOPs. This allowed unequivocal assignment of all so far known HLA-A2 subtypes, including A*0209 and A*0215N which differ for nucleotide substitutions in exon 4, without the need for two separate amplifications. Using this approach, HLA-A*02 subtype distribution was analyzed in 218 samples from unrelated, healthy individuals from northern Italy enrolled in the Italian Bone Marrow Registry and typed as HLA-A2 by serology or generic molecular analysis. As expected, A*0201 was found in the majority (92.6%) of samples. However, a significant number (6.8%) of individuals carried A*0205. Furthermore, A*0202, A*0208, A*0209 and A*0217, so far not described in Caucasians, were detected in a low number of samples (frequency ranging from 0.45% to 1.8%). Finally, a novel HLA-A*02 subtype, A*0220, was detected in 0.9% of the samples. As confirmed by DNA sequencing of exons 2 and 3, this allele is identical to A*0201 except for a single nucleotide substitution in codon 66 which changes the predicted amino acid sequence form Lys to Asn. The findings of this study have implications for the selection of HLA-A*02+ donors in unrelated bone marrow transplantation and of patients for specific immunotherapy with HLA-A*02 restricted peptide vaccines.     

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.     

Sequence analysis of the novel HLA-Cw*08 variant allele, Cw*0820, in a Chinese Han individual

A novel human leukocyte antigen (HLA) allele, HLA-Cw*0820, was identified in a Chinese Han individual. It differs from the closest allele Cw*080101 by single nucleotide change at genomic nucleotide (nt) 1615 G>A (coding sequence nt 652 G>A, codon 194 GTC>ATC) in exon 4, which results in an amino acid change Val194Ile.     

A new HLA-B*51 variant, B*5158, identified by sequence-based typing in a Korean individual

A novel human leukocyte antigen (HLA)-B*51 allele, officially named HLA-B*5158, was identified in the cord blood from Korean. HLA-B*5158 allele shows single nucleotide difference from B*510101 in exon 2 at nucleotide position 214 (C/T), resulting in an amino acid substitution, Trp48Arg.     

A new HLA-A*26 variant, A*2637 identified by haplotype-specific extraction and sequencing-based typing

The novel allele A*2637 differs from the common A*260101 by a single nucleotide substitution in exon 2 (position 186 C>G) causing an amino acid exchange (SER>ARG).     

Identification of a variant HLA-A*3401 allele, A*340102, in an educational DNA typing sample

A*340102 was first identified in an ASEATTA Educational DNA typing sample, which typed as A*3401, 3401variant. The variant differs from A*3401 by a single silent substitution in exon 2 at nucleotide 309, codon 79 (GGG-->GGT).     

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.     

HLA-A*020115 and HLA-Cw*030203 show new synonymous mutations in exon 4

Two novel human leukocyte antigen (HLA) class I alleles, A*020115 and Cw*030203, were completely characterized by sequencing-based typing. Both present synonymous new HLA polymorphisms at exon 4. A*020115 shows a single nucleotide change regarding A*02010101 at codon 245 GCG > GCC). In contrast, Cw*030203 differs from Cw*030202 in a point mutation at codon 271 (ACC > ACT).     

Identification of HLA-A*11 variant (A*1107) in the Korean population

We report here a new HLA-A*11 allele, A*1107, identified by sequencing based typing in the Korean population. The full-length sequencing of A*1107 was conducted on cDNA. HLA-A*1107 differs from HLA-A*1101 by a single nucleotide at position 399 of codon 109 in exon3 (TTC-->TTA), leading to an amino acid change from phenylalanine to leucine. But the serological profile of HLA-A*1107 did not exhibit the altered HLA-A11.     

Identification of a novel HLA-B*40 null allele, HLAB*40:155N

The novel HLA (human leukocyte angiten)-A*26 allele differs from A*26:01:01 by a single nucleotide substitution at position 292 of exon 2 where a 'G' change to 'C'.     

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.