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.     

Identification by sequencing based typing and complete coding region analysis of three new HLA class II alleles: DRB3*0210, DRB3*0211 and DQB1*0310

The study of HLA class II polymorphism by direct exon 2 DNA sequencing analysis has been established to be a reliable and accurate high-resolution typing procedure. This approach shows some advantages in relation to previous methods, polymerase chain reaction using sequence-specific oligonucleotides (PCR-SSO) and sequence-specific primers (PCR-SSP), basically due to the capability of analysis for the complete sequenced genomic region, including non-polymorphic motifs. DRB3 and DQB1 sequencing based typing (SBT) in unrelated bone marrow donor searching allowed us to detect three new alleles. The complete coding region sequences were characterised from cDNA. Two new DRB3 alleles, DRB3*0210 and DRB3*0211, were described in two Caucasian bone marrow donors. Both sequences showed single point mutations regarding DRB3*0202, producing amino acid replacements at positions 51 (Asp to Thr) and 67 (Leu to Ile), respectively. These two point mutations can be found in other DRB alleles, and suggest that gene conversion would be involved in the origin of both alleles. A new DQB1 sequence was found in a Spanish patient that showed two nucleotide differences, positions 134 and 141, with regard to its close similar DQB1*03011 allele. Only substitution at position 134 provoked amino acid replacement at residue 45, Glu to Gly. This single amino acid change would be involved in the lack of serologic recognition of this new molecule by DQ7-specific reagents.     

Novel HLA-DRB3 alleles discovered during routine sequencing based typing,DRB3*02023, DRB3*0212, DRB3*0213 and DRB3*03012

We report the discovery of four HLA-DRB3 alleles during routine sequencing based typing (SBT); DRB3*02023, DRB3*0212, DRB3*0213 and DRB3*03012. These alleles differ from other HLA-DRB3 alleles by previously undescribed single nucleotide polymorphisms.     

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.     

Three new DRB alleles routinely identified by sequence-based typing: DRB1*010103, DRB1*0326 and DRB3*0219

We describe here two additional DRB1 alleles found in two Caucasoid recipient candidates for organ transplant and a new DRB3 allele found in a Caucasoid unrelated bone marrow donor from the German file. HLA-DRB generic and allele typing were performed using commercial kits, subsequently exon 2 was sequenced. We found a DRB1*010101 with a silent mutation at codon 68 and a DRB1*0306 with a mutation at codon 38 (T-C) which causes an amino acid substitution from Val to Ala. DRB3*0219 differs from DRB3*020201 by two-point mutations at codons 60 and 74 (A/C and A/G, respectively). These mutations at positions 266 and 308 were responsible for two amino acid substitutions (Tyr to Ser and Gln to Arg).     

Two DR2-associated novel alleles arose from the silent mutation of codon 72: DRB1*16012, DRB5*01012

Two DRB1*02-associated alleles, DRB1*16012 and DRB5*01012, are described. Both alleles carry the same silent substitution at codon 72.     

Detection of four novel alleles: DRB1*1130, DRB1*13072, DRB1*1315 and DRB1*1331

Four new DR52-associated DRB1 alleles are described. One allele, DRB1*1130, is a hybrid between a DRB3*02 allele and a DRB1*11011 allele. The other alleles, DRB1*13072, DRB1*1315, and DRB1*1331, are simple reshufflings of known polymorphic motifs.     

Two new HLA Cw* alleles,Cw*0105 and Cw*1405, detected by sequence based typing

During recent years, the view of the relative importance of the HLA Cw locus has undergone substantial change. From being an HLA locus with both limited polymorphism and biological significance there are now more than a hundred different alleles known and the biological importance of HLA Cw, both as a transplantation antigen and as a receptor for NK cells, is well established. Sequence based typing has been shown to be a powerful tool, especially for HLA Cw typing. Here we describe two new HLA Cw* alleles found during routine typing of potential bone marrow donors and hematological patients. The HLA Cw*0105 differs from Cw*0102 at positions 361 and 368 in exon 3 leading to a Trp to Arg and Cys to Ser substitution, respectively. HLA Cw*1405 differs from Cw*14021 by a single nucleotide substitution at position 368. This mutation results in an amino acid substitution of Phe for Tyr.     

Polymorphism of HLA-DRw52-associated DRB1 genes as defined by sequence-specific oligonucleotide probe hybridization and sequencing

We have used group-specific DNA amplification and sequence-specific oligonucleotide probe (SSOP) hybridization to study DRB1 sequence polymorphisms associated with DR3, DRw11(5), DRw12(5), DRw13(w6), DRw14(w6) and DRw8 alleles. Group-specific amplification of DRw52-associated DRB1 alleles was achieved using a 5' amplification primer designed to hybridize with a first hypervariable region (HVR) sequence common to all known alleles in this group, together with a 3' intron primer. Prospective SSOP typing of DR3, DRw11, DRw12, DRw13, DRw14 and DRw8 alleles was performed in 318 individuals, including 124 patients, 46 family members and 148 unrelated marrow donors. Among the 395 DRw52-associated DRB1 alleles tested in our study, a subtype corresponding to the previously defined alleles DRB1*0301-2 (DR3), DRB1*1101-4 (DR5), DRB1*1201-2 (DR5), DRB1*1301-5 (DRw6), DRB1*1401-2 and 1404 (DRw6), and DRB1*0801-4 (DRw8) could be assigned in all but 6 individuals (1.9%) tested. In addition to the 22 known alleles, we identified two new DRw6-associated alleles, DRB1*13.MW(1) and DRB1*14.GB(1). DRB1*13.MW typed serologically as DRw13 and was identical to DRB1*1301 except at codon 71 where AGG encodes arginine instead of GAG encoding glutamic acid. DRB1*14.GB represents a DRB1*1402 variant whose sequence at codon 86 encodes valine (GTG) instead of glycine (GGT). These results demonstrate that SSOP methods represent an efficient and precise approach for typing DRB1 alleles and for identifying potential novel variants previously unrecognized by conventional typing methods.     

Group-specific amplification of cDNA from DRB1 genes. Complete coding sequences of partially defined alleles and identification of the new alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113

We present here the complete coding sequences, previously unavailable, of the DRB1 alleles DRB1*030102, *0306, *040701, *0408, *1327, *1356, *1411, *1446, *1503, *1504, *0806, *0813, and *0818. For cDNA isolation, new group-specific primers located at the 5′UT and 3′UT regions were used to carry out allele-specific amplification and a convenient method for determining full-length sequences for DRB1 alleles. Complete coding sequencing of samples previously typed as DRB1*0406, DRB1*080101, and DRB1*1111 revealed new alleles with noncoding nucleotide changes at exons 1 and 3. In addition, we found a novel allele, DRB1*0113, whose second exon carries a sequence motif characteristic of DRB1*07 alleles. The predicted class II haplotypic associations of all alleles are reported and discussed.     

Identification of a novel HLA-DRB1*12 allele, DRB1*1218, in Chinese population

Here, we report the identification of a novel human leukocyte antigen-DRB1*12 variant, DRB1*1218 allele, in a Chinese Han individual. The novel DRB1*12 variant allele differed from the closest allele DRB1*120201 by nucleotide 262 G>C (codon 59 GAG>CAG) missense mutation in exon 2, which resulted in an amino acid substitution of Glu>Gln.     

Three new DP alleles identified in sub-Saharan Africa: DPB1*74O1, DPAl*02013, and DPAl*0302

Abstract: HLA-DP genotyping of over 400 individuals from sub-Saharan Africa identified three new DP alleles: DPB1*7401, DPAl*02013, and DPAl*0302. DNA sequencing confirmed that DPB1*7401, found in one individual, is a novel combination of previously described sequence motifs in the six variable regions of DPB1. DPA1*02013, found in one individual, is identical to DPAl*02012 except for two silent substitutions, a T to C transition in codon 37, and an A to G transition in codon 38. DPAl*0302, identified in seven individuals, is identical to DPAl*0301 except for a C to T transition at the second position of codon 66. The identification of these novel alleles brings the total number of reported DPB1 alleles to 77 and DPA1 alleles to 11.     

Identification of four new DR52-associated DRJB1 alleles: DRB1*1424, *1425, *1323 and *1324

Four previously unreported DR52-associated DRB1 alleles have been characterized through DNA sequencing, contributing to the diversity of the HLA system. DRB1*1424 is nearly identical to DRB1*1402 in the second exon, except that it contains the "I—A" motif found at codons 67–71 common to the DRB1*15 alleles. DRB1*1425 contains the "A—H" motif, found in DRB1*1401 at codons 57–60, in a sequence otherwise identical with the second exon of DRB1*1307. Compared with DRB1*11012, DRB1*1323 contains three predicted amino acid changes at codons 58 (ala→glu), 67 (phe→ile), and 71 (arg→glu). The sequence of DRB1*1324 is identical to exon 2 of DRB1*1103, except that DRB1*1324 does not contain the GAG at codon 58 characteristic of the DRB1*11 alleles. These new alleles may have arisen through gene conversion, and they contribute to the complexity of the DR6 family.     

High-resolution DNA typing in immunoglobulin A deficiency confirms a positive association with DRB 1*0301, DQBl*02 haplotypes

Selective immunoglobulin A (IgA) deficiency, the most common form of primary immunodeficiency, is related to the HLA genes. Previous studies demonstrated associations with particular HLA-DR-DQ haplotypes and a neutral amino acid at position 57 of the DQß chain was implicated in the susceptibility to selective IgA deficiency. In this study we reanalyzed the reported findings by high-resolution DNA typing of the loci DRB1, DQB1 and DQA1. We compared the typing results of 74 IgA-deficient individuals, detected by screening of blood donors, with those taken from 111 healthy controls. Results confirmed a strong positive association with DRB 1*0301, DQB1*02 and a negative association with DRB1*1501, DQB 1*0602. Considering the molecular interactions between HLA class II alleles and the peptides bound we conclude that the amino acid at position 57 of the DQß chain may contribute to the susceptibility to selective IgA deficiency, but not determine it. An extended statistical analysis strengthened the hypothesis that selective IgA deficiency might be communicated by the distinct haplotype DRB1*0301, DQB1*02.