HLA‐A*2607: sequence of a novel A*26 subtype predicted by DNA typing which shares the MA2.1 epitope with A*02, B*57 and B*58

Arnett, Kelly L.; Moses, J. H.; Williams, Fionnuala; Marsh, Steven G.E.; Bodmer, J.; Parham, Peter; Middleton, Derek

doi:10.1111/j.1399-0039.1996.tb02578.x

Cited by 11 publications

(8 citation statements)

References 14 publications

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“…The NN was not trained with outputs including multiple specificities other than broad and split assignments. For example, the NN was not trained with A*2607, which carries both a short A26 assignment and a A2 + B57 + B58 specificity (9), nor was it trained with DRB1*1107, which bears both DR11 and DR3 reactivity. Incorporation of this complexity into the training of the NN may refine the analysis further, particularly if this information is used to predict structure–function relationships.…”

Section: Discussionmentioning

confidence: 99%

“…Serologic testing had assigned a short A26 (10) to this allele although reactivity with an A2 reactive monoclonal antibody was also noted (9). The allele did not receive any NN assignments above the 0. a Serologic reaction patterns are provided as comments from the serology DNA dictionary (5).…”

Section: Hla-amentioning

confidence: 99%

“…The single inconsistent assignment was A*2607 (Tables 1 and 5). Serologic testing had assigned a short A26 (10) to this allele although reactivity with an A2 reactive monoclonal antibody was also noted (9). The allele did not receive any NN assignments above the 0.55 threshold (i.e.…”

mentioning

confidence: 99%

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Use of a neural network to assign serologic specificities to HLA‐A, ‐B and ‐DRB1 allelic products

Maiers

Schreuder

Lau³

et al. 2003

Tissue Antigens

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A computational method was used to predict the serologic specificities of HLA molecules encoded by the HLA-A, -B, and -DRB1 loci. The polypeptide sequences of a subset of alleles (numbering 149) with well-defined serologic assignments were used to train a neural network to predict broad and split serologic assignments for each HLA allelic product. The resultant neural network assignments were compared with those of a validation set containing the sequences of 74 HLA-A, 175 HLA-B, and 117 HLA-DRB1 alleles that had previous serologic test assignments but were not part of the training set. The network was able to correctly predict at least one of the serologic assignments of the majority of the validation alleles (99% of the HLA-A set, 86% HLA-B, 94% HLA-DRB1). The remainder received either no assignment (1% HLA-A, 13% HLA-B, 5% HLA-DRB1) or a different but closely related assignment (1% HLA-B and -DRB1). Overall, the variation in serologic assignment by the network appeared comparable to the assignments seen among different laboratories using serologic techniques. When used to predict the serologic assignments of 393 HLA alleles without known serologic types, the network was able to predict assignments for most alleles (95% HLA-A, 85% HLA-B, 96% HLA-DRB1). The majority of these assignments were consistent with assignments predicted by sequence homologies with known alleles. The remainder did not receive an assignment and likely represent new combinations of epitopes.

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Section: Discussionmentioning

confidence: 99%

Section: Hla-amentioning

confidence: 99%

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Use of a neural network to assign serologic specificities to HLA‐A, ‐B and ‐DRB1 allelic products

Maiers

Schreuder

Lau³

et al. 2003

Tissue Antigens

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“…The mabs used were: MA2.1 (IgG1) recognizing HLA-A2, B17 and A*2607; PA2.1 (IgG1) and BB7.2 (IgG2b) recognizing HLA-A2 and A69 but not HLA-A*0210. W6/32 (IgG2a) recognizing all MHC class I molecules was used as a positive control (32)(33)(34)(35).…”

Section: Flow Cytometric Analysis For Preselection Of Hla-a2-positivementioning

confidence: 99%

A PCR‐SSP method to specifically select HLA‐A*0201 individuals for immunotherapeutic studies

2000

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HLA-A*0201 is an important restriction element for peptide presentation to T cells in disease and cancer. Mutation studies and analyses using cytotoxic T lymphocytes have shown the functional relevance of subtype-specific differences in HLA-A2 molecules for peptide binding and T-cell receptor recognition. Therefore, many immunotherapeutic studies need to accurately select HLA-A*0201-positive individuals. We designed an easy, robust approach based on the polymerase chain reaction using sequence-specific primers (PCR-SSP) to specifically distinguish A*0201-positive individuals from other HLA-A2 subtypes described to date. The first step includes reactions that give information whether the sample donor is HLA-A2 and, if so, whether the individual is homozygous or heterozygous for HLA-A2. Further, it is determined whether the sample has an HLA-A*0209 or an HLA-A*0201 sequence at the corresponding position in exon 4. Samples that may contain an HLA-A*0201 allele according to the results of this first step are subtyped in a second step nested PCR. Here the strategy is focussed on the discrimination of HLA-A*0201 from the other subtypes by considering divergent nucleotide positions in two ways. One SSP combination amplifies the HLA-A*0201 sequence while a corresponding SSP combination specifically amplifies the subtype or group of subtypes differing from HLA-A*0201 at this position. Thus, at relevant polymorphic nucleotide positions the HLA-A*0201 sequence is both directly and indirectly confirmed. This strategy strongly enhances the reliability of the subtyping and allows better verification of HLA-A*0201-positive patient selection for clinical studies.

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“…A'Blank' D50068, L43536, L43537 (Maruya et al, 1996;Dale et al, 1996) A*2606 A26(10) -KHB102 L43534, L43535 (Dale et al, 1996) A*2607 A26(10) A26mic MIC-ND L48341 (Arnett et al, 1996b) (Blasczyk et al, 1996) A*7403…”

Section: A*2409nmentioning

confidence: 99%

Nomenclature for Factors of the HLA System, 1996

Bodmer¹,

Marsh²,

Albert³

et al. 1997

Vox Sanguinis

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HLA‐A2607: sequence of a novel A26 subtype predicted by DNA typing which shares the MA2.1 epitope with A02, B57 and B*58

Cited by 11 publications

References 14 publications

Use of a neural network to assign serologic specificities to HLA‐A, ‐B and ‐DRB1 allelic products

Use of a neural network to assign serologic specificities to HLA‐A, ‐B and ‐DRB1 allelic products

A PCR‐SSP method to specifically select HLA‐A*0201 individuals for immunotherapeutic studies

Nomenclature for Factors of the HLA System, 1996

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