Optimization of high resolution DNA typing of HLA-A and B loci

Lazaro, AM; Fernandez-Viña, M.A.; Nulf, CJ; Fish, VM; McGarry, JE; Marcos, CY; Miller, SN; Šťastný, Peter

doi:10.1016/0198-8859(96)84910-x

Cited by 2 publications

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“…Each pair of alleles was mapped to the set of allele pairs that had identical probe hit patterns, then the typing was compressed to NMDP allele code format. For HLA-A and HLA-B loci we used kits described at the 12th International Histocompatibility Workshop [29] , and for HLA-DRB1 locus we used a kit described at the 11th International Histocompatibility Workshop [15] , [30] . SBT simulation mapped allele pairs to a list of ambiguous genotypes with identical heterozygous sequence in exons 2 and 3 published by IMGT-HLA ( http://www.ebi.ac.uk/imgt/hla/ambig.html ) and reported the typing in the genotype list format.…”

Section: Methodsmentioning

confidence: 99%

Measuring Ambiguity in HLA Typing Methods

et al. 2012

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In hematopoietic stem cell transplantation, donor selection is based primarily on matching donor and patient HLA genes. These genes are highly polymorphic and their typing can result in exact allele assignment at each gene (the resolution at which patients and donors are matched), but it can also result in a set of ambiguous assignments, depending on the typing methodology used. To facilitate rapid identification of matched donors, registries employ statistical algorithms to infer HLA alleles from ambiguous genotypes. Linkage disequilibrium information encapsulated in haplotype frequencies is used to facilitate prediction of the most likely haplotype assignment. An HLA typing with less ambiguity produces fewer high-probability haplotypes and a more reliable prediction. We estimated ambiguity for several HLA typing methods across four continental populations using an information theory-based measure, Shannon's entropy. We used allele and haplotype frequencies to calculate entropy for different sets of 1,000 subjects with simulated HLA typing. Using allele frequencies we calculated an average entropy in Caucasians of 1.65 for serology, 1.06 for allele family level, 0.49 for a 2002-era SSO kit, and 0.076 for single-pass SBT. When using haplotype frequencies in entropy calculations, we found average entropies of 0.72 for serology, 0.73 for allele family level, 0.05 for SSO, and 0.002 for single-pass SBT. Application of haplotype frequencies further reduces HLA typing ambiguity. We also estimated expected confirmatory typing mismatch rates for simulated subjects. In a hypothetical registry with all donors typed using the same method, the entropy values based on haplotype frequencies correspond to confirmatory typing mismatch rates of 1.31% for SSO versus only 0.08% for SBT. Intermediate-resolution single-pass SBT contains the least ambiguity of the methods we evaluated and therefore the most certainty in allele prediction. The presented measure objectively evaluates HLA typing methods and can help define acceptable HLA typing for donor recruitment.

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Section: Methodsmentioning

confidence: 99%

Measuring Ambiguity in HLA Typing Methods

et al. 2012

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“…All individuals included in the present study were typed for HLA‐A locus alleles by polymerase chain reaction using sequence‐specific oligonucleotide probes (PCR‐SSOP). The PCR was performed using the A‐locus specific primers RAP 1007 (AGG ATC CAG ACG CCG AGG ATG GCCG) and DB 337 (CAG GAT CCC TCC TTC CCG TTC TCC AGGT) described by Bugawan et al ( 35) and was followed by dot‐blot hybridization with a set of 93 SSOPs for the analysis of exon 2 and 3 polymorphism ( 36). All subjects were also typed for HLA‐B locus alleles using the procedure described previously ( 37) with some modifications.…”

Section: Methodsmentioning

confidence: 99%

Novel HLA‐A and HLA‐B alleles in South American Indians

et al. 1999

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The human leukocyte antigen (HLA) complex includes the most polymorphic genes in humans. More than 600 allelic variants have been described in different populations. The HLA-B locus has contributed the largest number of alleles. Although Native American populations display a restricted number of HLA-alleles, many novel HLA class I alleles have been identified in indigenous communities of Central and South America. We have studied 248 unrelated individuals from three tribes of North-East Argentina and one from South-West Brazil, as well as 80 related individuals from the Brazilian tribe. In the course of this work, we found 8 new B-locus alleles and 2 novel A-locus alleles in these populations. Here we report the nucleotide sequences of A*0219, A*0222, B*3519, B*3520, B*3521, B*3912, B*4009 and B*4803 and we show their relationship with similar alleles. The new alleles B*35092 and B*3518 have been described by us in a previous paper. The possible mechanisms that may have produced these alleles over evolutionary time are discussed.

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Optimization of high resolution DNA typing of HLA-A and B loci

Cited by 2 publications

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Measuring Ambiguity in HLA Typing Methods

Measuring Ambiguity in HLA Typing Methods

Novel HLA‐A and HLA‐B alleles in South American Indians

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