High-resolution sequence-based typing strategy for HLA-DQA1 using SSP-PCR and subsequent genotyping analysis with novel spreadsheet program.

S K Cordovado; A E Simone; P W Mueller

doi:10.1034/j.1399-0039.2001.580504.x

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High-resolution sequence-based typing strategy for HLA-DQA1 using SSP-PCR and subsequent genotyping analysis with novel spreadsheet program.

S K Cordovado·A E Simone·P W Mueller

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Abstract

We present a new sequence-based typing (SBT) strategy for the polymorphic HLA-DQA1 locus that is based on sequence-specific primer - polymerase chain reaction (SSP-PCR) amplification from genomic DNA. This method allows high-resolution genotyping in the second exon of the DQA1 gene. This gene presents a unique situation in which half of the known alleles contain an inframe three base pair deletion of codon 56. This deletion confounds direct SBT methodologies of heterozygous individuals containing both a deletion and nondeletion allele. The primary HLA haplotype associated with type 1 diabetes susceptibility is DR3/DR4. The DQA1 genotype for these two haplotypes are DQA1 *0501, a non-deletion allele and *0301, a deletion allele, thus creating a situation that cannot be resolved using a direct sequencing approach. Our group-specific SBT strategy isolates the deletion alleles from the nondeletion alleles, allowing them to be resolved by direct sequencing. Additionally, we present a novel spreadsheet program that accurately assigns the genotype of both homozygous and heterozygous persons.

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Alleles Base Sequence DNA Primers Exons HLA-DQ Antigens HLA-DQ alpha-Chains Histocompatibility Testing Humans Molecular Sequence Data Polymerase Chain Reaction Software Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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S K Cordovado, A E Simone, P W Mueller. 2001. High-resolution sequence-based typing strategy for HLA-DQA1 using SSP-PCR and subsequent genotyping analysis with novel spreadsheet program.. https://doi.org/10.1034/j.1399-0039.2001.580504.x

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