A comprehensive approach for typing the alleles of the HLA-B locus by automated sequencing

Authors

  • E. W. Petersdorf,

    Corresponding author
    1. Division of Clinical Research, Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, USA
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  • J. A. Hansen

    1. Division of Clinical Research, Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, USA
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**Fred Hutchinson Cancer Research Center 1124 Columbia Street, M718 Seattle, WA 98104 USA, Fax +1 (206) 667–5255

Abstract

Abstract: We describe an approach for typing alleles of the HLA-B locus by using automated sequencing technology. The exon 2 and exon 3 nucleotide sequence of each allele is determined directly from genomic DNA in two steps. In the first step, HLA-B exon 2, intron 2 and exon 3 sequences are amplified with one or two primer pairs out of a panel of 5 primer pairs that describe all known HLA-B alleles. In the second step, templates are sequenced in 5′ and 3′ orientations in a PCR assay that utilizes Taq polymerase to incorporate fluorescent dye-labeled nucleotides into each new strand synthesized. Gel electrophoresis of the labeled products is performed in an automated DNA sequencer. The derived sequences are aligned against reference sequences and each nucleotide position is evaluated for homology to consensus sequence. Using this strategy, the HLA-B allele sequence is directly ascertained with precision and efficiency. The automated sequencing strategy can be readily applied in the clinical laboratory as a practical tool for high resolution typing of HLA-B alleles.

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