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Novel procedures for high-throughput analysis of a frequent insertion-deletion polymorphism in the human T-cell receptor beta locus

Conrad, Bernard

In: Immunogenetics, 2004, vol. 56, no. 3, p. 220-224

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    Titre
    • Novel procedures for high-throughput analysis of a frequent insertion-deletion polymorphism in the human T-cell receptor beta locus
    Auteur
    • Conrad, Bernard. Department of Microbiology and Molecular Medicine, CMU, University of Geneva, 1 rue Michel Servet, 1211, Geneva 4, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Immunogenetics, 2004, vol. 56, no. 3, p. 220-224. Springer-Verlag; http://www.springer.de
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:320485
    Summary
    The human T-cell receptor beta locus (TRB) contains two frequent insertion-deletion polymorphisms. In one, the insertion comprises two functional variable beta genes, TRBV6-2/TRBV6-3 and TRBV4-3, and the pseudogene TRBV3-2. Deletion of these TRBV genes may confer resistance and/or susceptibility to autoimmunity, analogously to findings in rodent models. Curiously, the TRBV domains in the insertion react with the HERV-K18 superantigen associated with type1 diabetes. While this region has been extensively characterized before, typing methods compatible with high-throughput analysis are not yet available. Here, two novel procedures are reported that are suitable for large-scale association analysis of this polymorphism. One features a duplex TaqMan 5′-exonuclease assay that quantifies the gene dosage of TRBV3-2 present at 0, 1 or 2 copies, with its closely related diploid relative TRBV3-1 as an internal reference, using the 2-ΔΔC T method. The other technique consists of two complementary long PCRs with primers specific for unique regions in the locus. The first discriminates individuals heterozygous or homozygous for the deletion, and the second, individuals heterozygous or homozygous for the insertion from other genotypes. These simple, solid, and cross-validated procedures can now be used in conjunction with flanking single-nucleotide polymorphisms for large-scale linkage studies