Resolution of cis-trans ambiguities between HLA-DRB1 alleles using single-strand conformation polymorphisms and sequencing

DNA-based typing of HLA alleles occasionally results in the inability to as sign a specific allele because of ambiguity in associating two or more poly morphisms to the same or to alternate homologs (cis/trans ambiguity). Since most individuals are heterozygous at a given HLA locus, the highest level of confidence in definition is obtained when the alleles are tested in isol ation. By using single-strand conformation polymorphisms (SSCP) to separate heterozygous HLA-DRB1 alleles, followed by sequencing of separated conform ers, we have achieved resolution of previously ambiguous assignments withou t the need for additional probes or primers.