How many probes are needed for HLA-DPB1 typing with sequence-specific oligonucleotide probes? A theoretical approach using computer simulation.

HLA-DP genotyping with sequence-specific oligonucleotides is used to detect known sequence variations in the polymorphic segments of the DPB1 second exon. This approach is a valuable method replacing the tedious cellular definition of DP polymorphism. We have addressed, by computer simulation, the question: what is the minimum number of probes needed to provide an unambiguous assignment of HLA-DP alleles by genotyping of heterozygous individuals? We were able to reduce the number of probes in a set defining the presently known 22 different alleles and most of the heterozygous combinations to 18 probes. Only two pairs of allelic combinations cannot be distinguished by this method, neither with our optimized set of probes nor with any larger set comprising probes of reasonable length. This is because two pairs of alleles may be the result of a reciprocal genetic exchange. These two pairs, however, could be distinguished by family analysis, direct sequencing, or DNA amplification using specific primers chosen from the polymorphic ends of the DPB1 second exon.