HLA class II typing by digestion of PCR-amplified DNA with allele-specific restriction endonucleases will fail to unequivocally identify the genotypes of many homozygous and heterozygous individuals.
Recently, a new technique for HLA class II genotyping has been introduced, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, claimed to be a practical alternative to conventional serological and cellular HLA class II typing (1-3). The PCR-RFLP technique is ingenious, relatively rapid and does not require hybridization with sequence-specific oligonucleotide probes. However, analysis of whether homozygous and heterozygous combinations of PCR-RFLP patterns for the various investigated HLA class II loci are unique or not unfortunately shows that only 19% of DRB homozygous and heterozygous combinations are unique. The figures for the DQA1, DQB and DPB loci are 56%, 29% and 65%, respectively. As not all nucleotide sequences analyzed in the above-mentioned studies (1-3) gave rise to unique PCR-RFLPs and as more sequences now are known, for the DRB1, DRB3, DRB5 and DPB1 loci (4), the frequencies of unique PCR-RFLP patterns for the different HLA class II loci will be reduced even further. Thus, the present analysis demonstrates that the PCR-RFLP technique, performed as described in references 1-3, is not yet ready to be used for routine HLA class II genotyping. The resolution of the PCR-RFLP method can be improved by various modifications. However, the role of a modified PCR-RFLP technique in HLA class II typing still remains to be shown.
Olerup
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Center for BioTechnology, Karolinska Institute, NOVUM, Huddinge, Sweden.
D000483:Alleles; D015343:DNA Probes, HLA; D004262:DNA Restriction Enzymes / Q000378:metabolism; D005838:Genotype; D006681:HLA-D Antigens / Q000235:genetics*; D006682:HLA-DP Antigens / Q000235:genetics; D006683:HLA-DQ Antigens / Q000235:genetics; D006684:HLA-DR Antigens / Q000235:genetics; D006579:Heterozygote; D006650:Histocompatibility Testing / Q000379:methods*; D006720:Homozygote; D006801:Humans; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D015203:Reproducibility of Results; D013379:Substrate Specificity
D015343:DNA Probes, HLA; D006681:HLA-D Antigens; D006682:HLA-DP Antigens; D006683:HLA-DQ Antigens; D006684:HLA-DR Antigens; D004262:DNA Restriction Enzymes