Identification of the HLA-DRB1*04, -DRB1*07, and -DRB1*09 alleles by PCR amplification with sequence-specific primers (PCR-SSP) in 2 hours.

The clinical applicability of genomic HLA class II typing techniques has increased after the introduction of PCR-based typing strategies. In typing by PCR amplification using sequence-specific primers (PCR-SSP), amplification of specific alleles or groups of alleles is achieved, provided that the mismatch(es) of the SSP is located in the 3' end of the primer. Thus, the specificity of the typing system becomes part of the amplification step, which reduces the total typing time to a minimum by simplifying the postamplification processing of samples. The set of primers presented here identifies all of the alleles of the DR4 group, DRB1*0401-DRB1*0411, as well as the DRB1*07 and DRB1*0901 alleles. In the present study of DR4 alleles, PCR-SSP was compared with hybridization with sequence-specific oligonucleotide probes following group-specific PCR amplification (PCR-SSO). The two typing strategies gave completely concordant results in the 90 DR4-positive and the 32 DR4-negative individuals and cell lines studied. DR7,DQ9/DR9,DQ9 discrimination using PCR-SSP, was compared with MspI DQA RFLP typing, also with concordant results in the 33 DR7- and/or DR9-positive and 36 DR7- and DR9-negative individuals and cell lines tested. No false-negative or false-positive typing results were obtained. Genomic typing by PCR-SSP was performed in the overall time of 2 hours, including rapid DNA preparation, PCR amplification, postamplification processing, documentation, and interpretation of results. This makes the PCR-SSP strategy for HLA class II typing attractive not only in population- and disease-association studies, but also in routine clinical practice, including donor-recipient matching prior to cadaveric transplantation.