Sequence-based typing of HLA-A2 alleles using a primer with an extra base mismatch.

A PCR-SBT method using genomic DNA for HLA-A2 alleles was established. To achieve specific amplification for detecting a single base difference between A2 alleles and other HLA-A alleles, a primer having one extra mismatch at the second position from its 3'-end was designed. The primer exhibited a high specificity with annealing temperatures from 64 degrees C to 68 degrees C. Thirty-eight Japanese samples were screened using this method. The majority of Japanese A2 antigens were coded by A*0201. A*0206 and A*0207 were observed at relatively high frequencies. Serologically defined split antigens, A2S and A2AK, which we have recently identified, corresponded to A*0203 and A*0210, respectively. Moreover, A*0207 was strongly associated with B46 and DR8.1.