Using HLA sequence analysis and HLAMatchmaker to examine CREGs

Cross-reactive antigen groups (CREGs) were examined by similarity analysis of HLA sequences and by mismatched antibody-accessible triplets. The methods used were: (1) To count the number of main different and minor different positions in the amino acid sequences of exon 2 and exon 3 between each antigen pair in CREG; (2) Using HLAMatches program to count mismatched antibody-accessible triplets between each antigen pair in CREG. It was found that, in most situation, both the major and the minor differences between strong cross reactive antigen pairs were apparently fewer than those between weaker cross reactive antigen pairs. The main and minor different positions derived from sequence analysis have a good coincidence with the positions of mismatched HLATriplets. We also discussed the discrepancy between two different CREG schemes. It was concluded that similarity analysis of HLA allelic sequences is helpful for finding a better criteria of HLA matching.