DNA polymorphisms and haplotypes in the 5′-upstream region of the ABO blood group gene

We investigated the polymorphisms in the 5′-upstream region between nucleotide position (nt) -9600 and nt-4105 of the ABO blood group gene using PCR and direct sequencing methods. We found 16 single nucleotide polymorphisms, two insertion–deletion polymorphisms and two sequence polymorphisms. One of the insertion–deletion polymorphisms was found at nts from -9605 to -9204, and the alleles of that locus were named ABORR*L (non-deletion) and ABORR*S (52-base-deletion). There were two haplotypes constructed from 14 polymorphisms in the region between nt-9600 and nt-7565; they were tentatively named ABORR*L-associated and ABORR*S-associated haplotypes. The ABORR*L-associated haplotype may link with ABO*O(A) (also known as ABO*O201), and the ABORR*S-associated haplotype links with the other common alleles. This indicates the existence of two major lineages of the Japanese ABO alleles in the 5′-upstream region from nt-7565. In contrast to these findings, we observed six haplotypes in the region between nt-6371 and nt-4105, and we assume that the sequence in that region is variable as compared with those in the other 5′-upstream regions. We examined the generation of two sequence polymorphisms found in the present study. In the both cases, the formation of a hairpin loop caused by palindrome in a single-stranded DNA molecule may play an important role in generating the polymorphism.