Combined polymorphism associated with a 3-bp deletion in the 5'-flanking region of a tetrameric short tandem repeat at the CYP19 locus.

Allele frequencies for a tetrameric short tandem repeat locus, CYP19, were determined in 220 unrelated Japanese individuals. The frequency distribution was similar to that of a previous report. However, PCR amplification using two sets of primers suggested that one allele consisting of 7 TTTA repeats (the allele 7) was divided into two separate ones, 7P (standard) and 7(-3), which differed in length for 3 bp. Sequence analysis of the two alleles revealed that the smaller 7(-3) had a 3-bp deletion in the 5'-flanking region of the tetrameric repeat. The deletion was also observed as the allele 7(-3) in non-Japanese such as Caucasians and Africans; it was only found in a part of the allele 7 [7(-3)], but not in the other alleles, in all examined populations. In the Japanese population, the deletion was observed in 39.6% of the allele 7, or 24.8% of all of the alleles. When the STR polymorphism at the CYP19 locus was combined with the polymorphic deletion adjacent to the repeat region, the numerical indices of genetic polymorphisms (heterozygosity, polymorphism information content and the power of discrimination) in Japanese rose from 0.541, 0.46 and 0.723 to 0.723, 0.66 and 0.864, respectively. Accordingly, the combined polymorphism at the CYP19 locus can be considered appropriate for hereditary analysis in the field of forensic science.