Investigating SNPs Flanking the D1S80 Locus in a Tamil Population from India

D1S80 is a 16-bp variable number of tandem repeats minisatellite. We analyzed single nucleotide polymorphisms (SNPs) flanking this locus in a Tamil population. Alleles ranged from 15 through 41 repeats, with alleles 18 and 24 being predominant with frequencies of 31% and 34.5%, respectively, suggesting a bimodal allelic distribution. All the 18-repeat alleles are associated with Hin fI(+) and Fnu 4HI(-) restriction site polymorphisms at the 5. and 3. ends, respectively. Allele 24 is associated with Hin fI(-) and Fnu 4HI(+). Of the alleles tested, 98.5% have a linkage of two specific SNP polymorphisms. If an allele is positive for Hin fI, then it is negative for Fnu 4HI, and if an allele is negative for Hin fI, it is then positive for Fnu 4HI, which demonstrates strong linkage disequilibrium between the two polymorphic SNPs. This suggests that reciprocal crossover is not involved in changes in the number of repeats, as few exchanges are seen in the flanking regions. The repeat allele- SNP association might be involved with the internal structure of the locus micropolymorphisms, possibly a double-strand break hotspot.