Specificity of genetic diversity in D1S80 revealed by SNP-VNTR haplotyping

Background: The allele frequency patterns of the D1S80 variable number tandem repeat (VNTR) locus have been shown to be multimodal in many different human populations. Aim: To explore the complex allele distribution of the D1S80 polymorphic locus in different populations comparing the derived single nucleotide polymorphism (SNP) rs16824398D1S80 haplotype frequencies in samples of European (Russians), Asian (Yakuts) and sub-Saharan African origin. Subjects and methods: The D1S80 locus together with its 50-flanking region including SNP rs16824398 was amplified using allele-specific polymerase chain reaction (PCR). Results: Haplotype phase determination sub-divided the total D1S80 allele spectrum into two allele sets marked by the corresponding SNP rs16824398 alleles. In non-African samples, the most frequent D1S80 alleles had 24 and 18 repeats that were associated with different SNP backgrounds (T and G alleles, respectively). Both combinations also occurred in Africans, but these samples exhibited an expanded spectrum of VNTR alleles on both SNP backgrounds. Conclusions: The sub-division of the D1S80 allele spectrum shape on the linked SNP background is indicative of populations of the main human groups. The reported differences in D1S80 allele spectra between populations of different ethnic origins can be explained by the ratios of chromosomes with T and G alleles.