[Correlations between haplogroup membership and Y-STR haplotype as a potential measure of quality control in forensic...

A correlation between particular Y-STR alleles from the so-called "minimal haplotype" and haplogroup membership of the Y chromosome was tested. We collected 146 Y chromosomes from haplogroups R1*, R1a1* and 1* and estimated the frequency of Y-STR alleles in each haplogroup. We then used different algorithms to assign a haplogroup to a haplotype, and tested their accuracy. Generally, a method based on calculation of haplotype similarity using the highest allele frequencies as modal values and assigning a score to each locus based on a ratio of allele frequencies turned out to give the most precise matches. However, using the same rules for Y chromosomes from other populations did not allow for precise estimation of their Y chromosome haplogroup frequencies. Possible explanations for this failure include interpopulation differences in haplotypes correlated with particular haplogroups, as well as a relatively small number of chromosomes analyzed. Potential uses for the presented method in forensics were also described.