A convenient guideline to determine if two Y-STR profiles are from the same lineage

Y chromosome STR loci are used in forensics primarily for identification purposes by determining the male lineages. The Henan province in China has established a large Y-STR (>200 000 profiles) database for criminal investigations. A large proportion of the Y-STR profiles in the database were generated using either the Applied Biosystems Yfiler^ۛ or Yfiler^ۛ Plus PCR Amplification kits. The additional loci in the Yfiler Plus kit as compared to the Yfiler kit results in a concomitant cumulative mutation rate increase across the loci. Therefore, in those cases when two profiles have one to a few mismatched loci, it is difficult to determine if they are from the same lineage. In this study, 7405 unrelated male profiles were manually selected from the database. Analysis showed higher power of discrimination than the corresponding Yfiler haplotypes. Further, the distributions of the number of mismatched loci and the mismatched steps were generated for father-son, grandfather-grandson, uncle-nephew, and cousins (i.e. one, two, three, and four meioses, respectively) by exhaustive pairwise comparison of the unrelated profiles using a dynamic programming approach. The same distributions were generated for unrelated pairs with mutation rates of the loci. With the distributions, the false negative and false positive rates were determined. Two Yfiler profiles with ≤2 mismatched loci or ≤2 steps are more likely from the same lineage than unrelated lineages, and two Yfiler Plus profiles with ≤4 mismatched loci or ≤5 mismatched steps are more likely from the same lineage.