Abstract
The male-specific region of the human Y chromosome is a useful genetic marker for genealogical searching, male inheritance testing, and male DNA mixture deconvolution in forensic studies. However, the Y chromosomal short tandem repeats (Y-STRs) are difficult to distinguish among related males due to their low/medium mutation rate. In contrast, rapidly mutating (RM) Y-STRs exhibit unusually high mutation rates and possess great potential for differentiating male lineages. In this study, we developed a novel Y-STRs multiplex amplification assay of 32 RM Y-STRs by fragment analysis using six dye-labeled technologies (FAM, HEX, TAMRA, ROX, VIG, and SIZ). The development and the validation of the kit were carried out in accordance with the Scientific Working Group guidelines on DNA Analysis Methods. Identical allelic profiles of the 32 RM Y-STRs using a DNA 9948 sample as the positive control could be observed at different concentrations of PCR reagents. Further, the RM Y-STRs did not show cross-reactions with other common animal species, and the developed assay could tolerate interferences from common PCR inhibitors and mixed DNA samples. More importantly, the kit showed relatively high sensitivity and could detect trace DNA samples. Genetic distributions of 32 RM Y-STRs in the Guizhou Han population revealed that these RM Y-STRs showed relatively high genetic diversities. In conclusion, the RM Y-STR assay developed here showed good species specificity, high sensitivity, tolerance to inhibitors, and sample compatibility, which can be viewed as a highly efficient tool with high discrimination capacity for forensic male differentiation.
Highlights
The majority of the human Y chromosome regions does not recombine and exhibit a strict male inheritance pattern from father to son (Kayser, 2017)
Haplotype match probability (HMP), discrimination capacity (DC), and haplotype diversity (HD) of 32 rapidly mutating (RM) Y chromosomal short tandem repeats (Y-Short tandem repeat (STR)) in the Guizhou Han population were calculated on the basis of a previous study (Liu et al, 2020b)
The amplicon ranges of these 32 RM Y-STRs are illustrated in Supplementary Figure S1
Summary
The majority of the human Y chromosome regions does not recombine and exhibit a strict male inheritance pattern from father to son (Kayser, 2017). Genetic markers on the Y chromosome serve as powerful tools that are widely employed in forensics to determine the lineage of the male pedigree and perform DNA mixture deconvolution of forensic samples related to sexual assaults (Ruitberg et al, 2001). Short tandem repeat (STR) loci exhibit alleles defined by variable numbers of short sequence motifs and can possess many allele variations in populations that lead to extremely high genetic diversities. STRs found on the Y chromosome can provide male identification, pedigree searching, and paternity analysis, and commercial Y-STR kits have been developed.
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