Amy E. Decker

Chromosomal Duplications Along the Y-Chromosome and their Potential Impact on Y-STR Interpretation

Y-chromosome short tandem repeat (Y-STR) markers are being used as potential tools for distinguishing low levels of male DNA in the presence of excess female DNA as is present in many sexual assault samples. Usually single copy Y-STR loci produce a single amplicon in single source samples, and thus the observation of multiple peaks at such a locus could suggest to an analyst that a mixture of more than one male contributor is present in the tested sample. However, many regions of the Y-chromosome are duplicated or even triplicated in some individuals and this fact can thus complicate potential mixture interpretation. Reasons for the presence of duplications at multiple loci within a single sample are explored in the context of Y-STR marker location along the chromosome. True male-male mixtures commonly exhibit more than one locus-specific PCR product across multiple Y-STR loci that are not adjacent to one another on the Y-chromosome. In addition, duplicated loci typically possess alleles that differ by only a single repeat unit and possess similar peak heights.

Analysis of mutations in father–son pairs with 17 Y-STR loci

We have examined 389 father/son sample pairs from U.S. Caucasians, African Americans, Hispanics and Asians using the 17 Y-STR loci in the Yfilertrade mark kit and observed a total of 24 differences between father and son. Thirteen mutations resulted in the gain of a repeat in the son and 11 resulted in a loss of a repeat. All samples resulted in single repeat mutations except one sample which contained a two repeat loss at Y-GATA-H4. Furthermore, two different sample pairs were found to have two mutations. An African American sample pair had a mutation at DYS458 and a second at DYS635 and an Asian sample pair had mutations at DYS439 and Y-GATA-H4.

Autosomal SNP typing of forensic samples with the GenPlex TM HID System: Results of a collaborative study

The GenPlex™ HID System (Applied Biosystems - AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex™ HID System using 250-500pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex™ HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex™ HID System with the most commonly used STR kits, 500pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler™ kit (AB), GenPlex™ HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex™ HID showed a very low mean mach probability, while all STR kits except MiniFiler™ had very limited discriminatory power.

The impact of additional Y-STR loci on resolving common haplotypes and closely related individuals ☆

Commercial Y-STR kits have permitted laboratories to go beyond the original nine minimal haplotype loci (MHL) and to discover the advantage of additional Y-STR loci in resolving common haplotypes. In an effort to examine the impact of Y-STR markers beyond the 17 loci now available in commercial kit form, new Y-STR loci are being investigated on a common set of samples representative of the major U.S. population groups. Additional Y-STRs can also increase the power of discrimination between closely related male individuals, which is important not only in forensics but also in the paternity and genetic genealogy communities.