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Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains

Abstract

Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies. In this comparative study, Y-STR typing with both Yfiler™ and Yfiler™ Plus (Thermo Fisher Scientific, Waltham, MA, USA) was performed on a variety of human skeletal remains, including samples from the American Civil War (1861–1865), the late nineteenth century gold rush era in Deadwood, SD, USA (1874–1877), the Seven Years’ War (1756–1763), a seventeenth-century archaeological site in Raspenava, Bohemia (Czech Republic), and World War II (1939–1945). The skeletal remains used for this study were recovered from a wide range of environmental conditions and were extracted using several common methods. Regardless of the DNA extraction method used and the age/condition of the remains, 22 out of 24 bone samples yielded a greater number of alleles using the Yfiler™ Plus kit compared to the Yfiler™ kit using the same quantity of input DNA. There was no discernable correlation with the degradation index values for these samples. Overall, the efficacy of the Yfiler™ Plus assay was demonstrated on degraded DNA from skeletal remains. Yfiler™ Plus increases the discriminatory power over the previous generation multiplex due to the larger set of Y-STR markers available for analysis and buffer modifications with the newer version kit. Increased haplotype resolution is provided to infer or refute putative genetic relationships.

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Acknowledgements

This project was supported in part by Thermo Fisher Scientific, the City of Deadwood, Deadwood Historical Preservation Society, Department of Forensic Medicine at the University of Helsinki, and the Czech Science Foundation (grant No. 14-36938G). We would like to thank Thermo Fisher Scientific for donation of reagents for amplification and genotyping; and Andrea Carbonaro, Laura Pelleymounter, Lisa Calandro, and Julio Mulero for their technical assistance, expertise, and accurate amplicon sizing data for the Y-STR kits used in this study. The opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect those of Thermo Fisher Scientific, the City of Deadwood, Deadwood Historical Preservation Society, University of Helsinki, or the Czech Science Foundation.

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Ambers, A., Votrubova, J., Vanek, D. et al. Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains. Int J Legal Med 132, 1545–1553 (2018). https://doi.org/10.1007/s00414-018-1794-8

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  • DOI: https://doi.org/10.1007/s00414-018-1794-8

Keywords

  • Skeletal remains
  • Y-STR typing
  • Degraded DNA
  • Yfiler™ Plus
  • Lineage testing
  • Historical remains
  • Rapidly mutating Y-STRs