Biomedical Science Letters (대한의생명과학회지)

The Korean Society for Biomedical Laboratory Sciences (대한의생명과학회)
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Improvement of the Discrimination Capacity through the Expansion of Y Chromosomal STR Markers

  • Dong Gyu Lee (Forensic DNA Division, National Forensic Service) ;
  • So Eun Lee (Department of Forensic Sciences, Sungkyunkwan University) ;
  • Ji Hwan Park (Forensic DNA Division, National Forensic Service) ;
  • Si-Keun Lim (Department of Forensic Sciences, Sungkyunkwan University) ;
  • Ju Yeon Jung (Forensic DNA Section, National Forensic Service Jeju Branch)
  • Received : 2023.10.04
  • Accepted : 2023.11.01
  • Published : 2023.12.31
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Abstract

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

Keywords

Acknowledgement

This work was supported by the Korean Government and the Forensic Research Program of the National Forensic Service (NFS) [grant number NFS2023DNA03].

References

  1. Ambers A, Votrubova J, Vanek D, Sajantila A, Budowle B. Improved y-str typing for disaster victim identification, missing persons investigations, and historical human skeletal remains. International Journal of Legal Medicine. 2018. 132: 1545-1553. https://doi.org/10.1007/s00414-018-1794-8
  2. Cho NS, Choi DH, Kim YJ, Hong SB, Kim SH, Lee WH, Han MS. An expanded korean reference db of y-chromosome str haplotype for forensic application. Journal of Scientific Criminal Investigation. 2016. 10: 48-54. https://doi.org/10.20297/jsci.2016.10.1.48
  3. Henry J, Simon C, Linacre A. The benefits and limitations of expanded y-chromosome short tandem repeat (y-str) loci. Forensic Science International: Genetics Supplement Series. 2015. 5: e28-e30. https://doi.org/10.1016/j.fsigss.2015.09.012
  4. Jung JY, Park J-H, Oh Y-L, Kwon H-S, Park H-C, Park K-H, Kim EH, Lee D-S, Lim S-K. Forensic genetic study of 29 y-strs in korean population. Legal Medicine. 2016. 23: 17-20. https://doi.org/10.1016/j.legalmed.2016.09.001
  5. Lee DG, Kim SJ, Cho W-C, Cho Y, Park JH, Lee J, Jung JY. Analysis of mutation rates and haplotypes of 23 ychromosomal strs in korean father-son pairs. Forensic Science International: Genetics. 2023. 65: 102875.
  6. Lee H, Hwang IK, Park M-S, Jeong K-S, Park S-H, Kang P-W, Cho NS, Choi D-H. A validation study to apply of powerplex®y23 kit in y-str genotyping of sexual assault samples. Korean Journal of Scientific Criminal Investigation. 2015. 9: 181-186.
  7. Lee HJ, Lee SD, Lee SH, Park SJ, Jeong SJ, Lee JW. Statistical evaluation of lineage markers in individual identification. The Korean Journal of Laboratory Medicine. 2014. 38: 39-47. https://doi.org/10.7580/kjlm.2014.38.2.39
  8. Lee HY, Park MJ, Chung U, Lee HY, Yang WI, Cho S-H, Shin K-J. Haplotypes and mutation analysis of 22 y-chromosomal strs in korean father-son pairs. International Journal of Legal Medicine. 2007. 121: 128-135. https://doi.org/10.1007/s00414-006-0130-x
  9. Li M, Zhou W, Zhang Y, Huang L, Wang X, Wu J, Meng M, Wang H, Li C, Bian Y. Development and validation of a novel 29-plex y-str typing system for forensic application. Forensic Science International: Genetics. 2020. 44: 102169.
  10. Nei M. Molecular evolutionary genetics. 1987. Columbia university press.
  11. Oh YN, Lee HY, Lee EY, Kim EH, Yang WI, Shin K-J. Haplotype and mutation analysis for newly suggested y-strs in korean father-son pairs. Forensic Science International: Genetics. 2015. 15: 64-68. https://doi.org/10.1016/j.fsigen.2014.09.023
  12. Park MJ, Lee HY, Kim NY, Sim JE, Yang WI, Cho SH, Shin KJ. Genetic characteristics of 22 y-str loci in koreans. Korean J Leg Med. 2007. 31: 162-170.
  13. Park MJ, Lee HY, Yoo J-E, Chung U, Lee SY, Shin K-J. Forensic evaluation and haplotypes of 19 y-chromosomal str loci in koreans. Forensic Science International. 2005. 152: 133-147. https://doi.org/10.1016/j.forsciint.2004.07.016
  14. Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B. A global analysis of y-chromosomal haplotype diversity for 23 str loci. Forensic Science International: Genetics. 2014. 12: 12-23. https://doi.org/10.1016/j.fsigen.2014.04.008
  15. Ralf A, Lubach D, Kousouri N, Winkler C, Schulz I, Roewer L, Purps J, Lessig R, Krajewski P, Ploski R. Identification and characterization of novel rapidly mutating y-chromosomal short tandem repeat markers. Human Mutation. 2020. 41: 1680-1696. https://doi.org/10.1002/humu.24068
  16. Song F, Xie M, Xie B, Wang S, Liao M, Luo H. Genetic diversity and phylogenetic analysis of 29 y-str loci in the tibetan population from sichuan province, southwest china. International Journal of Legal Medicine. 2020. 134: 513-516. https://doi.org/10.1007/s00414-019-02043-y
  17. Turrina S, Caratti S, Ferrian M, De Leo D. Are rapidly mutating y-short tandem repeats useful to resolve a lineage? Expanding mutability data on distant male relationships. Transfusion. 2016. 56: 533-538. https://doi.org/10.1111/trf.13368
  18. Yang IS, Lee HY, Park MJ, Yang WI, Shin K-J. Web-based y-str database for haplotype frequency estimation and kinship index calculation. Korean Journal of Legal Medicine. 2012. 36: 45-55. https://doi.org/10.7580/KoreanJLegMed.2012.36.1.45
  19. Yoo SY, Han S, Hwang JH, Park MJ, Kwon JA, Kim NS, Park JH, Cho NS. Population genetics of 23 y-chromosomal str loci in south koreans. Korean Journal of Scientific Criminal Investigation. 2014. 8: 16-30.
  20. Zhang AH, Lee HY, Seo SB, Lee HJ, Jin HX, Cho SH, Lyoo SH, Kim KH, Lee JW, Lee SD. Y haplogroup distribution in korean and other populations. Korean Journal of Legal Medicine. 2012. 36: 34-44. https://doi.org/10.7580/KoreanJLegalMed.2012.36.1.34
  21. Zhang J, Mo X, Shang L, Jin X, Chen D, Zhu H, Zhang Y, Kang B, Li W, Ye J. Genetic analysis of 29 y-str loci in han population from dongfang, southern china. International Journal of Legal Medicine. 2019. 133: 1033-1035. https://doi.org/10.1007/s00414-018-1899-0
  22. Zhao Y, Zhang J, He T, Chen C, Guo D, Jiao Z, Yang Z, Yu Z, Ma W, Zhang Q. Validation of the microreaderTM 29y prime id system for forensic use. Forensic Science International. 2020. 309: 110147.
  23. Zhou Y, Shao C, Li L, Zhang Y, Liu B, Yang Q, Tang Q, Li S, Xie J. Genetic analysis of 29 y-str loci in the chinese han population from shanghai. Forensic Science International: Genetics. 2018. 32: e1-e4. https://doi.org/10.1016/j.fsigen.2017.11.003