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Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples

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Abstract

The SureID® PathFinder Plus is a new 6-dye, 41-plex Y-STR system that includes the 17 loci from the Yfiler® kit (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4) plus 14 rapidly mutating Y-STR loci (DYS449, DYS481, DYS518, DYS527a/b, DYS533, DYS549, DYS570, DYS576, DYS627, DYF387S1a/b, and DYF404S1), and 10 low-medium mutation loci (DYS388, DYS444, DYS447, DYS460, DYS522, DYS557, DYS593, DYS596, DYS643, and DYS645). The inclusion of the 14 rapidly mutating Y-STR loci improves the discrimination of related individuals. Conversely, the 10 low-medium mutation loci are suitable not only for familial searching but also for providing a higher refinement in the construction of Y chromosome phylogenetic relationships among lineages. The 41-plex Y-STR system is designed for direct amplification of reference samples, such as blood samples on an FTA® Card, gauze, tissue, or cotton substrates as well as hair root or buccal samples on swabs. We performed developmental validation work including accuracy, stability, stutter precision, species specificity, sensitivity, PCR inhibitors, reproducibility, parallel testing of the system, and suitability for use on DNA mixtures. In addition, mutations of the loci were analyzed by 754 DNA-confirmed father–son pairs. The results demonstrate that this kit, developed in-house, is time-efficient, accurate, reliable, and highly informative for forensic database, familial searching, and distinguishing related males.

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References

  1. Gopinath S, Zhong C, Nguyen V, Ge J, Lagace RE, Short ML, Mulero JJ (2016) Developmental validation of the Yfiler® Plus PCR Amplification Kit: an enhanced Y-STR multiplex for casework and database applications. Forensic Sci Int Genet 24:164–175

  2. Hedman M, Pimenoff V, Lukka M, Sistonen P, Sajantila A (2004) Analysis of 16 Y STR loci in the Finnish population reveals a local reduction in the diversity of male lineages. Forensic Sci Int 142:37–43

    Article  CAS  Google Scholar 

  3. Hedman M, Neuvonen AM, Sajantila A, Palo JU (2010) Dissecting the Finnish male uniformity: the value of additional Y-STR loci. Forensic Sci Int Genet 5:199–201

    Article  Google Scholar 

  4. Kayser M, Vermeulen M, Knoblauch H, Schuster H, Krawczak M, Roewer L (2007) Relating two deep-rooted pedigrees from Central Germany by high-resolution Y-STR haplotyping. Forensic Sci Int Genet 1:125–128

    Article  Google Scholar 

  5. Lin H, Ye Q, Tang P, Mo T, Yu X, Tang J (2020) Analyzing genetic polymorphism and mutation of 44 Y-STRs in a Chinese Han population of Southern China. Legal Med 42:101643

    Article  Google Scholar 

  6. Thompson JM, Ewing MM, Frank WE, Pogemiller JJ, Nolde CA, Koehler DJ, Shaffer AM, Rabbach DR, Fulmer PM, Sprecher CJ, Storts DR (2012) Developmental validation of the PowerPlex® Y23 System: a single multiplex Y-STR analysis system for casework and database samples. Forensic Sci Int Genet 7:240–250

  7. Westen AA, Kraaijenbrink T, Clarisse L, Grol LJW, Willemse P, Zuniga SB, Robles De Medina EA, Schouten R, van der Gaag KJ, Weiler NEC, Kal AJ, Kayser M, Sijen T, de Knijff P (2014) Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males. Forensic Sci Int Genet 14:174–181

    Article  Google Scholar 

  8. Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, de Knijff P, Kayser M (2012) A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages. Forensic Sci Int Genet 6:208–218

    Article  CAS  Google Scholar 

  9. Butler JM, Schoske R (2005) U.S. population data for the multi-copy Y-STR locus DYS464. J Forensic Sci 50:975

    CAS  PubMed  Google Scholar 

  10. Robino C, Ralf A, Pasino S, De Marchi MR, Ballantyne KN, Barbaro A, Bini C, Carnevali E, Casarino L, Di Gaetano C, Fabbri M, Ferri G, Giardina E, Gonzalez A, Matullo G, Nutini AL, Onofri V, Piccinini A, Piglionica M, Ponzano E, Previderè C, Resta N, Scarnicci F, Seidita G, Sorçaburu-Cigliero S et al (2014) Development of an Italian RM Y-STR haplotype database: results of the 2013 GEFI collaborative exercise. Forensic Sci Int Genet 15:56–63

    Article  Google Scholar 

  11. Mo XT, Zhang J, Ma WH, Bai X, Li WS, Zhao XC, Ye J (2019) Developmental validation of the DNATyperTM Y26 PCR amplification kit: an enhanced Y-STR multiplex for familial searching. Forensic Sci Int Genet 38:113–120

    Article  CAS  Google Scholar 

  12. Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, Hennessy LK (2006) Development and validation of the AmpFlSTR® YfilerTM PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci 51:64–75

  13. Shi MS, Tang JP, Bai RF, Yu XJ, Lv JY, Hu B (2007) Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area). Int J Legal Med 121:455–462

    Article  Google Scholar 

  14. Dai HL, Wang XD, Li YB, Wu J, Zhang J, Zhang HJ, Dong JG, Hou YP (2004) Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population. Forensic Sci Int 145:47–55

    Article  CAS  Google Scholar 

  15. Hanson EK, Ballantyne J (2007) Population data for 48 'Non-Core' Y chromosome STR loci. Legal Med 9:221–231

    Article  CAS  Google Scholar 

  16. Jarve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, Khusnutdinova EK, Kivisild T, Sanchez JJ (2009) Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit. PLoS One 4:e7276

    Article  Google Scholar 

  17. Du W, Feng P, Huang H, Wu W, Zhang L, Guo Y, Liu C, Liu H, Liu C, Chen L (2019) Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci. Int J Legal Med 133:1015–1027

    Article  Google Scholar 

  18. Alghafri R, Goodwin W, Ralf A, Kayser M, Hadi S (2015) A novel multiplex assay for simultaneously analysing 13 rapidly mutating Y-STRs. Forensic Sci Int Genet 17:91–98

    Article  CAS  Google Scholar 

  19. Baeta M, Nunez C, Villaescusa P, Ortueta U, Ibarbia N, Herrera RJ, Blazquez-Caeiro JL, Builes JJ, Jimenez-Moreno S, Martinez-Jarreta B, de Pancorbo MM (2018) Assessment of a subset of Slowly Mutating Y-STRs for forensic and evolutionary studies. Forensic Sci Int Genet 34:e7–e12

    Article  CAS  Google Scholar 

  20. Ballantyne K, Ralf A, Aboukhalid R, Achakzai N, Anjos T, Ayub Q, Balažic J, Ballantyne J, Ballard D, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho E, Carvalho M, Cheng B, Coble M, Comas D, Corach D, D'Amato M, Davison S et al (2014) Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats. Hum Mutat 35:1021–1032

    Article  CAS  Google Scholar 

  21. SWGDAM (2004) Report on the current activities of the Scientific Working Group on DNA Analysis Methods Y-STR Subcommitee. Available at http://www2.fbi.gov/hq/lab/fsc/backissu/july2004/standards/2004_03_standards03.htm. Accessed 10.12.12

  22. SWGDAM (2012) Validation Guidelines for DNA Analysis Methods. Available at http://swgdam.org/SWGDAM_Validation_Guidelines_APPROVED_Dec_2012.pdf. Accessed 04.05.15

  23. SWGDAM (2014) Interpretation Guidelines for Y-Chromosome STR Typing. Available at http://swgdam.org/SWGDAM_YSTR_Guidelines_APPROVED_01092014_v_02112014_FINAL.pdf. Accessed 04.05.15

  24. Nei M, Tajima F (1981) DNA polymorphism detectable by restriction endonucleases. Genetics 97:145–163

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Hedman J, Nordgaard A, Rasmusson B, Ansell R, Radstrom P (2009) Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles. Biotechniques 47:951–958

    Article  CAS  Google Scholar 

  26. Opel KL, Chung D, McCord BR (2010) A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci 55:25–33

    Article  CAS  Google Scholar 

  27. Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58:2292–2295

    Article  CAS  Google Scholar 

  28. Akane A, Matsubara K, Nakamura H, Takahashi S, Kimura K (1994) Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci 39:362

    Article  CAS  Google Scholar 

  29. Shutler GG, Gagnon P, Verret G, Kalyn H, Korkosh S, Johnston E, Halverson J (1999) Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case. J Forensic Sci 44:623–626

    Article  CAS  Google Scholar 

  30. Schlotterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:211–215

    Article  CAS  Google Scholar 

  31. Viguera E, Canceill D, Ehrlich SD (2001) In vitro replication slippage by DNA polymerases from thermophilic organisms. J Mol Biol 312:323–333

    Article  CAS  Google Scholar 

  32. Walsh PS, Fildes NJ, Reynolds R (1996) Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res 24:2807–2812

    Article  CAS  Google Scholar 

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Acknowledgments

We thank all of the participants in this study. The authors would like to gratefully acknowledge the following laboratories for beta-testing of the SureID® PathFinder Plus Kit: Medical Research Center of Shaoxing University, Forensic Center of Shaoxing University, Human DNA Diagnostics Laboratory of Ningbo Health Gene Technologies Co. Ltd., and Forensic DNA laboratory of Shaoxing Municipal Public Security Bureau.

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Authors and Affiliations

  1. Forensic Center, College of Medicine, Shaoxing University, No. 508 Huancheng West Road, Shaoxing, 312000, China

    Guangyao Fan

  2. Shaoxing Municipal Public Security Bureau, Shaoxing, 312000, China

    Lipeng Pan

  3. Ningbo Health Gene Technologies Co. Ltd., Ningbo, 315040, China

    Peizhi Tang & Xiangmin Luo

  4. College of Medicine, Shaoxing University, Shaoxing, 312000, China

    Yijun Zhou & Mengnan Liu

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  1. Guangyao Fan
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  4. Yijun Zhou
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Correspondence to Guangyao Fan.

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Informed consent was obtained from all participating subjects, and this work was approved by the Ethics Committee of the Medical College, Shaoxing University.

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Fan, G., Pan, L., Tang, P. et al. Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples. Int J Legal Med 135, 409–419 (2021). https://doi.org/10.1007/s00414-020-02326-9

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  • DOI: https://doi.org/10.1007/s00414-020-02326-9

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