Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449

Abstract

In forensic casework, Y-chromosome short tandem repeats (Y-STRs) are essential for differentiating between unrelated males and resolving the male component of admixed biological evidence. While the majority of Y-STRs are adequate for discriminating between different paternal lineages, rapidly mutating Y-STRs are necessary for improving discrimination between males within populations of low Y-chromosome diversity and between paternal relatives. Alternatively, sequencing of Y-STRs may also improve the discrimination between isometric Y-STR alleles by identifying variation in the repeat unit pattern arrangements and by identifying SNPs in the flanking region or within the STR repeat unit itself. In this report, a total of 153 DNA sequences are presented across the Y-STR loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. A total of 94 Y-STR sequences provided herein are reported for the first time, of which 37 sequences represent alleles showing size homoplasy, 34 sequences of known alleles for which sequence data has been unavailable and a total of 23 novel allele sequences across loci DYS644, DS447, DYS710 and DYS504. This study further encountered a rare sequence variant in the 5′ flanking region of DYS385 and a total of two SNPs in the repeat structure at DYS481 and DYS449.

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Abbreviations

Y-STR:

Y-chromosome short tandem repeat

STR:

Short tandem repeat

CE:

Capillary electrophoresis

DNA:

Deoxyribonucleic acid

SNP:

Single nucleotide polymorphism

PCR:

Polymerase chain reaction

SH:

Size homoplasy

NAS:

Novel allele sequence

KA:

Known alleles

PM:

Pattern match

RPV:

Repeat pattern variant

RFU:

Relative fluorescent unit

References

  1. 1.

    Roewer L, Arnemann J, Spurr NK et al (1992) Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts. Hum Genet 89:389–394. https://doi.org/10.1007/bf00194309

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Roewer L (2009) Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 5:77–84. https://doi.org/10.1007/s12024-009-9089-51

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635. https://doi.org/10.1007/s00439-017-1776-91

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Oota H, Settheetham-Ishida W, Tiwawech D, Ishida T, Stoneking M (2001) Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nat Genet 29:201–221. https://doi.org/10.1038/ng711

    CAS  Article  Google Scholar 

  5. 5.

    Nuñez C, Baeta M, Fernández M, Zarrabeitia M, Martinez-Jarreta B, de Pancorbo MM (2015) Highly discriminatory capacity of the PowerPlex® Y23 system for the study of isolated populations. Forensic Sci Int Genet 17:104–107. https://doi.org/10.1016/j.fsigen.2015.04.005

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    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. https://doi.org/10.1016/j.fsigen.2011.04.017

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal microsatellites: rates , characteristics , molecular bases and forensic implications. Am J Hum Genet 87:341–353. https://doi.org/10.1016/j.ajhg.2010.08.00

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Gopinath S, Zhong C, Nguyen V, Ge J, Lagacé 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. https://doi.org/10.1016/j.fsigen.2016.07.006

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Thompson JM, Ewing MM, Frank WE, Pogemiller JJ, Nolde CA, Koehler DJ, Shaffer AM, Rabbach DR, Fulmer PM, Sprecher CJ, Storts DR (2013) 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

    CAS  Article  Google Scholar 

  10. 10.

    Garza JC, Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res 6:211–217. https://doi.org/10.1101/gr.6.3.211

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Claerhout S, Van der Haegen M, Vangeel L et al (2018) A game of hide and seq: identification of parallel Y-STR evolution in deep-rooting pedigrees. Eur J Hum Genet 27:637–646. https://doi.org/10.1038/s41431-018-0312-2

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Warshauer DH, Churchill JD, Novroski N, King JL, Budowle B (2015) Novel Y-chromosome short tandem repeat variants detected through the use of massively parallel sequencing. Genomics Proteomics Bioinform 13:250–257. https://doi.org/10.1016/j.gpb.2015.08.001

    Article  Google Scholar 

  13. 13.

    Huszar TI, Jobling MA, Wetton JH (2018) A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing. Forensic Sci Int Genet 35:97–106. https://doi.org/10.1016/j.fsigen.2018.03.012

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 14.

    ForenSeq™ DNA Signature Prep Kit Reference Guide (2015). V01:15049528 https://support.illumina.com/downloads/forenseq-dna-signature-prep-guide-15049528.html. Accessed 9 June 2018

  15. 15.

    D’Amato ME, Bajic VB, Davison S (2011) Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system. Forensic Sci Int Genet 5:122–125. https://doi.org/10.1016/j.fsigen.2010.08.015

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    D’Amato ME, Ehrenreich L, Cloete K, Benjeddou M, Davison S (2010) Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710. Forensic Sci Int Genet 4:104–110. https://doi.org/10.1016/j.fsigen.2009.06.011

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    D’Amato ME, Benjeddou M, Davison S (2009) Evaluation of 21 Y-STRs for population and forensic studies. Forensic Sci Int Genet Suppl Ser 2:446–447. https://doi.org/10.1016/j.fsigss.2009.08.091

    Article  Google Scholar 

  18. 18.

    D’Amato ME, Kasu M (2017) Population analysis of African Y-STR profiles with UniQ TYPER™ Y-10 genotyping system. Forensic Sci Int Genet Suppl Ser 6:e84–e85. https://doi.org/10.1016/j.fsigss.2017.09.048

    Article  Google Scholar 

  19. 19.

    Burrows AM, Ristow PG, Amato MED (2017) Preservation of DNA from saliva samples in suboptimal conditions. Forensic Sci Int Genet Suppl Ser 6:e80–e81. https://doi.org/10.1016/j.fsigss.2017.09.050

    Article  Google Scholar 

  20. 20.

    Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215

    CAS  Article  Google Scholar 

  21. 21.

    Tsiana KJ (2015) Y-STR profiling of four south African populations using the University of the Western Cape 10 locus set, Msc, University of the Western Cape, South Africa

  22. 22.

    Kasu M (2019) Validation and application of a highly discriminating and rapid 10-locus Y-STR DNA profiling system, PhD, University of the Western Cape, South Africa

  23. 23.

    Ruitberg CM, Reeder DJ, Butler JM (2001) A short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res 29:320–322. https://doi.org/10.1093/nar/29.1.320

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Novroski NMM, King JL, Churchill JD, Seah LH, Budowle B (2016) Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 25:214–226. https://doi.org/10.1016/j.fsigen.2016.09.007

    CAS  Article  PubMed  Google Scholar 

  25. 25.

    Kwon SY, Lee HY, Kim EH, Lee EY, Shin KJ (2016) Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. Forensic Sci Int Genet 25:132–141. https://doi.org/10.1016/j.fsigen.2016.08.010

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Park MJ, Lee HY, Yang WI (2012) Understanding the Y chromosome variation in Korea — relevance of combined haplogroup and haplotype analyses. Int J Legal Med 126:589–599. https://doi.org/10.1007/s00414-012-0703-9

    Article  PubMed  Google Scholar 

  27. 27.

    Rodig H, Grum M, Grimmecke H-D (2007) Population study and evaluation of 20 Y-chromosome STR loci in Germans. Int J Legal Med 121:24–27. https://doi.org/10.1007/s00414-005-0075-5

    Article  PubMed  Google Scholar 

  28. 28.

    Redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, de Knijff P, Butler JM, Hammer MF (2002) Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int 130:97–11. https://doi.org/10.1016/S0379-0738(02)00347-X

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306. https://doi.org/10.1093/bib/bbn017

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Cloete KW, Ristow PG, Kasu M, D’Amato ME (2016) Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis. Electrophoresis 38:617–623. https://doi.org/10.1002/elps.201600257

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Leat N, Ehrenreich L, Benjeddou M, Cloete K, Davison S (2007) Properties of novel and widely studied Y-STR loci in three South African populations. Forensic Sci Int 168:154–161. https://doi.org/10.1016/j.forsciint.2006.07.009

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, de Ungria MCA, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MHD, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Škaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EPH, Yong RYY, Pajnič IZ, Kayser M (2014) Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 35:1021–1032.

    CAS  Article  Google Scholar 

  33. 33.

    Willuweit S, Roewer L (2015) The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15:43–48. https://doi.org/10.1016/j.fsigen.2014.11.024

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, Graziosi G, Heidorn F, Herrmann S, Herzog B, Hidding M, Honda K, Jobling M, Krawczak M, Leim K, Meuser S, Meyer E, Oesterreich W, Pandya A, Parson W, Penacino G, Perez-Lezaun A, Piccinini A, Prinz M, Schmitt C, Schneider PM, Szibor R, Teifel-Greding J, Weichhold G, de Knijff P, Roewer L (1997) Evaluation of Y-chromosomal STRs: a multicenter study. Int J Legal Med 110:125–133. https://doi.org/10.1007/s004140050051

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Kayser M, Kittler R, Erler A, Hedman M, Lee AC, Mohyuddin A, Mehdi SQ, Rosser Z, Stoneking M, Jobling MA, Sajantila A, Tyler-Smith C (2004) A comprehensive survey of human Y-chromosomal microsatellites. Am J Hum Genet 74:1183–1197 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182082/

    CAS  Article  Google Scholar 

  36. 36.

    Lim S-K, Xue Y, Parkin JE, Tyler-Smith C (2007) Variation of 52 new Y-STR loci in the Y chromosome consortium worldwide panel of 76 diverse individuals. Int J Legal Med 121:124–127. https://doi.org/10.1007/s00414-006-0124-8

    Article  PubMed  Google Scholar 

  37. 37.

    Gusmão L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr WR, Morling N, Prinz M, Roewer L, Tyler-Smith C, Schneider PM, DNA Commission of the International Society of Forensic Genetics (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Forensic Sci Int 157:187–197. https://doi.org/10.1016/j.forsciint.2005.04.002

    CAS  Article  PubMed  Google Scholar 

  38. 38.

    Parkin EJ, Kraayenbrink T, van Driem GL, Tshering of Gaselô K, de Knijff P, Jobling MA (2006) 26-Locus Y-STR typing in a Bhutanese population sample. Forensic Sci Int 161:1–7. https://doi.org/10.1016/j.forsciint.2005.10.008

    CAS  Article  PubMed  Google Scholar 

  39. 39.

    Tishkoff SA, Williams SM (2002) Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 3:611–621. https://doi.org/10.1038/nrg865

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Ristow PG, Cloete KW, D’Amato ME (2016) GlobalFiler® express DNA amplification kit in South Africa: extracting the past from the present. Forensic Sci Int Genet 24:194–201. https://doi.org/10.1016/j.fsigen.2016.07.007

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank the University of the Free State, University of Limpopo, University of Venda, the Tshwane University of Technology, the Regiment Botha military base Nelspruit for hosting our sampling, and all the voluntary donors from the University of the Western Cape and numerous locations across South Africa and Lesotho.

Funding

This work was supproted by The National Research Foundation of South Africa (NRF) (IFRR, UID 104726 and THRIP UID 80134 grants to MED), the Technology Innovation Agency (TIA) Seed Fund Programme grant to MED, the South African Medical Research Council (MRC) Research Development Grant and South Africa Network for Bioscience (SANBio) BioFISAII (V6LFD03/11214/04400/044LP/FORENSIC_KIT). The NRF provided the PhD bursary to MK.

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Correspondence to Maria Eugenia D’Amato.

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Ethical approval was granted by the University of the Western Cape Senate Research Committee (BM15/4/97 and BM/16/3/18).

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Kasu, M., Fredericks, J., Fraser, M. et al. Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. Int J Legal Med 133, 1681–1689 (2019). https://doi.org/10.1007/s00414-019-02056-7

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Keywords

  • Forensic
  • Y-chromosome; haplotype
  • Rapidly mutating
  • Size homoplasy
  • Sequence variation