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

  • Mohaimin Kasu
  • Jamie Fredericks
  • Mischa Fraser
  • Christiaan Labuschagne
  • Mpasi Lesaoana
  • Maria Eugenia D’AmatoEmail author
Original Article


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.


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



Y-chromosome short tandem repeat


Short tandem repeat


Capillary electrophoresis


Deoxyribonucleic acid


Single nucleotide polymorphism


Polymerase chain reaction


Size homoplasy


Novel allele sequence


Known alleles


Pattern match


Repeat pattern variant


Relative fluorescent unit



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 information

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.

Compliance with ethical standards

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

Conflict of interest

The authors declare that they have no conflict of interest

Supplementary material

414_2019_2056_MOESM1_ESM.fas (8 kb)
ESM 1 (FAS 8 kb)
414_2019_2056_MOESM2_ESM.fas (7 kb)
ESM 2 (FAS 7 kb)
414_2019_2056_MOESM3_ESM.fas (7 kb)
ESM 3 (FAS 6 kb)
414_2019_2056_MOESM4_ESM.fas (3 kb)
ESM 4 (FAS 3 kb)
414_2019_2056_MOESM5_ESM.fas (4 kb)
ESM 5 (FAS 4 kb)
414_2019_2056_MOESM6_ESM.fas (4 kb)
ESM 6 (FAS 3 kb)
414_2019_2056_MOESM7_ESM.fas (3 kb)
ESM 7 (FAS 3 kb)
414_2019_2056_MOESM8_ESM.fas (4 kb)
ESM 8 (FAS 4 kb)
414_2019_2056_MOESM9_ESM.fas (13 kb)
ESM 9 (FAS 13 kb)
414_2019_2056_MOESM10_ESM.fas (5 kb)
ESM 10 (FAS 5 kb)
414_2019_2056_MOESM11_ESM.docx (817 kb)
ESM 11 (DOCX 795 kb)
414_2019_2056_MOESM12_ESM.docx (15 kb)
ESM 12 (DOCX 13.2 kb)


  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. CrossRefGoogle Scholar
  2. 2.
    Roewer L (2009) Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 5:77–84. CrossRefGoogle Scholar
  3. 3.
    Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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 7:240–250CrossRefGoogle Scholar
  10. 10.
    Garza JC, Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res 6:211–217. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle Scholar
  14. 14.
    ForenSeq™ DNA Signature Prep Kit Reference Guide (2015). V01:15049528 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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 16:1215CrossRefGoogle 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 AfricaGoogle Scholar
  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 AfricaGoogle Scholar
  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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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.CrossRefGoogle Scholar
  33. 33.
    Willuweit S, Roewer L (2015) The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15:43–48. CrossRefGoogle 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. CrossRefGoogle 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 CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle 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. CrossRefGoogle Scholar
  39. 39.
    Tishkoff SA, Williams SM (2002) Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 3:611–621. CrossRefGoogle 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. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Mohaimin Kasu
    • 1
  • Jamie Fredericks
    • 1
    • 2
  • Mischa Fraser
    • 3
  • Christiaan Labuschagne
    • 3
  • Mpasi Lesaoana
    • 1
    • 4
  • Maria Eugenia D’Amato
    • 1
    Email author
  1. 1.Forensic DNA Laboratory, Department of BiotechnologyUniversity of the Western CapeBellvilleSouth Africa
  2. 2.Department of ChemistryEastern Kentucky UniversityRichmondUSA
  3. 3.Inqaba Biotechnical IndustriesPretoriaSouth Africa
  4. 4.Lesotho Mounted Police Service, Technical Support ServicesMaseruLesotho

Personalised recommendations