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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

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.

Keywords

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

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

Notes

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 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

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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

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