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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

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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

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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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Author notes

  1. Jamie Fredericks

    Present address: Department of Chemistry, Eastern Kentucky University, Richmond, KY, 40475, USA

Authors and Affiliations

  1. Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa

    Mohaimin Kasu, Jamie Fredericks, Mpasi Lesaoana & Maria Eugenia D’Amato

  2. Inqaba Biotechnical Industries, Muckleneuk, Pretoria, 0002, South Africa

    Mischa Fraser & Christiaan Labuschagne

  3. Lesotho Mounted Police Service, Technical Support Services, Maseru, 100, Lesotho

    Mpasi Lesaoana

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  1. Mohaimin Kasu
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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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