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Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

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journal contribution
posted on 17.10.2019, 14:20 by Yahya M. Khubrani, Pille Hallast, Mark A. Jobling, Jon H. Wetton
While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen's ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally.

Funding

YMK was supported by the Saudi Arabian Ministry of Interior, and by a PhD studentship grant from the Saudi Arabian Cultural Bureau, London. PH was supported by Estonian Research Council Grants PUT1036 and IUT34-12. We thank all DNA donors, NUCLEUS Genomic Services at the University of Leicester for access to FGx sequencing, and Tunde Huszar and Verogen (Nicola Oldroyd-Clark, Sarah Naif, Richard Kessell and Cydne Holt) for useful discussions. We also thank Chris Phillips for sharing STR sequence data on the HGDP samples, and Chris Tyler-Smith for allowing the extraction of iiSNP genotypes from the HGDP WGS data. This research used the SPECTRE High Performance Computing Facility at the University of Leicester for data analysis.

History

Citation

Forensic Science International: Genetics, 2019, 43:102164

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/Biological Sciences/Genetics and Genome Biology

Version

AM (Accepted Manuscript)

Published in

Forensic Science International: Genetics

Publisher

Elsevier for International Society for Forensic Genetics (ISFG)

issn

1872-4973

eissn

1878-0326

Acceptance date

20/09/2019

Copyright date

2019

Publisher version

https://www.sciencedirect.com/science/article/pii/S1872497319303151?via=ihub

Notes

The file associated with this record is under embargo until 12 months after publication, in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above.;Supplementary material related to this article can be found, in the online version, at doi: https://doi.org/10.1016/j.fsigen.2019.102164

Language

en