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A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage

  • Author Footnotes
    1 Present address: Forensic Science SA, Adelaide, South Australia, 5000, Australia.
    Felicia Bardan
    Footnotes
    1 Present address: Forensic Science SA, Adelaide, South Australia, 5000, Australia.
    Affiliations
    Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
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  • Denice Higgins
    Affiliations
    Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia

    School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
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  • Jeremy J. Austin
    Correspondence
    Corresponding author.
    Affiliations
    Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
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  • Author Footnotes
    1 Present address: Forensic Science SA, Adelaide, South Australia, 5000, Australia.
Published:December 11, 2022DOI:https://doi.org/10.1016/j.fsigen.2022.102822

      Highlights

      • Single nucleotide polymorphisms (SNPs) can provide forensic intelligence.
      • Existing forensic SNP panels are inflexible and may perform poorly on degraded DNA.
      • We developed and tested a customisable, SNP hybridisation enrichment panel.
      • The panel provides valuable biological profiles and forensic intelligence.

      Abstract

      Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.

      Keywords

      Abbreviations:

      MPS (massively parallel sequencing), mtDNA (mitochondrial DNA), SNP (single nucleotide polymorphism), STR (short tandem repeat)
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