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)To read this article in full you will need to make a payment
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Article info
Publication history
Published online: December 11, 2022
Accepted:
December 9,
2022
Received in revised form:
November 2,
2022
Received:
July 13,
2022
Identification
Copyright
© 2022 Published by Elsevier B.V.
