A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry,hair and eye colour,and Y chromosome lineage |
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| Institution: | 1. Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia;2. School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia;1. MPS’s Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China;2. Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan 030001, Shanxi, People’s Republic of China;3. Chinese Center For Disease Control And Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China;4. Marine College, Shandong University, Weihai 264209, Shandong, China;1. Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA;2. Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA;1. Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, PR China;2. School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan 250117, PR China;3. Jinan City Blood Center, Jinan 250001, PR China;4. Jinan Municipal Public Security Bureau, Jinan 250115, PR China;5. Queen Mary School, Nanchang University, Nanchang 330031, PR China;6. Shanxi Medical University, Taiyuan 030001, PR China |
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| 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. |
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| Keywords: | Forensic intelligence SNPs Biogeographic ancestry Phenotype Hybridisation enrichment MPS"} {"#name":"keyword" "$":{"id":"key0035"} "$$":[{"#name":"text" "_":"massively parallel sequencing mtDNA"} {"#name":"keyword" "$":{"id":"key0045"} "$$":[{"#name":"text" "_":"mitochondrial DNA SNP"} {"#name":"keyword" "$":{"id":"key0055"} "$$":[{"#name":"text" "_":"single nucleotide polymorphism STR"} {"#name":"keyword" "$":{"id":"key0065"} "$$":[{"#name":"text" "_":"short tandem repeat |
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