Forensic inference of biogeographical ancestry from genotype: The Genetic Ancestry Lab

Abstract

Short tandem repeat (STR) profiling of DNA has become ubiquitous in forensic practice and is used to associate people, objects, and places with each other and with crimes. STRs can include or exclude a suspect or victim as the donor of biological evidence. In the absence of a matching profile, however, STRs have limited value. It is possible, then, to extract other information from the DNA that might lead forensic investigators to an offender. Examples include biogeographical ancestry (BGA) and externally visible characteristics (EVCs). These require alternative genetic markers including single nucleotide polymorphisms and microhaplotypes which can be genotyped on many different platforms including capillary electrophoresis, microarrays, and massively parallel sequencing (MPS). The Genetic Ancestry Lab (GAL) in Australia provides estimates of BGA and EVCs derived from DNA that is extracted from biological evidence and then subjected to targeted amplicon enrichment and subsequent MPS. This review will describe the process of BGA prediction employed by the GAL as well as describing alternative practices. Limitations are addressed and future directions highlighted, including resolution of genetic admixture. It is highly likely that inference of BGA will become standard forensic practice, performed simultaneously with or in addition to STR profiling, and it is hoped that this review might provide a road map. This article is categorized under: Forensic Anthropology > Ancestry Determination Forensic Science in Action/Crime Scene Investigation > From Traces to Intelligence and Evidence Forensic Biology > Ancestry Determination using DNA Methods Forensic Biology > Forensic DNA Technologies

The National Significance of a DNA Revolution: A Call for Policy Action towards Sustainable Development Goals (SDGs)

“…The use of DNA in the determination of ancestry has helped in the establishment of family relations in countries such as Australia, the US and the UK. In most cases where a reference sample is available, to predict the Biogeographical Ancestry (BGA) of a biological sample, genetic markers are selected based on their ability to differentiate between BGAs [47]. This technology has been applied in the identification of anonymous bodies, disaster victims, race and ethnicity, and other archaeological activities in developed countries.…”

The Y chromosome and its use in forensic DNA analysis

“…Direct-to-consumer testing has led to a lay expectation of certainty in BGA but a broad continental ancestry from a broad view across an individual's genome is likely the best that can be done [ 43 ].…”

Why most Principal Component Analyses (PCA) in population genetic studies are wrong

“…It is used to examine the population structure of a cohort to determine ancestry, analyze the demographic history and admixture, decide on the similarity of samples and exclude outliers, decide how to model the populations in downstream analyses, describe the relationships between the samples, infer kinship, identify clines of ancestries in the data (e.g., Patterson et al 2010;Yang et al 2010;Moorjani et al 2011;Ramstetter et al 2017), detect genomic signatures of natural selection (e.g., Duforet-Frebourg et al 2015), and identify convergent evolution (e.g., Galinsky et al 2016). It is used by direct-toconsumer companies to estimate ethnicity (Ball et al 2020) and in forensics to infer ancestry and biogeography (e.g., McNevin 2020). PCA is embedded in databases like gnomAD (Karczewski et al 2020), MR-Base (Hemani et al 2018), and the UK Biobank (Bycroft et al 2018), where PCA loadings are offered.…”