Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool.

We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia.

Performance of ancestry-informative SNP and microhaplotype markers.

The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured.

Prediction of biogeographical ancestry in admixed individuals.

Estimation of ancestral affiliation for human genotypes is now possible for major geographic populations and has been employed for forensic casework. Prediction algorithms, such as the Snipper Bayesian classifier, have the ability to classify non-admixed BGA in African (AFR), European (EUR), East Asian (EAS), and most Amerindian (NAM) individuals, but are not always appropriate for admixed individuals. Artificial admixture was simulated for all possible admixture ratios (1:1, 3:1, 2:1:1, and 1:1:1:1) from four grandparents.

Prediction of biogeographical ancestry from genotype: a comparison of classifiers.

DNA can provide forensic intelligence regarding a donor's biogeographical ancestry (BGA) and other externally visible characteristics (EVCs). A number of algorithms have been proposed to assign individual human genotypes to a BGA using ancestry informative marker (AIM) panels. This study compares the BGA assignment accuracy of the population clustering program STRUCTURE and three generic classification approaches including a Bayesian algorithm, genetic distance, and multinomial logistic regression (MLR).