Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference

Peter Resutik; Simon Aeschbacher; Michael Krützen; Adelgunde Kratzer; Cordula Haas; Christopher Phillips; Natasha Arora

doi:10.1016/j.fsigen.2023.102850

Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference

Forensic Sci Int Genet. 2023 May:64:102850. doi: 10.1016/j.fsigen.2023.102850. Epub 2023 Feb 25.

Authors

Peter Resutik¹, Simon Aeschbacher², Michael Krützen³, Adelgunde Kratzer⁴, Cordula Haas⁴, Christopher Phillips⁵, Natasha Arora⁶

Affiliations

¹ Zurich Institute of Forensic Medicine, University of Zurich, Switzerland. Electronic address: peter.resutik@irm.uzh.ch.
² Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.
³ Department of Evolutionary Anthropology, University of Zurich, Switzerland.
⁴ Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
⁵ Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
⁶ Zurich Institute of Forensic Medicine, University of Zurich, Switzerland. Electronic address: natasha.arora@irm.uzh.ch.

PMID: 36924679
DOI: 10.1016/j.fsigen.2023.102850

Abstract

Biogeographical ancestry (BGA) inference from ancestry-informative markers (AIMs) has strong potential to support forensic investigations. Over the past two decades, several forensic panels composed of AIMs have been developed to predict ancestry at a continental scale. These panels typically comprise fewer than 200 AIMs and have been designed and tested with a limited set of populations. How well these panels recover patterns of genetic diversity relative to larger sets of markers, and how accurately they infer ancestry of individuals and populations not included in their design remains poorly understood. The lack of comparative studies addressing these aspects makes the selection of appropriate panels for forensic laboratories difficult. In this study, the model-based genetic clustering tool STRUCTURE was used to compare three popular forensic BGA panels: MAPlex, Precision ID Ancestry Panel (PIDAP), and VISAGE Basic Tool (VISAGE BT) relative to a genome-wide reference set of 10k SNPs. The genotypes for all these markers were obtained for a comprehensive set of 3957 individuals from 228 worldwide human populations. Our results indicate that at the broad continental scale (K=6) typically examined in forensic studies, all forensic panels produced similar genetic structure patterns compared to the reference set (G'≈90%) and had high classification performance across all regions (average AUC-PR > 97%). However, at K= 7 and K= 8, the forensic panels displayed some region-specific clustering deviations from the reference set, particularly in Europe and the region of East and South-East Asia, which may be attributed to differences in the design of the respective panels. Overall, the panel with the most consistent performance in all regions was VISAGE BT with an average weighted AUC̅_W score of 96.26% across the three scales of geographical resolution investigated.

Keywords: Ancestry informative markers (AIMs); Biogeographical ancestry (BGA); Classification performance; Forensic BGA panels; Genetic structure.

MeSH terms

DNA Fingerprinting
Genetics, Population*
Genotype
Humans
Polymorphism, Single Nucleotide
Population Groups
Racial Groups* / genetics