Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference. (May 2023)

• Record Type: Journal Article
• Authors: Resutik, Peter; Aeschbacher, Simon; Krützen, Michael; Kratzer, Adelgunde; Haas, Cordula; Phillips, Christopher; Arora, Natasha
• Is Part Of: Forensic science international. Volume 64(2023)
• Publication Date: 2023-05
• Subjects: Biogeographical ancestry (BGA) -- Ancestry informative markers (AIMs) -- Genetic structure -- Classification performance -- Forensic BGA panels; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2023.102850
• Languages: English
• ISSNs: 1872-4973

Abstract

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 AUC ̅ W score of 96.26% across the three scales of geographical resolution investigated. Highlights: New global reference dataset generated by collating genotypes from 3, 957 individuals and 228 populations. Evaluation leverages an extensive reference marker set comprising 10k Human Origins Array-based SNPs. Analyses were used to examine patterns of genetic diversity and differentiation, and classification performance with STRUCTURE. Presented workflow paves the way for further comparative evaluations of forensic BGA panels. We make our extensive global reference dataset available for the scientific community.