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Open AccessArticle

Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System

by Leire Palencia-Madrid 1,2, Catarina Xavier 1, María de la Puente 1,3, Carsten Hohoff 4, Christopher Phillips 3, Manfred Kayser 5 and Walther Parson 1,6,*,† on behalf of the VISAGE Consortium
1
Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Tirol, Austria
2
BIOMICs Research Group, Lascaray Research Center, University of the Basque Country, 01006 Vitoria-Gasteiz, Basque Country, Spain
3
Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
4
Institut für Forensische Genetik GmbH, 48161 Münster, Nordrhein-Westfalen, Germany
5
Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, The Netherlands
6
Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
*
Author to whom correspondence should be addressed.
A complete list of the centers and investigators in the VISAGE GROUP is provided in Appendix A.
Genes 2020, 11(6), 708; https://doi.org/10.3390/genes11060708
Received: 11 May 2020 / Revised: 9 June 2020 / Accepted: 11 June 2020 / Published: 26 June 2020
(This article belongs to the Special Issue Genes at Ten)
The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose. View Full-Text
Keywords: forensic DNA phenotyping; appearance; ancestry; BGA; HIrisPlex-S; EVC prediction; phenotype prediction; DNA phenotyping; PowerSeq; VISAGE forensic DNA phenotyping; appearance; ancestry; BGA; HIrisPlex-S; EVC prediction; phenotype prediction; DNA phenotyping; PowerSeq; VISAGE
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Palencia-Madrid, L.; Xavier, C.; de la Puente, M.; Hohoff, C.; Phillips, C.; Kayser, M.; Parson, W., on behalf of the VISAGE Consortium; Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System. Genes 2020, 11, 708.

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