Titre:	Development and evaluations of the ancestry informative markers of the VISAGE enhanced tool for appearance and ancestry
Auteur(s):	Ramírez, Jorge Ruiz Puente, María de la Xavier, Catarina Ambroa-Conde, Adrián Álvarez Dios, Jose Aradas, Ana Freire Mosquera Miguel, Ana Ralf, Arwin Amory, Cristina Katsara, Maria Alexandra Khellaf, Tarek Nothnagel, Michael Cheung, Elaine Y. Y. Gross, Theresa E. Schneider, Peter M. Uacyisrael, Jolame Oliveira, Silviene Fabiana de Guimarães, Maria de Nazaré Klautau Gontijo, Carolina Carvalho Pośpiech, Ewelina Branicki, Wojciech Parson, Walther Kayser, Manfred Carracedo, Ángel Lareu, Maria Victoria Phillips, Christopher
metadata.dc.contributor.affiliation:	University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit Medical University of Innsbruck, Institute of Legal Medicine University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit University of Santiago de Compostela, Faculty of Mathematics University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit University Medical Center Rotterdam, Erasmus MC, Department of Genetic Identification Medical University of Innsbruck, Institute of Legal Medicine University of Cologne, Cologne Center for Genomics University of Cologne, Cologne Center for Genomics University of Cologne, Cologne Center for Genomics University Hospital Cologne University of Cologne, Faculty of Medicine and University Clinic, Institute of Legal Medicine University of Cologne, Faculty of Medicine and University Clinic, Institute of Legal Medicine University of Cologne, Faculty of Medicine and University Clinic, Institute of Legal Medicine Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji Universidade de Brasília, Departamento Genética e Morfologia Universidade de Brasília, Departamento Genética e Morfologia Universidade de Brasília, Departamento Genética e Morfologia Jagiellonian University, Malopolska Centre of Biotechnology Uniwersytet Jagielloński, Krakow, Poland Medical University of Innsbruck, Institute of Legal Medicine University Medical Center Rotterdam, Erasmus MC, Department of Genetic Identification Fundación Pública Galega de Medicina Xenómica (FPGMX), Instituto de Investigación Sanitaria (IDIS),15706 Santiago de Compostela, Spain University of Santiago de Compostela, Genomics Group, CIBERER, CIMUS University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit University of Santiago de Compostela, Institute of Forensic Sciences, Forensic Genetics Unit
Assunto::	Ancestralidade biogeográfica Marcadores genéticos
Date de publication:	5-mar-2023
Editeur:	Elsevier B. V.
Référence bibliographique:	RAMÍREZ, et al. Jorge Ruiz. Development and evaluations of the ancestry informative markers of the VISAGE enhanced tool for appearance and ancestry. Forensic Science International: Genetics, [S. l.], v. 64, 102853, 2023. DOI: https://doi.org/10.1016/j.fsigen.2023.102853. Disponível em: https://www.sciencedirect.com/science/article/pii/S1872497323000285. Acesso em: 28 jun. 2024.
Abstract:	The VISAGE Enhanced Tool for Appearance and Ancestry (ET) has been designed to combine markers for the prediction of bio-geographical ancestry plus a range of externally visible characteristics into a single massively parallel sequencing (MPS) assay. We describe the development of the ancestry panel markers used in ET, and the enhanced analyses they provide compared to previous MPS-based forensic ancestry assays. As well as established autosomal single nucleotide polymorphisms (SNPs) that differentiate sub-Saharan African, European, East Asian, South Asian, Native American, and Oceanian populations, ET includes autosomal SNPs able to efficiently differentiate populations from Middle East regions. The ability of the ET autosomal ancestry SNPs to distinguish Middle East populations from other continentally defined population groups is such that characteristic patterns for this region can be discerned in genetic cluster analysis using STRUCTURE. Joint cluster membership estimates showing individual co-ancestry that signals North African or East African origins were detected, or cluster patterns were seen that indicate origins from central and Eastern regions of the Middle East. In addition to an augmented panel of autosomal SNPs, ET includes panels of 85 Y-SNPs, 16 X-SNPs and 21 autosomal Microhaplotypes. The Y- and X-SNPs provide a distinct method for obtaining extra detail about co-ancestry patterns identified in males with admixed backgrounds. This study used the 1000 Genomes admixed African and admixed American sample sets to fully explore these enhancements to the analysis of individual co-ancestry. Samples from urban and rural Brazil with contrasting distributions of African, European, and Native American co-ancestry were also studied to gauge the efficiency of combining Y- and X-SNP data for this purpose. The small panel of Microhaplotypes incorporated in ET were selected because they showed the highest levels of haplotype diversity amongst the seven population groups we sought to differentiate. Microhaplotype data was not formally combined with single-site SNP genotypes to analyse ancestry. However, the haplotype sequence reads obtained with ET from these loci creates an effective system for de-convoluting two-contributor mixed DNA. We made simple mixture experiments to demonstrate that when the contributors have different ancestries and the mixture ratios are imbalanced (i.e., not 1:1 mixtures) the ET Microhaplotype panel is an informative system to infer ancestry when this differs between the contributors.
metadata.dc.description.unidade:	Instituto de Ciências Biológicas (IB) Departamento de Genética e Morfologia (IB GEM)
Licença::	This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
DOI:	https://doi.org/10.1016/j.fsigen.2023.102853
Collection(s) :	Artigos publicados em periódicos e afins

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