Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel

Pereira, Vânia; Freire-Aradas, Ana; Ballard, David J.; Børsting, Claus; Diez, Vladímir Rodríguez; Pruszkowska–Przybylska, Paulina; Ribeiro, João Victor; Achakzai, Niaz M; Aliferi, Anastasia; Bülbül, Özlem; Cárceles, María Dolores Pérez; Triki-Fendri, Soumaya; Rebai, Ahmed; Court, Denise Syndercombe; Morling, Niels; Lareu, Marı́a Victoria; Carracedo, Ángel; Phillips, C.

doi:10.1016/j.fsigen.2019.06.010

Cited by 35 publications

(37 citation statements)

References 28 publications

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“…The most successful studies developed models for eye, hair and skin color with promising prediction performance analyzing only a few dozen single nucleotide polymorphisms (SNPs) [ 12 , 13 , 14 ]. It has been demonstrated that the analysis of nuclear SNPs also aids the estimation of the biogeographical ancestry (BGA) by using at least thirty or more SNPs to obtain reliable results [ 15 , 16 , 17 , 18 , 19 ]. Targeted Massively Parallel Sequencing (MPS) technologies enable the simultaneous amplification of hundreds of DNA markers at low DNA input levels thus providing sensitive tools that keep sample consumption low, which has started to be applied for forensic purposes including appearance and/or ancestry prediction from DNA, e.g., [ 20 , 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

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

Palencia-Madrid

Xavier

Puente

et al. 2020

Genes

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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.

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Section: Introductionmentioning

confidence: 99%

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

Palencia-Madrid

Xavier

Puente

et al. 2020

Genes

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“…Genetic structure PCA and STRUCTURE analyses were performed with different reference data according to the availability of information concerning the markers. For the EUROFORGEN NAME markers, reference data included samples from the 1000 Genomes Project and HGDP-CEPH 20 (Supplementary Table S2). For the combined dataset of EUROFORGEN NAME and Precision ID Ancestry Panels (referred to as 'Combined' in the following sections), PCA and STRUCTURE analyses were carried out using the reference data from the 1000 Genomes Project (Supplementary Table S3).…”

Section: Discussionmentioning

confidence: 99%

“…The authors con rm that all methods were performed in accordance with the relevant guidelines and regulations. A total of 336 individuals from Albania, Denmark, Greece, Iraq, Slovenia, Somalia, and Turkey were previously typed with the MassARRAY ® EUROFORGEN NAME assay 20 . To reach a minimum of 75 individuals per population 23 , samples from 220 individuals from these populations were typed with the AmpliSeq™ EUROFORGEN NAME panel (Supplementary Table S1).…”

Section: Methodsmentioning

confidence: 99%

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

Truelsen

Tvedebrink

Mogensen

et al. 2021

Preprint

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The EUROFORGEN NAME panel is a second-tier ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY® system and included 111 SNPs. Here, a custom AmpliSeq™ EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1,098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with the first-tier Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.

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“…These subsets were then used [37,38] and mitochondrial DNA variation [39], and to some extent on additional non-genetic tools such as cranial morphometric analysis [40]. However, identification by high-density SNP genotyping of putative autochthonous ancestral components in Eastern and Northern Africa [28,35] suggests the future possibility to implement current worldwide AIM panels with complementary assays improving ancestry inference within this specific geographical area, in a similar way to what was previously achieved for the Mediterranean basin [41], Eurasia [33,42] and the Pacific region [43].…”

Section: Classification Success Of Aim Panelsmentioning

confidence: 98%

Characterization of ancestry informative markers in the Tigray population of Ethiopia: A contribution to the identification process of dead migrants in the Mediterranean Sea

Kumar

Haddish

Lacerenza

et al. 2020

Forensic Science International: Genetics

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel

Cited by 35 publications

References 28 publications

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

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

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

Characterization of ancestry informative markers in the Tigray population of Ethiopia: A contribution to the identification process of dead migrants in the Mediterranean Sea

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