PIMA: A population informative multiplex for the Americas

Gontijo, Carolina Carvalho; Porras-Hurtado, Liliana; Freire-Aradas, Ana; Fondevila, M.; Santos, C.; Salas, Antonio; Henao, Julieta; Isaza, Carlos; Beltrán, Leonardo; Silbiger, Vivian Nogueira; Castillo, A.; Ibarra, A.; Chavez, F. Moreno; Söchtig, Jens; Ruiz, Y.; Barreto, Guillermo; Rondón, Fernando Valle; Zabala, William; Borjas, Lisbeth; Oliveira, Silviene Fabiana de; Carracedo, Ángel; Lareu, Marı́a Victoria

doi:10.1016/j.fsigen.2019.102200

Cited by 9 publications

(11 citation statements)

References 37 publications

(53 reference statements)

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“…The VISAGE Basic Tool (herein BT) is the first forensic MPS test combining markers for predicting eye, hair, and skin colour with those for BGA inference in a single assay, along with a saliva-blood focused age estimation assay requiring a parallel assay and workflow due to the bisulphite conversion steps needed to measure methylation. The VISAGE BT was founded on marker panels which have been shown to be informative for the three pigmentation traits [5][6][7] and for continental-scale population differentiation [8][9][10][11][12]. The level of multiplexing necessary to accommodate sufficient SNPs to yield optimum predictions of both EVCs and continental BGA was in part dictated by experience of building multiplexes for forensic MPS analysis [8,12,13].…”

Section: Introductionmentioning

confidence: 99%

“…FigureS2.1 summarises the same type of population analyses as Figure3applied to unadmixed(8)(9)(10)(11)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25) and admixed(12)(13)(26)(27)(28)(29) 1000 Genomes samples (30X coverage genotypes) analysed against the reference population set. In nearly all cases, unadmixed samples show low levels of joint cluster membership.…”

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confidence: 99%

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Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

Puente

Ruiz-Ramírez

Ambroa-Conde

et al. 2021

Genes

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We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

Puente

Ruiz-Ramírez

Ambroa-Conde

et al. 2021

Genes

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“…The bulk of autosomal BGA SNPs selected for ET were identified from previous forensic ancestry panels, using HGDP-CEPH human diversity panel [15][16][17] and 1000 Genomes Phase III SNP data [18], (HGDP-CEPH population descriptions, grouping and sample sizes as outlined in [19]; and for 1000 Genomes populations in [18] also see Section 2.2.1). Such population sample sets are increasingly being enhanced with more detailed and comprehensive whole-genome-sequence based variant catalogs.…”

Section: Autosomal Bga Snpsmentioning

confidence: 99%

Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry

Ruiz-Ramírez

Puente

Xavier

et al. 2023

Forensic Science International: Genetics

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“…a panel of 29 AIMs for differentiating Oceanian populations; and the 26-plex Population Informative Multiplex for the Americas (PIMA) dedicated to Indigenous American populations [122]. Other most used sets in this eld are the Kidd's lab panel, containing 55 SNPs that can distinguish seven to eight continental regions [108], and the EUROFORGEN Global AIM-SNP set which is composed of 128 autosomal SNPs to differentiate the main ve global groups (Africa, Europe, East Asia, Native America, and Oceania) [95].…”

Section: Bga-related Literaturementioning

confidence: 99%

Forensic DNA Phenotyping: a review on SNP panels, genotyping techniques, and prediction models

Ortuño

2023

Preprint

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In the past few years, forensic DNA phenotyping (FDP) has attracted a strong interest in the forensic research. Among the increasing publications, many have focused on testing the available panels to infer biogeographical ancestry (BGA) on less represented populations and understanding the genetic mechanisms underlying externally visible characteristics (EVC). However, there are currently no publications that gather all the existing panels limited to FDP and discuss the main technical limitations of the technique. In this review, we performed a bibliographic search in Scopus database of FDP-related literature, which resulted in a total of 48, 43 and 15 panels for BGA, EVC and both BGA and EVC inference, respectively. Here we provide a list of commercial and non-commercial FDP panels and the FDP limitations regarding the lack of harmonization in terms of terminology (i.e., categorization and measurement of traits) and reporting, the lack of genetic knowledge and environment influence to select markers and develop panels, and the debate surrounding the selection of genotyping technologies and prediction models and algorithms. In conclusion, this review aims to be an updated guide and to present an overview of the current FDP-related literature.

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PIMA: A population informative multiplex for the Americas

Cited by 9 publications

References 37 publications

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry

Forensic DNA Phenotyping: a review on SNP panels, genotyping techniques, and prediction models

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