HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms

Breslin, Krystal; Wills, Bailey; Ralf, Arwin; García, Marina Ventayol; Kukla-Bartoszek, Magdalena; Pośpiech, Ewelina; Freire-Aradas, Ana; Xavier, Catarina; Ingold, Sabrina; Puente, M. de la; Gaag, Kristiaan J. van der; Herrick, Noah; Haas, Cordula; Parson, Walther; Phillips, C.; Sijen, Titia; Branicki, Wojciech; Walsh, Susan; Kayser, Manfred

doi:10.1016/j.fsigen.2019.102152

Cited by 59 publications

(76 citation statements)

References 34 publications

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“…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 ]. The need for combining more and more SNPs for combined appearance and ancestry prediction and the suitability of targeted MPS has triggered the development of a panel consisting of 153 markers for predicting appearance and ancestry in the framework of the VISAGE (VISible Attributes through GEnomics) Consortium ( ).…”

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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“…Early prediction studies evaluated the accuracy of predicting eye color from SNP data [7][8][9][10] and these analyses have been more recently extended to hair [11,12], and skin pigmentation [13]. As a result, sets of SNPs have now been proposed for the simultaneous prediction of eye, hair and skin color [14,15]. However, so far, these studies have had a strong European bias [7,10,11,14,16].…”

Section: Introductionmentioning

confidence: 99%

Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

Palmal

Adhikari

Mendoza‐Revilla

et al. 2020

Preprint

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We report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.

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“…[ 17 ]. The progress of research in this direction could, in the near future, lead to the discovery of new IFs that are not predictable today [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

New Frontiers and Old Challenges: How to Manage Incidental Findings When Forensic Diagnosis Goes Beyond

2020

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Incidental findings (IFs) are well known in medical research and clinical practice as unexpected findings having potential health or reproductive importance for an individual. IFs are discovered under different contexts but do not fall within the aim of a study, and/or are unanticipated or unintentionally revealed, and/or are not the specific focus or target of the particular research or clinical query. Today, in forensic settings, we can consider as incidental findings all the information that is neither related to the cause of death nor to the dynamic of the event or the scope of the forensic investigation. The question whether and how professionals should consider traditional values as guiding notions in the reporting of IFs in the context of forensic assessments is the focus of this article. We propose a descriptive analysis, which focuses on the forensic field, describing forensic situations in which IFs may occur, and whether and to whom they may be disclosed. Some considerations will be provided regarding forensic experts concerning their moral commitment to warn relatives about IFs.

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HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms

Cited by 59 publications

References 34 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

Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

New Frontiers and Old Challenges: How to Manage Incidental Findings When Forensic Diagnosis Goes Beyond

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