The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Kukla-Bartoszek, Magdalena; Szargut, Maria; Pośpiech, Ewelina; Diepenbroek, Marta; Zielińska, Grażyna; Jarosz, Agata; Piniewska-Róg, Danuta; Arciszewska, Joanna; Cytacka, Sandra; Spólnicka, Magdalena; Branicki, Wojciech; Ossowski, Andrzej

doi:10.1016/j.fsigen.2020.102301

Cited by 21 publications

(23 citation statements)

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“…In the presented study, only one autosomal SNP (rs1470608) dropped out at 125 pg input due to low coverage. Observations about the weak amplification rate of rs1470608 have been previously reported in the development of the SNapShot and MPS versions of the HIrisPlex-S (HPS) Panel [11,17,56]. However, the drop-out of rs1470608 causes minimal AUC loss of 0.001 and does not affect the final skin color prediction.…”

Section: Discussionmentioning

confidence: 78%

“…When working with the same DNA quantity obtained from a degraded bone, a consensus profile did not allow for phenotype prediction, demonstrating the strong impact of DNA quality. A study from Kukla-Bartoszek and Szargut [56] also presents the results of forensic phenotyping of high degraded bone samples and suggests that full genotypes can be obtained down to 50 pg of DNA input. In the case of the mentioned study, an additional challenge was a lack of reference data for most of the individuals (almost all of the remains belonged to the victims of communism crimes in Poland in the 1950s) so the reliability of the predictions could not be entirely evaluated.…”

Section: Discussionmentioning

confidence: 99%

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Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

Diepenbroek

Bayer

Schwender

et al. 2020

Genes

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As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable “eye-witness” and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay’s sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.

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Section: Discussionmentioning

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

Diepenbroek

Bayer

Schwender

et al. 2020

Genes

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“…For amplification, the PCR primer couples described in the original studies [ 9 , 27 ] were used. Table S3 shows the panel of the 24 SNPs that can be typed by sequencing the 17 amplicons produced by a single round of multiplex PCR.…”

Section: Methodsmentioning

confidence: 99%

“…In particular, a panel of EVC markers was typed in ancient remains using a set of different skeletal element types from each skeleton and tested to determine whether a reliable prediction can be achieved through generation of a consensus genotype. For more recent samples from the Second World War, it was tested whether a single test-based approach, with no repetition of analysis [ 27 ], could lead to reliable EVC typing. Only one skeletal element type that is the highest DNA-yielding bone type in the human body—the petrous bone—was selected for this purpose.…”

Section: Introductionmentioning

confidence: 99%

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

Pajnič

Zupanc

Leskovar

et al. 2022

Genes

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To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

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“…Increasing understanding of human genome variability is enabling better use of DNA's predictive potential [1]. Besides clinical applications, predictive DNA analysis can be useful in forensics for intelligence purposes [2], in molecular anthropology [3] and in identification of historical figures [4][5][6]. In recent years, intensive research has been carried out on the prediction of various human appearance characteristics [e.g.…”

Section: Introductionmentioning

confidence: 99%

Searching for improvements in predicting human eye colour from DNA

et al. 2021

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Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.

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The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Cited by 21 publications

References 50 publications

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

Searching for improvements in predicting human eye colour from DNA

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