Phenotype prediction accuracy – A Swedish perspective

Junker, Klara; Staadig, Adam; Sidstedt, Maja; Tillmar, Andreas; Hedman, Jonas

doi:10.1016/j.fsigss.2019.10.022

Cited by 4 publications

(2 citation statements)

References 10 publications

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“…The molecular structure of these changes is still not clear [ 16 , 30 ]. The brown hair color prediction success was lower in other European population studies compared to our results [ 16 , 29 , 31 ]. Blond hair phenotypes are more common in Europe than in the Turkish population.…”

Section: Resultscontrasting

confidence: 99%

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

Simsek

Filoğlu

et al. 2022

Genes

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Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color.

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Section: Resultscontrasting

confidence: 99%

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

Simsek

Filoğlu

et al. 2022

Genes

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show abstract

“…However, the AUC value for blond hair (0.72) was considerably lower than reported by HIrisPlex (0.81). This may be because the most common incorrect prediction across all hair colours were for individuals with brown hair who were predicted to have blond hair, which is also in line with data from a Swedish population [51]. Kukla-Bartoszek et al suggested that incorrect predictions may be the result of age-dependent hair colour darkening [52].…”

Section: Hair Colour Predictions In a Norwegian Study Populationsupporting

confidence: 53%

Predicting eye and hair colour in a Norwegian population using Verogen’s ForenSeq™ DNA signature prep kit

Salvo

Janssen

Kirsebom

et al. 2022

Forensic Science International: Genetics

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Prediction of eye and hair colour from DNA can be an important investigative tool in forensic cases if conventional DNA profiling fails to match DNA from any known suspects or cannot obtain a hit in a DNA database. The HIrisPlex model for simultaneous eye and hair colour predictions was developed for forensic usage. To genotype a DNA sample, massively parallel sequencing (MPS) has brought new possibilities to the analysis of forensic DNA samples. As part of an in-house validation, this study presents the genotyping and predictive performance of the HIrisPlex SNPs in a Norwegian study population, using Verogen's ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system and the HIrisPlex webtool. DNA-profiles were successfully typed with DNA input down to 125 pg. In samples with DNA input < 125 pg, false homozygotes were observed with as many as 92 reads. Prediction accuracies in terms of AUC were high for red (0.97) and black (0.93) hair colours, as well as blue (0.85) and brown (0.94) eye colours. The AUCs for blond (0.72) and brown (0.70) hair colour were considerably lower. None of the individuals was predicted to have intermediate eye colour. Therefore, the error rates of the overall eye colour predictions were 37% with no predictive probability threshold (pmax) and 26% with a probability threshold of 0.7. We also observed that more than half of the incorrect predictions were for individuals carrying the rs12913832 GG genotype. For hair colour, 65% of the individuals were correctly predicted when using the highest probability category approach. The main error was observed for individuals with brown hair colour that were predicted to have blond hair. Utilising the prediction guide approach increased the correct predictions to 75%. Assessment of phenotype-genotype associations of eye colours using a quantitative eye colour score (PIEscore), revealed that rs12913832 AA individuals of Norwegian descent had statistically significantly higher PIEscore (less brown eye colour) than individuals of non-northern European descent. To our knowledge, this has not been reported in other studies. Our study suggests that careful assessment of the target population prior to the implementation of forensic DNA phenotyping to case work is beneficial.

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A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences

Frégeau

2021

Canadian Society of Forensic Science Journal

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Phenotype prediction accuracy – A Swedish perspective

Cited by 4 publications

References 10 publications

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

Predicting eye and hair colour in a Norwegian population using Verogen’s ForenSeq™ DNA signature prep kit

A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences

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