The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction

Pośpiech, Ewelina; Wojas‐Pelc, Anna; Walsh, Susan; Liu, Fan; Maeda, Hitoshi; Ishikawa, Takaki; Skowron, Małgorzata; Kayser, Manfred; Branicki, Wojciech

doi:10.1016/j.fsigen.2014.01.012

Cited by 61 publications

(80 citation statements)

References 57 publications

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“…Amongst HIrisPlex SNPs, it has the strongest predictive effect for non-red hair colour together with rs16891982 and rs12203592 [29]. Several other studies identified rs12913832 as the strongest marker for hair colour inference [21,46,47] while a recent study by Branicki identified several SNP-SNP interactions for rs12913832 influencing hair colour [48]. Apart from mild synergistic interactions between rs12913832 and rs28777, we did not detect comparable interactions.…”

Section: Discussioncontrasting

confidence: 93%

“…It is well known that hair colour often changes during an individual's lifetime, and such shifts include the darkening of blond hair colour in particular [19]. This effect, as well as its implication for hair colour inference in forensic analysis, was described previously by Walsh [27] and Branicki [48]. Finally, it is important to highlight several limitations to the present study.…”

Section: Discussionmentioning

confidence: 60%

“…Branicki reported a similar frequency in a Polish cohort of 385 but did not detect a significant association to any hair colour [21]. However, more recently, the same group found significant association to black hair colour from multivariate binary logistic regression analysis [48]. Moreover, Branicki found synergistic epistatic interactions between rs35264875 and rs1042602 in TYR.…”

Section: Discussionmentioning

confidence: 90%

“…Furthermore, use of the Fischer-Saller chart seems to be more appropriate for phenotyping populations of northern Europe compared to the south since the fair hair colour range (fair/dark blond) is overrepresented in contrast to the limited dark hair sample range (dark brown/black). A lower brown hair colour predictive power could be further attributed to a lack of full marker coverage, epigenetic effects [48] and/or environmental influences. It is well known that hair colour often changes during an individual's lifetime, and such shifts include the darkening of blond hair colour in particular [19].…”

Section: Discussionmentioning

confidence: 99%

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Exploration of SNP variants affecting hair colour prediction in Europeans

et al. 2015

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DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.

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Section: Discussioncontrasting

confidence: 93%

Section: Discussionmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

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Exploration of SNP variants affecting hair colour prediction in Europeans

et al. 2015

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“…However, externally visible characteristics (EVCs) are difficult to understand due to their high complexity derived from their multifactorial nature, involving various genes, gene-environment interactions, and epistasis phenomena [4,5]. EVCs are also not widely used at present because some phenotypic loci may provide ancestral or clinical information that may raise ethical concerns in the forensic field.…”

Section: Introductionmentioning

confidence: 99%

Assessment of IrisPlex-based multiplex for eye and skin color prediction with application to a Portuguese population

et al. 2015

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DNA phenotyping research is one of the most emergent areas of forensic genetics. Predictions of externally visible characteristics are possible through analysis of single nucleotide polymorphisms. These tools can provide police with "intelligence" in cases where there are no obvious suspects and unknown biological samples found at the crime scene do not result in any criminal DNA database hits. IrisPlex, an eye color prediction assay, revealed high prediction rates for blue and brown eye color in European populations. However, this is less predictive in some non-European populations, probably due to admixing. When compared to other European countries, Portugal has a relatively admixed population, resulting from a genetic influx derived from its proximity to and historical relations with numerous African territories. The aim of this work was to evaluate the utility of IrisPlex in the Portuguese population. Furthermore, the possibility of supplementing this multiplex with additional markers to also achieve skin color prediction within this population was evaluated. For that, IrisPlex was augmented with additional SNP loci. Eye and skin color prediction was estimated using the multinomial logistic regression and binomial logistic regression models, respectively. The results demonstrated eye color prediction accuracies of the IrisPlex system of 90 and 60% for brown and blue eye color, respectively, and 77% for intermediate eye color, after allele frequency adjustment. With regard to skin color, it was possible to achieve a prediction accuracy of 93%. In the future, phenotypic determination multiplexes must include additional loci to permit skin color prediction as presented in this study as this can be an advantageous tool for forensic investigation.

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Forensic DNA Analysis

Prinz¹,

Lessig²

2022

Handbook of Forensic Medicine

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The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction

Cited by 61 publications

References 57 publications

Exploration of SNP variants affecting hair colour prediction in Europeans

Exploration of SNP variants affecting hair colour prediction in Europeans

Assessment of IrisPlex-based multiplex for eye and skin color prediction with application to a Portuguese population

Forensic DNA Analysis

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