DNA-based predictive models for the presence of freckles. (September 2019)

• Record Type: Journal Article
• Authors: Kukla-Bartoszek, Magdalena; Pośpiech, Ewelina; Woźniak, Anna; Boroń, Michał; Karłowska-Pik, Joanna; Teisseyre, Paweł; Zubańska, Magdalena; Bronikowska, Agnieszka; Grzybowski, Tomasz; Płoski, Rafał; Spólnicka, Magdalena; Branicki, Wojciech
• Is Part Of: Forensic science international. Volume 42(2019)
• Page Start: 252
• Page End: 259
• Publication Date: 2019-09
• Subjects: Freckles -- Forensic DNA phenotyping -- Externally visible characteristics -- DNA prediction -- Targeted massively parallel sequencing; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2019.07.012
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: Ephelides are hyperpigmented spots on skin observed in Europeans and Asians. Pigmentation genes explain significant portion of freckles heritability. Binomial and multinomial models for prediction of freckles are developed. Non- medium- and heavy-freckled people predicted with AUC = 0.75, 0.66 and 0.79. Several epistatic effects and sex important for freckles prediction. Abstract: Freckles or ephelides are hyperpigmented spots observed on skin surface mainly in European and Asian populations. Easy recognition and external visibility make prediction of ephelides, the potentially useful target in the field of forensic DNA phenotyping. Prediction of freckles would be a step forward in sketching the physical appearance of unknown perpetrators or decomposed cadavers for the forensic DNA intelligence purposes. Freckles are especially common in people with pale skin and red hair and therefore it is expected that predisposition to freckles may partially share the genetic background with other pigmentation traits. The first proposed freckle prediction model was developed based on investigation that involved variation of MC1R and 8 SNPs from 7 genes in a Spanish cohort [19 ]. In this study we examined 113 DNA variants from 46 genes previously associated with human pigmentation traits and assessed their impact on freckles presence in a group of 960 individuals from Poland. Nineteen DNA variants revealed associations with the freckle phenotype and the study also revealed that females have ∼1.8 higher odds of freckles presence comparing to males ( p -value = 9.5 × 10 −5 ). Two alternative prediction models were developed using regression methods. A simplified binomial 12-variable model predicts the presence of ephelides with cross-validated AUC = 0.752. A multinomial 14-variable model predicts one of three categories – non-freckled, medium freckled and heavily freckled. The two extreme categories, non-freckled and heavily freckled were predicted with moderately high accuracy of cross-validated AUC = 0.754 and 0.792, respectively. Prediction accuracy of the intermediate category was lower, AUC = 0.657. The study presents novel DNA models for prediction of freckles that can be used in forensic investigations and emphasizes significance of pigmentation genes and sex in predictive DNA analysis of freckles.