DNA-based predictive models for the presence of freckles.
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.
['Kukla-Bartoszek|Magdalena|M|', 'Pośpiech|Ewelina|E|', 'Woźniak|Anna|A|', 'Boroń|Michał|M|', 'Karłowska-Pik|Joanna|J|', 'Teisseyre|Paweł|P|', 'Zubańska|Magdalena|M|', 'Bronikowska|Agnieszka|A|', 'Grzybowski|Tomasz|T|', 'Płoski|Rafał|R|', 'Spólnicka|Magdalena|M|', 'Branicki|Wojciech|W|']
D024722:Cardiac Myosins D015331:Cohort Studies D004268:DNA-Binding Proteins D016326:Extracellular Matrix Proteins D005260:Female D006023:Glycoproteins D020662:Guanine Nucleotide Exchange Factors D034482:Heterogeneous-Nuclear Ribonucleoprotein Group C D059014:High-Throughput Nucleotide Sequencing D006801:Humans D050835:Interferon Regulatory Factors D016015:Logistic Models D008297:Male D008548:Melanosis D026901:Membrane Transport Proteins D008957:Models, Genetic D014442:Monophenol Monooxygenase D018995:Myosin Heavy Chains D009687:Nuclear Proteins D056918:Nuclear Receptor Coactivators D010641:Phenotype D020641:Polymorphism, Single Nucleotide D044102:Receptor, Melanocortin, Type 1 D012680:Sensitivity and Specificity D017422:Sequence Analysis, DNA D012737:Sex Factors D012880:Skin Pigmentation D044767:Ubiquitin-Protein Ligases
Freckles Forensic DNA phenotyping DNA prediction Externally visible characteristics Targeted massively parallel sequencing