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Exploration of SNP variants affecting hair colour prediction in Europeans

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Abstract

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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Acknowledgments

The authors are very grateful to all the sample donors who participated in the project. JS would like to acknowledge the support of the German FAZIT foundation. MVL was supported by funding from Xunta de Galicia, Incite 09208163 PR.

Conflict of interest

The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, A Coruña, Spain

    Jens Söchtig, Chris Phillips, Olalla Maroñas, Yarimar Ruiz, Manuel Fondevila, Ángel Carracedo & María V. Lareu

  2. Faculty of Mathematics, University of Santiago de Compostela, A Coruña, Spain

    Antonio Gómez-Tato, Jose Alvarez-Dios & María-Ángeles Casares de Cal

  3. CIBERER, Genomic Medicine Group, University of Santiago de Compostela, A Coruña, Spain

    Raquel Cruz & Ángel Carracedo

  4. Dermatologikum Hamburg, Hamburg, Germany

    Kristian Reich

  5. Clinic for Dermatology, Allergology and Venerology, University Medical Center Göttingen, Göttingen, Germany

    Kristian Reich

  6. Criminalistics Unit Against Violation of Fundamental Rights (UCCVDFAMC), Public Ministry, Caracas, Venezuela

    Yarimar Ruiz

  7. Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Ángel Carracedo

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  1. Jens Söchtig
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  2. Chris Phillips
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Correspondence to Chris Phillips.

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Söchtig, J., Phillips, C., Maroñas, O. et al. Exploration of SNP variants affecting hair colour prediction in Europeans. Int J Legal Med 129, 963–975 (2015). https://doi.org/10.1007/s00414-015-1226-y

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