Prediction of Human Pigmentation Traits from DNA Polymorphisms

Abstract

Driven by recent evolutionary history, pigmentation traits significantly contribute to the most obvious parts of the overall human phenotypic diversity with skin colour varying between worldwide individuals, while eye and hair colour differences only exist in individuals of European (and neighbouring region) descent. Genetic association studies have discovered various DNA variants that together explain large proportion of phenotypic variance in eye, hair and skin colouration. Besides providing leads in the molecular understanding of human pigmentation, multiple associated DNA variants have also been used for prediction modelling of pigmentation traits. The success of DNA‐based pigmentation prediction laid the foundation for a new subfield of forensic genetics known as Forensic DNA Phenotyping, which aims to help finding unknown perpetrators. Pigmentation DNA prediction is further relevant in anthropological research from old and ancient human remains for reconstructing colour phenotypes of deceased persons including those of historical importance.

Key Concepts

  • Driven by recent evolutionary history, differences in pigmentation significantly contribute to the phenotypic diversity in humans.
  • Eye, hair and skin colour reflect complex traits with multiple genes and environmental factors determining phenotypic variation distributed differently around the world.
  • Gene mapping studies identified a number of pigmentation genes that typically but not necessarily determine all three pigmentation traits in humans.
  • Multiple pigmentation‐associated DNA variants have proven useful to predict all three human pigmentation traits with varying accuracies.
  • Several DNA test systems are available for accurate prediction of blue and brown eyes, while for other eye colours further research is needed.
  • Available DNA test systems for hair colour provide accurate prediction of red and (albeit less so) of black hair, while the DNA prediction of blond and brown hair is troubled by age‐dependent hair colour changes in some (but not all) individuals not yet understood on the molecular level.
  • Of the three human pigmentation traits, DNA prediction of skin colour is least advanced, requiring considerable further research.
  • Current DNA prediction on the level of categorical eye, hair and skin colour shall be improved towards more detailed colour phenotypes, if the necessary DNA predictors become available via dedicated future research.
  • Forensic science is a major recipient of pigmentation predictive DNA tests, where they are used to trace unknown perpetrators unidentifiable via conventional DNA profiling.
  • Pigmentation DNA prediction is also relevant in anthropological and human evolutionary research particularly from old and ancient human remains.

Keywords: human appearance; eye colour; hair colour; skin colour; pigmentation genetics; genotype to phenotype; prediction modelling; molecular anthropology; forensic genetics; forensic DNA phenotyping

Figure 1. Illustration of HIrisPlex‐based eye and hair colour DNA prediction. Eye and hair images of 12 individuals selected to vary strongly in hair and eye colour with their eye colour probabilities as obtained with the enhanced IrisPlex model and their hair colour probabilities obtained with the enhanced HIrisPlex model (http://hirisplex.erasmusmc.nl) from complete 24‐loci DNA profiles generated with the HIrisPlex genotyping assay. Those probabilities that led to the predicted eye and hair colour categories are highlighted in grey following guidelines described in Walsh . (, ). Individual numbering is 1–6 on the left side and 7–12 on the right side. DNA‐based prediction conclusions are as follows: 1: black hair and brown eyes, 2: dark brown/black hair and brown eyes, 3: dark brown/black hair and blue eyes, 4: brown/dark brown hair and blue eyes, 5: Brown/medium brown hair and brown eyes, 6: Brown hair and brown eyes (likely with non‐brown parts), 7: Blond/dark blond hair and blue eyes, 8: blond hair and blue eyes, 9: blond/dark blond hair and blue eyes, 10: red hair and blue eyes, 11: red hair and brown eyes (likely with non‐brown parts), 12: red hair and blue eyes. Reproduced from Kayser (2015a) © Elsevier.
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Further Reading

Jablonski NG (2012) Living Colour: The Biological and Social Meaning of Skin Colour. Berkeley: University of California Press.

Kayser M (2015b) Forensic DNA phenotyping: predicting human appearance from crime scene material for investigative purposes. Forensic Science International: Genetics. 10.1016/j.fsigen.2015.02.003.

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Visser M, Kayser M, Grosveld F and Palstra R‐J (2014) Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation. Pigment Cell & Melanoma Research 27: 169–177.

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Branicki, Wojciech, and Kayser, Manfred(Oct 2015) Prediction of Human Pigmentation Traits from DNA Polymorphisms. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023851]