The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population.
Human pigmentation traits are of great interest to many research areas, from ancient DNA analysis to forensic science. We developed a gene-based predictive model for pigmentation phenotypes in a realistic target population for forensic case work from Northern Germany and compared our model with those brought forth by previous studies of genetically more heterogeneous populations. In doing so, we aimed at answering the following research questions: (1) do existing models allow good prediction of high-quality phenotypes in a genetically similar albeit more homogeneous population? (2) Would a model specifically set up for the more homogeneous population perform notably better than existing models? (3) Can the number of markers included in existing models be reduced without compromising their predictive capability in the more homogenous population? We investigated the association between eye, hair and skin colour and 12 candidate single-nucleotide polymorphisms (SNPs) from six genes. Our study comprised two samples of 300 and 100 individuals from Northern Germany. SNP rs12913832 in HERC2 was found to be strongly associated with blue eye colour (odds ratio=40.0, P<1.2 × 10(-4)) and to yield moderate predictive power (AUC: 77%; sensitivity: 90%, specificity: 63%, both at a 0.5 threshold for blue eye colour probability). SNP associations with hair and skin colour were weaker and genotypes less predictive. A comparison with two recently published sets of markers to predict eye and hair colour revealed that the consideration of additional SNPs with weak-to-moderate effect increased the predictive power for eye colour, but not for hair colour.
Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany.
Amke
A
Caliebe
Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany.
Melanie
M
Harder
Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany.
Rebecca
R
Schuett
Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany.
Michael
M
Krawczak
Institute of Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany.
Almut
A
Nebel
Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany.
Nicole
N
von Wurmb-Schwark
D000328:Adult; D005127:Eye Color / Q000235:genetics*; D005260:Female; D005858:Germany; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics*; D006200:Hair Color / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012880:Skin Pigmentation / Q000235:genetics*; D044767:Ubiquitin-Protein Ligases
D020662:Guanine Nucleotide Exchange Factors; C118566:HERC2 protein, human; D044767:Ubiquitin-Protein Ligases