Interactions Between HERC2, OCA2 and MC1R May Influence Human Pigmentation Phenotype

Branicki, Wojciech; Brudnik, Urszula; Wojas‐Pelc, Anna

doi:10.1111/j.1469-1809.2009.00504.x

Cited by 106 publications

(105 citation statements)

References 41 publications

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“…Similar results were observed for already published male and female eye colour frequency data in Icelandic and Dutch populations [8] but not in Australian [9] and Polish populations [10]. Martinez-Cadenas and co-workers [1] suggested that the prediction success of the IrisPlex model and other models used to predict eye colour phenotypes from DNA genotypes may be improved by including gender as a factor.…”

Section: Introductionsupporting

confidence: 86%

The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model

Pietroni

Andersen

Johansen

et al. 2014

Forensic Science International: Genetics

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. In this study, we investigate the role of gender as a factor that contributes to eye colour variation and suggest that the gender effect on eye colour is population specific.A total of 230 Italian individuals were typed for the six IrisPlex SNPs (rs12913832, rs1800407, rs12896399, rs1393350, rs16891982 and rs12203592). A quantitative eye colour score (Pixel Index of the Eye: PIE-score) was calculated based on digital eye images using the custom made DIAT software. The results were compared with those of Danish and Swedish population samples.As expected, we found HERC2 rs12913832 as the main predictor of human eye colour independently of ancestry. Furthermore, we found gender to be significantly associated with quantitative eye colour measurements in the Italian population sample. We found that the association was statistically significant only among Italian individuals typed as heterozygote GA for HERC2 rs12913832. Interestingly, we did not observe the same association in the Danish and Swedish population. This indicated that the gender effect on eye colour is population specific. We estimated the effect of gender on quantitative eye colour in the Italian population sample to be 4.9%. Among gender and the IrisPlex SNPs, gender ranked as the second most important predictor of human eye colour variation in Italians after HERC2 rs12913832. We, furthermore, tested the five lower ranked IrisPlex predictors, and evaluated all possible 3 6 (729) genotype combinations of the IrisPlex assay and their corresponding predictive values using the IrisPlex prediction model [4]. The results suggested that maximum three (rs12913832, rs1800407, rs16891982) of the six IrisPlex SNPs are useful in practical forensic genetic casework.

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Section: Introductionsupporting

confidence: 86%

The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model

Pietroni

Andersen

Johansen

et al. 2014

Forensic Science International: Genetics

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“…16,26,32,39 Analysis of the HERC2-OCA2 region enables prediction of extreme (blue or brown) eye colours from genetic data with a reasonably high accuracy and has already been applied in real cases concerning identification of human remains. 40,41 Several other genes have been found to contribute to a lesser degree to the continuous variation in iris colour from light blue through intermediate (green and hazel) to dark brown, which is observed in humans.…”

Section: Discussionmentioning

confidence: 99%

“…In case of the rs12913832 position additionally recessive categorisation was applied and this was chosen for reporting as more appropriate and giving clearer results, which is also supported by our previous study. 26 In the case of the MC1R gene, polymorphisms were divided into two groups: the high penetrance variants coded as 'R' (N29insA, V84E (rs1805006), R151C (rs1805007), R142H (rs11547464), R160W (rs1805008), D294H (rs1805009) and Y152OCH), and low penetrance variants coded as 'r' (V60L (rs1805005), V92M (rs2228479), I155T (rs1110400) and R163Q (rs885479)). For high penetrance variants ('R'), three states were considered, assuming the existence of major function mutations; that is, 0¼no 'R' variant carriers, 1¼one 'R' variant carrier and 2¼two 'R' variant carriers.…”

Section: Statistical Calculationsmentioning

confidence: 99%

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Gene–gene interactions contribute to eye colour variation in humans

et al. 2011

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Prediction of phenotypes from genetic data is considered to be the first practical application of data gained from association studies, with potential importance for medicine and the forensic sciences. Multiple genes and polymorphisms have been found to be associated with variation in human pigmentation. Their analysis enables prediction of blue and brown eye colour with a reasonably high accuracy. More accurate prediction, especially in the case of intermediate eye colours, may require better understanding of gene-gene interactions affecting this polygenic trait. Using multifactor dimensionality reduction and logistic regression methods, a study of gene-gene interactions was conducted based on variation in 11 known pigmentation genes examined in a cohort of 718 individuals of European descent. The study revealed significant interactions of a redundant character between the HERC2 and OCA2 genes affecting determination of hazel eye colour and between HERC2 and SLC24A4 affecting determination of blue eye colour. Our research indicates interactive effects of a synergistic character between HERC2 and OCA2, and also provides evidence for a novel strong synergistic interaction between HERC2 and TYRP1, both affecting determination of green eye colour.

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“…The most strongly associated variant, rs12913832, shows the homozygous A allele in the Iceman's genome (coverage depth ×31), which is associated with brown eye colour in over 80% of cases even when regarded alone 30 . Branicki et al 31 defined a haplotype of five SNPs as predictor: rs4778138, rs4778241, rs7495174, rs12913832 and rs916977. The Iceman's haplotype (for which TTTTC and TTTTT were addressed together as the last SNP is a clear heterozygote) in the Branicki study encompassed 46 individuals, 8 of which were blue eyed, the residual 38 having a non-blue eye colour.…”

Section: Snp Analysismentioning

confidence: 99%

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

et al. 2012

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The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and presentday inhabitants of the Tyrrhenian sea, that the Iceman probably had brown eyes, belonged to blood group o and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

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Interactions Between HERC2, OCA2 and MC1R May Influence Human Pigmentation Phenotype

Cited by 106 publications

References 41 publications

The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model

The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model

Gene–gene interactions contribute to eye colour variation in humans

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

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