DNA-based eye colour prediction across Europe with the IrisPlex system

Walsh, Susan; Wollstein, Andreas; Liu, Fan; Chakravarthy, Usha; Rahu, Mati; Seland, Johan H.; Soubrane, G.; Tomazzoli, Laura; Topouzis, Fotis; Vingerling, Johannes R.; Vioque, Jesús; Fletcher, Astrid; Ballantyne, Kaye N.; Kayser, Manfred

doi:10.1016/j.fsigen.2011.07.009

Cited by 114 publications

(162 citation statements)

References 26 publications

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“…Instead of sensitivity and specificity, the negative and positive predictive values of a given model are more important parameters for practical use, and these are a function of the prevalence. Nevertheless, at least for blue eye colour, our evaluation of the markers proposed by Walsh et al 30 gave similar results as a Europe-wide evaluation, by the same group, 46 of a similar prediction model proposed by Liu et al 47 However, since Northern Germany constitutes only a very small segment of the European gene pool, the general validity of our conclusion needs to be clarified in future studies. For worldwide samples, different models may be required and the addition of ancestral markers may be worthwhile in these instances, owing to the preponderance of brown eye colour and dark Prediction of human skin, eye and hair colour A Caliebe et al skin or hair colour in some regions.…”

Section: Discussionsupporting

confidence: 81%

“…One possibility to overcome this problem would be to apply a high and a low threshold in the first place, and to treat individuals between these thresholds as 'undetermined'. 29,46 In this case, specificity and sensitivity of the prediction model could be increased but would result in a large proportion of cases where no prediction is possible. A second option would be to discard thresholds altogether and for the scientist or forensic expert to merely communicate the actual phenotype probability.…”

Section: Discussionmentioning

confidence: 99%

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The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population

et al. 2015

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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, Po1.2 × 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.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population

et al. 2015

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“…We used the suggested threshold probability of p>0.7 for a conclusive prediction of blue, intermediate or brown eye colour [11] and compared it to a simple prediction model with only HERC2 rs12913832. The predictions of the simple model were calculated using the Snipper classifier [6] that allows prediction of the eye colour based on a subset of the IrisPlex SNPs (in this case, only HERC2 rs12913832).…”

Section: Accuracy Of the Irisplex Prediction Model In The Italian Popmentioning

confidence: 99%

“…As a reply to Martinez-Cadenas and coworker [3], the inventors of the IrisPlex assay tested whether the prediction of categorical eye colour (blue, intermediate and brown) was improved when gender was considered [3]. They used two large IrisPlex datasets with a total of over 9,000 European individuals [4,11]. The results showed that gender did not improve the prediction of the eye colour categories blue, intermediate and brown and concluded that gender had minimal effect on eye colour.…”

Section: Introductionmentioning

confidence: 99%

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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“…[4][5][6][7] The various ethnic groups on Madagascar are generally classified into two main subgroups: the Highlanders (HL), considered being more Asian in culture and phenotype, and the people from the coasts (CT), thought to be more African. 8 The determination of the phenotype, for example, eye colour, hair colour or skin colour, or the population origin from DNA has been an important research field in recent years, in which considerable progress has been accomplished (see for example [9][10][11][12][13][14][15] ). These techniques have already been applied successfully in the characterisation of ancient skeletal human remains.…”

Section: Introductionmentioning

confidence: 99%

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Poetsch¹,

Wiegand²,

Harder³

et al. 2013

Eur J Hum Genet

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Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.

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DNA-based eye colour prediction across Europe with the IrisPlex system

Cited by 114 publications

References 26 publications

The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population

The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population

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

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

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