The Mesolithic Cheddar Man andthe Neolithic sample from Carsington Pasture Cave,Derbyshire (‘Sven’) had sufficient coverage to estimate heterozygosity. Consistent with recent ancestry from larger or more admixed populations, Sven showed slightly higher levels of heterozygosity than Cheddar Man (Supplementary Figure S10).None of the Mesolithic and Neolithic British individuals analysed here had a derived lactase persistence allele (see Supplementary Table S2). We predicted pigmentation characteristics for Cheddar Man and Sven using Hirisplex and a recently-developed method for predicting skin pigmentation[26]
Previously, predictions on the level of skin pigmentation were mostly derived using two SNPs in SLC45A2 and SLC24A5 that indicate lack of hypo-pigmentation when in the ancestral state
. However, here we integrate 36 rather than 2 SNPs allowing more precise prediction
. Cheddar Man is predicted to have had dark or dark to black skin, blue/green eyes and dark brown possibly black hair, whereas Sven most likely had intermediate to dark skin pigmentation, brown eyes and black possibly dark brown hair (see Pigmentation section in the Supplementary Materials for a detailed discussion of the results). This is in line with the current hypothesis that alleles commonly as sociated with lighter skin were introduced in Western Europe by ANFs 19 .
Hum Genet. 2017 Jul;136(7):847-863. doi: 10.1007/s00439-017-1808-5. Epub 2017 May 12.
Global skin colour prediction from DNA.
Walsh S1, Chaitanya L2, Breslin K3, Muralidharan C3, Bronikowska A4, Pospiech E5,6, Koller J2, Kovatsi L7, Wollstein A8, Branicki W6,9, Liu F2,10,11, Kayser M12. Author information Erratum in
Erratum to: Global skin colour prediction from DNA. [Hum Genet. 2017]
Abstract
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.
Welcome to the Department of Genetic Identification of Erasmus MC
With the advancement of DNA phenotyping as a tool in Forensic and Anthropological usage, we now provide an easy to use interactive website to predict eye, hair and skin colour from DNA using the IrisPlex, HIrisPlex and HIrisPlex-S systems.
This work is in collaboration with the Walsh laboratory of Indiana-University-Purdue-University-Indianapolis (IUPUI), USA.
Please see the manual for instructions. We hope you enjoy using this tool and find it a useful addition to your analyses. If you have any issues regarding this website, please contact us at dnaphenotyping ... at ... gmail ... com
Funding support
The initial research and development that led to this resource was supported in part by funding from the Netherlands Forensic Institute (NFI), the Erasmus MC University Medical Center Rotterdam, and by a grant from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN). Development and maintenance of this web resource is supported by Erasmus MC University Medical Center Rotterdam.
The work of the Walsh laboratory is funded in part by the U.S. National Institute of Justice under grant number 2014-DN-BX-K031, the views presented here are for informational purposes only and do not constitute product approval or endorsement by the U.S. Department of Justice.
Forensic DNA Phenotyping (FDP), i.e. the prediction of human externally visible traits from DNA, has become a fast growing subfield within forensic genetics due to the intelligence information it can provide from DNA traces. FDP outcomes can help focus police investigations in search of unknown perpetrators, who are generally unidentifiable with standard DNA profiling. Therefore, we previously developed and forensically validated the IrisPlex DNA test system for eye colour prediction and the HIrisPlex system for combined eye and hair colour prediction from DNA traces. Here we introduce and forensically validate the HIrisPlex-S DNA test system (S for skin) for the simultaneous prediction of eye, hair, and skin colour from trace DNA. This FDP system consists of two SNaPshot-based multiplex assays targeting a total of 41 SNPs via a novel multiplex assay for 17 skin colour predictive SNPs and the previous HIrisPlex assay for 24 eye and hair colour predictive SNPs, 19 of which also contribute to skin colour prediction. The HIrisPlex-S system further comprises three statistical prediction models, the previously developed IrisPlex model for eye colour prediction based on 6 SNPs, the previous HIrisPlex model for hair colour prediction based on 22 SNPs, and the recently introduced HIrisPlex-S model for skin colour prediction based on 36 SNPs. In the forensic developmental validation testing, the novel 17-plex assay performed in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, as previously shown for the 24-plex assay. Sensitivity testing of the 17-plex assay revealed complete SNP profiles from as little as 63 pg of input DNA, equalling the previously demonstrated sensitivity threshold of the 24-plex HIrisPlex assay. Testing of simulated forensic casework samples such as blood, semen, saliva stains, of inhibited DNA samples, of low quantity touch (trace) DNA samples, and of artificially degraded DNA samples as well as concordance testing, demonstrated the robustness, efficiency, and forensic suitability of the new 17-plex assay, as previously shown for the 24-plex assay.
now allowing the estimation of individual probabilities for 3 eye, 4 hair, and 5 skin colour categories from HIrisPlex-S input genotypes. The HIrisPlex-S DNA test represents the first forensically validated tool for skin colour prediction, and reflects the first forensically validated tool for simultaneous eye, hair and skin colour prediction from DNA.
Posts: 42921 | From: , | Registered: Jan 2010
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quote:..Cheddar Man is predicted to have had dark or dark to black skin..
Which again verifies my point that these experts estimate a range of pigmentation. Really I don't know why you bother creating a whole other thread of the topic discussed here. Posts: 26243 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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This thread is about recent forensic techniques used in the article Global skin colour prediction from DNA by Walsh et all and the interactive program HIrisPlex (including a link to use it)
Cheddar man is just an example of use of these methods and new program
Posts: 42921 | From: , | Registered: Jan 2010
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