Improved eye- and skin-color prediction based on 8 SNPs

Abstract

AimTo improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions.MethodsAnalysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P = 0.007) but a rather poor strength of agreement (κ = 0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color.ResultsThe 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P = 6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set).ConclusionsWe can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.

Identification of individuals by trait prediction using whole-genome sequencing data

“…Similarly, skin color has an estimated heritability of 81% (40), with 11 genes predominantly contributing to pigmentation (41). For both eye and skin color, previous models predicted color categories rather than continuous values (10,13,42), often by using ad hoc decision rules. To our knowledge, none have used genome-wide variation to predict color.…”

“…The clinical and research community uses a fragmented system to enforce privacy that includes institutional review boards, ad hoc data access committees, and a range of privacy and security practices such as the Health Insurance Portability and Accountability Act (HIPAA) (9) and the Common Rule. These approaches are important, but may prove insufficient for genetic data (10). Even distribution of genomic data in summarized form, such as allele frequencies, carries some privacy risk (11).…”

“…Models exist for predicting individual traits such as skin color (5,10,12,13), eye color (10), and facial structure (14). We built models to predict 3D facial structure, voice, biological age, height, weight, body mass index (BMI), eye color, and skin color.…”

Crime investigation through DNA methylation analysis: methods and applications in forensics

“…The current research in DNA phenotyping (physical appearance because of the unique DNA) shows that 24 DNA markers (SNP) can be successfully used to predict the color of the hair as well as the eye of an individual from the DNA obtained from his/her body tissues (Walsh et al, 2013). Other genes responsible for skin color, hair structure, and baldness have been determined (Hart et al, 2013;Liu et al, 2015;Marcinska et al, 2015;Pospiech et al, 2015). In future, this technique can be combined with predicting method of age, biogeographic/ethnicity as well as behaviour of an individual from the DNA methylation data (Next Generation DNA Phenotyping), which can be used to accurately construct the inclusive facial picture who leaves behind the DNA mark but has no match for his/her DNA fingerprint.…”

Predicting Physical Features and Diseases by DNA Analysis: Current Advances and Future Challenges

“…There are at least ten published studies presenting methods to explore the predictive values of combinations of SNP alleles of pigmentation phenotypes (skin, eye and hair colour) and presence/absence of freckles [33][34][35][36][37][38][39][40][41][42], two of which [34,40] have already been validated [43][44][45]. Additional research is under development regarding these and other phenotypes, such as estimation of age [46][47][48][49], height [50,51], hair shape [52][53][54], facial features [55,56], baldness [54, 57,58], and adult stuttering [59,60].…”