Exploration of SNP variants affecting hair colour prediction in Europeans

Abstract

DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.

Development of a methylation marker set for forensic age estimation using analysis of public methylation data and the Agena Bioscience EpiTYPER system

“…Besides human pigmentation, other visible traits including facial morphology [6], stature [7] and hair shape [8] have all been proposed to provide useful data about an unidentified person. Prediction of externally visible characteristics such as hair colour [9,10] or early onset male pattern baldness [11] are potentially highly informative but are hindered by a lack of accuracy related to changes in phenotypic expression as a person gets older. Therefore, inference of a person's age can provide an important contribution to the following forensic analyses: i. to guide police investigations in the absence of eyewitness testimony or a national DNA database entry; ii.…”

The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation

“…In particular, the prediction of broad (i.e., categorical) eye and hair colour phenotypes from SNP genotypes is now achievable with practically useful accuracies, for instance by applying the IrisPlex and HIrisPlex DNA test systems that have been forensically validated [31][32][33][34], as well as tested and applied [35,36]. Similar tools for eye and hair colour DNA prediction that largely overlap in SNP predictors with the Iris/HIrisPlex systems have also been generated and used [21,[37][38][39][40][41][42]. This advancement in understanding the genetic basis and DNAbased predictability of eye and hair colour was achievable in part because these two pigmentation traits A C C E P T E D M A N U S C R I P T evolved in genetically homogeneous Europeans that were used in these genetic studies, and therefore are found today almost exclusively in people of (at least partial) European bio-geographic ancestry.…”

“…Therefore, the predictability of skin colour from DNA [37][38][39] lagged behind that of eye and hair colour [30][31][32][33][34][35][36][37][38][39][40][41][42]. Valenzuela et al [21] obtained a low R 2 value for skin reflectance of 45.7% based on three SNPs.…”

Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains

“…For this, the BioMark™ EP1™ real‐time PCR system (Fluidigm Corp., South San Francisco, CA) was used. Suitable SNPs were selected from various papers about FDP (Pneuman, Budimlija, Caragine, Prinz, & Wurmbach, ; Söchtig et al, ; Walsh et al, ) available through an online search using the National Centre for Biotechnology Information database (NCBI; Table S2). Based on these SNPs custom‐designed SNPtype™ assays were ordered at the Fluidigm® company.…”