A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model

To analyze two phenotype characteristics--eye and hair color--using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population. Twelve SNPs (OCA2 - rs1667394, rs7170989, rs1800407, rs7495174; HERC2 - rs1129038, rs12913832; MC1R - rs1805005, rs1805008; TYR -...

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Bibliographic Details
Published in:Croatian medical journal 2012-10, Vol.53 (5), p.401-408
Main Authors: Kastelic, Vanja, Drobnic, Katja
Format: Article
Language:English
Subjects:
Adult
Analysis
Bayes Theorem
Color of eyes
Criminal investigation
DNA - genetics
DNA Primers - genetics
Eye Color - genetics
Female
Forensic Science
Genetic aspects
Genetics, Population
Genotype
Hair Color - genetics
Humans
Male
Membrane Transport Proteins - genetics
Methods
Multiplex Polymerase Chain Reaction
Phenotype
Physiological aspects
Polymorphism, Single Nucleotide
Receptor, Melanocortin, Type 1 - genetics
Single nucleotide polymorphisms
Slovenia
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Description
Summary:To analyze two phenotype characteristics--eye and hair color--using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population. Twelve SNPs (OCA2 - rs1667394, rs7170989, rs1800407, rs7495174; HERC2 - rs1129038, rs12913832; MC1R - rs1805005, rs1805008; TYR - rs1393350; SLC45A2 - rs16891982, rs26722; SLC24A5 - rs1426654) were used for the development of a single multiplex assay. The single multiplex assay was based on SNaPshot chemistry and capillary electrophoresis. In order to evaluate the accuracy of the prediction of eye and hair color, we used the logistic regression model and the Bayesian network model, and compared the parameters of both. The new single multiplex assay displayed high levels of genotyping sensitivity with complete profiles generated from as little as 62 pg of DNA. Based on a prior evaluation of all SNPs in a single multiplex, we focused on the five most statistically significant in our population in order to investigate the predictive value. The two prediction models performed reliably without prior ancestry information, and revealed very good accuracy for both eye and hair color. Both models determined the highest predictive value for rs12913832 (P
ISSN:0353-9504
1332-8166
DOI:10.3325/cmj.2012.53.401