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Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations

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Abstract

DNA-based prediction for externally visible characteristics such as eye color is already a useful tool in forensic criminal investigations. The IrisPlex system, consisting of six single nucleotide polymorphisms (SNPs) and a prediction model, was developed based on individuals from several European populations. Other recent studies have developed a different prediction model, also based on European populations. In this study, we compared two prediction models using the data for the six IrisPlex SNPs genotyped on 905 individuals from 12 different Eurasian populations. All SNPs showed significant differences in allele frequencies among three groups of populations: European, genetically intermediate (Khanty, Uygur, and Yakut), and East Asian. The two prediction models, the FROG-kb calculation based on the formula of Walsh et al. (2011) and the Snipper calculation from Ruiz et al. (2013), gave identical predictions of brown eye color for the four East Asian populations with complete data but did not give concordant predictions for many individuals in the seven intermediate and European populations. Inconsistencies were mainly conclusive prediction by one model but not the other. Of the 714 individuals with complete 6-locus genotypes, the two models gave 22 % inconsistent predictions. Eliminating the 306 individuals in the Korean and three Chinese populations, in which the predictions were always consistent for brown eye color, the inconsistencies (among the remaining 408 individuals) were 38.7 %. We conclude that more attention should be paid to predictive uncertainty/error. Implementation of both prediction models in future forensic casework is one immediate way to highlight uncertainty.

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Acknowledgments

This work was supported by the Opening Project of Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education (2012KFKT06). The work at Yale was funded primarily by Grant 2010-DN-BX-K225 to KKK awarded by the National Institute of Justice, Office of Justice Programs, US Department of Justice. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the US Department of Justice. We would also like to thank all the collaborators who helped to collect the samples. Special thanks are due the hundreds of individuals who volunteered to give blood samples for studies of gene frequency variation.

Conflict of interest

The authors have declared no conflict of interest.

Ethical standards

The authors declared that the experiments comply with the current laws of China and the protocol was approved by the IRB at Yale.

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Authors and Affiliations

  1. Institute of Forensic Medicine, West China College of Preclinical and Forensic Medicine, Sichuan University, No.16. Section 3. RenMin Nan Road, 610041, Chengdu, Sichuan, People’s Republic of China

    Libing Yun & Yan Gu

  2. Department of Genetics, School of Medicine, Yale University, New Haven, CT, 06520-8005, USA

    Libing Yun, Haseena Rajeevan & Kenneth K. Kidd

Authors
  1. Libing Yun
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  2. Yan Gu
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  3. Haseena Rajeevan
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  4. Kenneth K. Kidd
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Corresponding author

Correspondence to Kenneth K. Kidd.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

The RFLP method, including primers and protocol (DOCX 23 kb)

Online Resource 2

Two spreadsheets of an Excel workbook giving data, calculations, and predictions for all individuals. The first sheet has the information for all fully genotyped individuals. The second sheet has the information for all incompletely genotyped individuals. (XLSX 146 kb)

Online Resource 3

The list of genotypes seen in each population and the numbers among the completely genotyped individuals. (XLSX 35 kb)

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Yun, L., Gu, Y., Rajeevan, H. et al. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. Int J Legal Med 128, 447–453 (2014). https://doi.org/10.1007/s00414-013-0953-1

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  • DOI: https://doi.org/10.1007/s00414-013-0953-1

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