Original Paper

Genotyping Error Detection in Samples of Unrelated Individuals without Replicate Genotyping
Nianjun Liu^a, Dabao Zhang^b, Hongyu Zhao<sup>c, d

a</sup>DepartmentofBiostatistics,UniversityofAlabamaatBirmingham, Birmingham, Ala.,
^bDepartment of Statistics, Purdue University, West Lafayette, Ind., and Departments of
^cEpidemiology and Public Health and
^dGenetics, Yale University School of Medicine, New Haven, Conn., USA

Address of Corresponding Author

Hum Hered 2009;67:154-162 (DOI: 10.1159/000181153)

  Key Words

• Genotyping error
• Single nucleotide polymorphisms (SNPs)
• Identifiability

  Abstract

Objective: Identifying genotyping errors is an important issue in genetic research, yet it has been relatively less studied in samples consisting of unrelated individuals. In this article, we consider several models of genotyping errors, which were originally proposed for pedigree data, for unrelated population samples with single nucleotide polymorphism (SNP) genotype data. The mathematical constraints are investigated for detecting genotyping errors without resampling replicates or genotyping relatives. Methods: For the various proposed genotyping error models, we unveil the conditions under which the parameters are identifiable. These results are verified through applications to simulated and real SNP data. Results: We show that, with constraints, two particular models provide both identifiable error rate and allele frequencies of an SNP for unrelated population data. The simulation study shows that these two models present unbiased estimates for the allele frequencies. One of the models also gives an unbiased estimate for the genotyping error rate. Conclusion: While the Hardy-Weinberg equilibrium test can be used to detect genotyping errors, a key advantage of these models is the explicit estimates of genotyping error rates and allele frequencies. This work may help researchers to estimate error rates and to use the estimates in their analysis to increase power and decrease bias, without the extra work of genotyping family members or replicates.

Copyright © 2008 S. Karger AG, Basel

  Author Contacts

Nianjun Liu
Department of Biostatistics, 420A Ryals Public Health Building
1665 University Boulevard, The University of Alabama at Birmingham
Birmingham, AL 35294 (USA)
Tel. +1 205 975 9190, Fax +1 205 975 2540, E-Mail nliu@uab.edu

  Article Information

Received: October 8, 2007
Accepted after revision: May 16, 2008
Published online: December 15, 2008
Number of Print Pages : 9
Number of Figures : 3, Number of Tables : 2, Number of References : 61