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Updated: Jun 17, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Accommodating population stratification in case-control association analysis: a new test and its application to
Yufang Zhang1, Xiangjun Xiao, Kai Wang
1Program of Public Health Genetics, University of Iowa, 200 Hawkins Drive E177 GH, Iowa City, Iowa 52242 USA. yufang-zhang@uiowa.edu.
Abstract:
It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained.
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