Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis

被引:0
作者
Yufang Zhang
Xiangjun Xiao
Kai Wang
机构
[1] University of Iowa,Program of Public Health Genetics
[2] University of Iowa,Department of Biostatistics
关键词
Population Stratification; Genetic Association Study; Likelihood Ratio Test Statistic; Genetic Analysis Workshop; Structure Association;
D O I
10.1186/1753-6561-3-S7-S111
中图分类号
学科分类号
摘要
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.
引用
收藏
相关论文
共 6 条
[1]  
Devlin B(1999)Genomic control for association studies Biometrics 55 997-1004
[2]  
Roeder K(2000)Association mapping in structured populations Am J Hum Genet 67 170-181
[3]  
Pritchard JK(2006)Principal components analysis corrects for stratification in genome-wide association studies Nat Genet 38 904-909
[4]  
Price AL(2008)The power of independent types of genetic information to detect association in a case-control study design Genet Epidemiol 32 731-756
[5]  
Won S(undefined)undefined undefined undefined undefined-undefined
[6]  
Elston RC(undefined)undefined undefined undefined undefined-undefined