Haplotype Frequency Comparison for Case-Parents Data  

作　　者：Caixia Li Peixing Li 

机构地区：[1]School of Mathematics, Sun Yat-sen University, Guangzhou, China [2]Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China

出　　处：《Open Journal of Statistics》2018年第4期721-730,共10页统计学期刊（英文）

摘　　要：For case-parents data, the information from offspring can be used to reduce the uncertainty of parents’ haplotype. In this article we develop likelihood ratio test to compare haplotype frequencies in transmitted and non-transmitted group. The maximum likelihood estimate of the haplotype frequencies for the family data is obtained via expectation-maximization (EM) algorithm. Our proposed method can handle the uncertainty of haplotypes and missing data. The simulations show that the method is more powerful to test association between haplotype and traits than TRANSMIT. We also demonstrated the method to detect the association between Megsin gene and immunoglobulin A nephropathy.For case-parents data, the information from offspring can be used to reduce the uncertainty of parents’ haplotype. In this article we develop likelihood ratio test to compare haplotype frequencies in transmitted and non-transmitted group. The maximum likelihood estimate of the haplotype frequencies for the family data is obtained via expectation-maximization (EM) algorithm. Our proposed method can handle the uncertainty of haplotypes and missing data. The simulations show that the method is more powerful to test association between haplotype and traits than TRANSMIT. We also demonstrated the method to detect the association between Megsin gene and immunoglobulin A nephropathy.

关 键 词：HAPLOTYPE Transmission Disequilibrium TEST LIKELIHOOD RATIO TEST EXPECTATION-MAXIMIZATION Algorithm 

分 类 号：R73[医药卫生—肿瘤]