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Haplotype Frequency Comparison for Case-Parents Data
School of Mathematics, Sun Yat-sen University, Guangzhou, China
Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China
- 1 School of Mathematics, Sun Yat-sen University, Guangzhou, China
- 2 Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China
Open Journal of Statistics·Volume 08 (2018)·Pages 721–730·Published 18 July 2018·DOI10.4236/ojs.2018.84047
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Abstract
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.
KeywordsHaplotypeTransmission Disequilibrium TestLikelihood Ratio TestExpectation-Maximization Algorithm
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