Author(s)

Caixia Li¹, Peixing Li^1,2*

¹School of Mathematics, Sun Yat-sen University, Guangzhou, China.
²Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China.

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.

Haplotype, Transmission Disequilibrium Test, Likelihood Ratio Test, Expectation-Maximization Algorithm

Li, C. and Li, P. (2018) Haplotype Frequency Comparison for Case-Parents Data. Open Journal of Statistics, 8, 721-730. doi: 10.4236/ojs.2018.84047.