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Likelihood ratio and score burden tests for detecting disease-associated rare variants

  • Woojoo Lee , Donghwan Lee and Yudi Pawitan EMAIL logo
Published/Copyright: September 30, 2015

Abstract

This paper presents two simple rare variant (RV) burden tests based on the likelihood ratio test (LRT) and score statistics. LRT is one of the commonly used tests in practical data analysis, and we show here that there is no reason to ignore it in testing RV associations. With the Bartlett correction, we have numerically shown that the LRT-based test can have a reliable distribution. Our simulation study indicates that if the non-null variants are as common as the null variants, then the LRT and score statistics have comparable performance to the C-alpha test, and if the former is rarer than the null variants, then they outperform the C-alpha test.


Corresponding author: Yudi Pawitan, Department of Medical Epidemiology, PO Box 281 Karolinska Institutet, 171 77 Stockholm, Sweden, e-mail:

Acknowledgments

This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (NRF-2013R1A1A1061332).

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Published Online: 2015-9-30
Published in Print: 2015-11-1

©2015 by De Gruyter

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