A comparison of the likelihood ratio test and the variance-stabilising transformation-based tests for detecting association of rare variants

Guan Xing, Hung Chih Ku, Chao Xing

Research output: Contribution to journalComment/debate

1 Scopus citations

Abstract

In a recent paper in this journal, the use of variance-stabilising transformation techniques was proposed to overcome the problem of inadequacy in normality approximation when testing association for a low-frequency variant in a case-control study. It was shown that tests based on the variance-stabilising transformations are more powerful than Fisher's exact test while controlling for type I error rate. Earlier in the journal, another study had shown that the likelihood ratio test (LRT) is superior to Fisher's exact test, Wald's test, and Pearson's X2 test in testing association for low-frequency variants. Thus, it is of interest to make a direct comparison between the LRT and the tests based on the variance-stabilising transformations. In this commentary, we show that the LRT and the variance-stabilising transformation-based tests have comparable power greater than Fisher's exact test, Wald's test, and Pearson's X2 test.

Original languageEnglish (US)
Pages (from-to)333-335
Number of pages3
JournalAnnals of Human Genetics
Volume77
Issue number4
DOIs
StatePublished - Mar 18 2013

Keywords

  • Likelihood ratio test
  • Low-frequency variants
  • Variance-stabilising transformation

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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