An optimal dose-effect mode trend test for SNP genotype tables

Genet Epidemiol. 2009 Feb;33(2):114-27. doi: 10.1002/gepi.20362.

Abstract

The genome-wide association studies have improved our understanding of the genetic basis of many complex traits. Two-by-three contingency tables are tested in these studies. The trend test for the additive mode is most often used, which is the test of 1 degree of freedom (df=1) and other tests, such as the genotype test (chi(2) (df=2)) and the chi(2) (df=1) tests for the dominant and recessive modes are also used to increase the power for markers in the non-additive modes. However, any one of them or combination of them is not perfect. We describe the relations among the chi(2) (df=2) test and chi(2) (df=1) tests for the dominant and recessive modes and the trend test for the additive mode and propose a new statistic based on their relations that tests the hypothesis that the disease-susceptible allele has a dose-effect somewhere between the recessive and dominant modes, which corresponds to the optimal dose-effect for the observed data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Genes, Dominant
  • Genes, Recessive
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study / statistics & numerical data*
  • Genotype
  • Heterozygote
  • Homozygote
  • Humans
  • Models, Genetic*
  • Models, Statistical
  • Molecular Epidemiology
  • Phenotype
  • Polymorphism, Single Nucleotide*