On the Different Ways to Handle the Trend of Disease Risk in Genetic Association Tests

Abstract

Genetic association studies usually apply the simple chi-square (χ 2 )-test for testing association between a single-nucleotide polymorphism (SNP) and a particular phenotype, assuming the genotypes and phenotypes are independent. So, the conventional χ 2 -test does not consider the increased risk of an individual carrying the increasing number of disease responsible allele (a particular genotype). But, the association tests should be performed with the consideration of this disease risk according to the mode of inheritance (additive, dominant, recessive). Practical demonstration of the two possible methods for considering such order or trends in contingency tables of genetic association studies using SNP genotype data is the purpose of this paper. One method is by pooling the genotypes, and the other is scoring the individual genotypes, based on the disease risk according to the inheritance pattern. The results show that the p-values obtained from both the methods are similar for the dominant and recessive models. The other important features of the methods were also extracted using the SNP genotype data for different inheritance patterns.