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

Genetic association studies usually apply the simple chi-square (χ2)-test for testing between a single-nucleotide polymorphism (SNP) and particular phenotype, assuming genotypes phenotypes are independent. So, conventional χ2-test does not consider increased risk of an individual carrying increasing number disease responsible allele (a genotype). But, tests should be performed with consideration this according to mode inheritance (additive, dominant, recessive). Practical demonstration two possible methods considering such order or trends in contingency tables genetic using SNP genotype data is purpose paper. One method by pooling genotypes, other scoring based on pattern. The results show that p-values obtained from both similar dominant recessive models. important features were also extracted different patterns.