Genetic
association studies usually apply the simple chi-square (χ2)-test for testing association between a
single-nucleotide polymorphism (SNP) and a particular phenotype, assuming the
genotypes and phenotypes are independent. So, the conventional χ2-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.
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