information:highlighting, structural:scholar_edition
Methods

When the allele frequency in the case group is much higher than in the control group, the odds ratio is higher than 1, and vice versa for lower allele frequency. Additionally, a P-value for the significance of the odds ratio is typically calculated using a simple chi-squared test. Finding odds ratios that are significantly different from 1 is the objective of the GWA study because this shows that a SNP is associated with disease. Because so many variants are tested, it is standard practice to require the p-value to be lower than 5 × 10 −8 to consider a variant significant.