I am reading a paper (link here) where they did a GWAS looking for Alzheimer's-associated genes. In their Table 2, a lot of the associated SNPs have an odds ratio that's less than 1. Does that mean that the minor allele is protective against Alzheimer's? Or, is this just because these are raw odds ratios and do not account for other covariates that were included in the main GWAS?
Yes, 'protective' in the sense that having the variant statistically means that you have a reduced 'risk' (or lower 'odds') of having an Alzheimer's diagnosis, but in the confines of those subjects who were in the study. As the OR approaches 0, the level of reduced 'risk' is strengthened. The way that the study's subjects are diagnosed is obviously important. Other criteria are also important in order for the results to be applied to the wider population.
Thus, there are very important things to consider here before one makes any wild statements about such variants:
- your study should be sufficiently powered such that interpretation of the statistical results can be done with confidence
- if the upper confidence limit interval for the variant goes above 1, then it is of less interest and this will reflected in th associated p-value
- if it doesn't have a statistically significant p-value, then it's not interesting; moreover, the p-value should reach genome-wide siginificance
- Replication - can the results be replicated in different cohorts / stages?
From what I can see, the Table 2 variants that have OR<1.0 (and the study, generally) fulfill these criteria.