Which SNP based association test to perform for case-control study design?

Question

[Gene]

I am analysing rare variants and I performed rare variant association testing using gene level tests (exmpl. SKAT).

I want to demontsrate that SNP based association tests are less powerfull that gene-based when rare variants are analysed. Which SNP based association test do you suggest?

My sample size is around 1 500, consisting of almost the same number of cases and controls.

Answer 1

[Kevin Blighe]

At the most simple level, it is just a Chi square or Fisher test on a 2 x 2 contingency table of minor and major alleles: A: SNP dataset and Z Score

Linear regression (continuous traits) and logistic regression (categorical traits) are also used, and, with these, one can technically control for the effect of covariates, which may include other SNPs.

One can improve these and elaborate them to a genetic context by assuming a dominantly or recessively inherited disease allele - PLINK goes over these and even more tests: https://www.cog-genomics.org/plink/1.9/assoc

For rare variants, there are already 'burden tests', of which I am sure you are aware.

Kevin