Hardy-Weinberg Equilbrium for multiple loci

Question

[QVINTVS_FABIVS_MAXIMVS]

I would like to test to see if a list of variants are in HWE

Say I have 100 loci with biallelic (AA/Aa/aa) genotypes for 1,000 samples. I would like to test that on average are the alleles in HWE.

Do I calculate a chi-squared statistic across each allele and then take the mean/median Chi-Sq stat to find the Pvalue?

I am assuming that each region is independent of each other (no linkage)

Answer 1

[anp375]

This sort of looks like a Multiple Testing problem. Get the chi-square/something-else p-values for all locations. With an alpha-threshold of 0.05, you can expect to get 5 p-values below 0.05 by chance.

The rest of this is pure speculation and I have no idea how correct it is:

Use a binomial distribution function to calculate the probability of obtaining your number of significant p-values (k) out of the total number of p-values (n=100), given an expected proportion of significant p-values of 0.05 (p=5/100).

If your probability is less than 0.05, then on average, your set of loci is not in Hardy-Weinberg equilibrium.

This is almost definitely not the most powerful test for your scenario, so you probably won't get a significant result.

Answer 2

[WouterDeCoster]

I seemed to have missed this question 11 days ago. I would definitely recommend using plink for jobs like this, and similar. The tool is intuitive and the documentation is amazing, see hardy-weinberg equilibrium test in plink