How do you compare HLA allele frequencies between two populations?

Question

[Moschi]

Hello,

I have HLA-typed cohort A (123 subjects), which has resulted in 23 HLA haplotypes. I have the frequency of each of these haplotypes in percentages. I want to compare these frequencies to a control group (cohort B) with 3000 subjects. These cohorts are of the same race and the studies were conducted in the same institution. I want to check if cohort A frequencies deviate from the control cohort B. Both cohorts are healthy and not diseased. Which test should I use please?

Answer 1

[dthorbur]

It sounds like you could apply a Chi-Squared test would be appropriate based on the data type you have mentioned.

Since the sample sizes are so different, I would also suggest a permutation analysis - randomly draw 123 subjects form cohort B and compare the HLA haplotype distribution back to cohort B. Repeat 1000 times. See how often you get a significant deviation from the original distribution.