Calculating frequencies of possible combinations of SNP genotypes in a population

Hi all,

I am looking to calculate the frequencies of all possible combinations of a group of SNP genotypes, in a population. This would be done based on the minor allele frequencies acquired in our population data. I just have a question on whether the following is the right way to do it:

If for example, we have three SNPs, their alleles, and their minor allele frequencies, with A2 being the minor allele:

SNP  A1  A2  MAF
SNPA  A   T  0.1
SNPB  C   G  0.3
SNPC  A   G  0.4

And I now have compiled the possible genotype combinations from the three SNPs:


and so on for 27 combinations.

In order to calculate the frequencies of each ‘profile’, would I simply multiply all the allele frequencies? For example, the first AA-CC-AA frequency would be:

(0.9)(0.9) x (0.7)(0.7) x (0.6)(0.6)

While for the AA-CC-AG combination it would be:

(0.9)(0.9) x (0.7)(0.7) x (0.6)(0.4)

Would this be correct?


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