How does genenomestudio's genotyping module calculate minor allele frequency (Minor Freq)?
Entering edit mode
2.1 years ago
curious ▴ 600

I am playing around with genomestudio to do genotyping of 32 SNP arrays from human samples just to learn the technique

One of my SNPs in genome studio is such:

Name: exm-rs10503253

# Calls: 32

SNP: [A/C]

AA Freq: .125

AB Freq .250

BB Freq: .625

Minor Freq (MAF): .250

I looked at a few SNPs and can’t seem to find a pattern for how MAF is calculated from these genotype frequencies. Or is it not calculated from the genotype frequencies of my study? Or rather is it looked up in a table from hapmap, 1000 genomes etc?

I am familiar with the formula MAF=(2Ref. allele)/(2(Ref.allele + alternate. allele)), but have not been able to figure out how to determine MAFstarting with genotype frequencies or any other numbers that I have from the output of genomestudio.

I am very new to these types of studies, any point in the right direction would be greatly appreciated.

genomestudio maf SNP gwas • 625 views
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I am not sure if I understood the question but by definition, the minor allele frequency for a given SNP is the proportion of the second most common allele of that SNP in the population. The formula you give doesn't compute the minor allele frequency but the frequency of the ref.allele in the situation where there are only two alleles. And the 2s on the numerator and denominator cancel out so they are not needed.

Entering edit mode

Thanks for taking the time to respond. I was trying to figure out how genomestudio calculates MAF. My guess was that they were calculating it from the genotype frequencies I gave, but I was not sure. I think I figured this out though

Allele frequency of A (minor allele):

Freq A = MAF (Minor Freq) = AA Freq + 1/2 AB Freq.

This works for every sample I tried, not sure how I didn't see this yesterday.


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