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Effect Allele Frequency in base summary statistics for PRSs calculation

I want to use summary statistics containing only the Effect Allele Frequency (EAF) and not the Minor Allele Frequency (MAF) as base dataset for PRS calculation in PRSice2. It would be possible to convert EAF to MAF and then filtering for a MAF threshold of 0.01?

Thanks in advance

gwas prs polygenic risk scores maf prsice
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updated by Sam Sam • written by bigfoot • bigfoot

1 answer

If you know the effective allele information, then you can simply filter the effective allele frequency as those > 0.99 and < 0.01. Because if the effective allele frequency is less than 0.01, it's the minor allele.

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written by Sam Sam

Opps, sorry, should be 0.99. Have now edited

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written by Sam Sam

Thanks Sam. So, in the end, only SNPs with EAF in the range 0.01-0.99 should be retained for the analyses.. right?

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written by bigfoot • bigfoot

If your goal is to filter by MAF of 0.01, then yes.

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written by Sam Sam

As a follow-up, what if our summary statistics only contain the alternative allele frequency and we would like to filter on a MAF threshold? Could we go through the same process of do we first need to transform the alternative allele frequency somehow?

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written by rem • rem

You can change the alternative allele frequency to MAF by making sure the frequency is less than 0.5. So for any frequency > 0.5, do 1- frequency and you'll have the MAF

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written by Sam Sam

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