How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual?
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3 months ago

Hi all,

I have an annotated vcf file for one individual which I want to estimate his polygenic risk score (PRS) for a certain trait, using the scoring files from the PGSCatalog. The scoring file contains the SNP ID, reference and alternative allele, and weights. How can I estimate the PRS using the scoring file without using the classical approach of having GWAS summary data, target data, etc...?

Thank you very much for your consideration.

prs genome snp • 843 views
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3 months ago
zx8754 10k

PGSCatalog has all you need to calculate the score, if individual has the effect allele then multiply it with beta, do the same for all SNPs, then sum.

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Thank you very much for your answer. One last question. Since the allele represent the single point mutation, should I use dummy coding to transform the nucleotides and then perform the multiplication with the betas or is there another approach?

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Yes, if effect allele is "A" and genotype is "A A", then 2 * beta

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Does anyone have any software or script that performs these calculations?

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It is a one-liner, multiply genotypes with coefficients and sum them

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Maybe try PRSice-2: https://www.prsice.info/

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