So, it's not as straightforward as simply calculating the PRS based on our genome's mapped SNPs, I see.
Thank you for the comprehensive answer!
Hi,
I'm very new in the GWAS and PRS analsysis, so my question is simple but I cannot find a straightforward answer anywhere: Is it possible, with a comprehensive database of risk scores associated with traits, to calculate polygenic risk scores for a specific genome? By this, I mean if I can "diagnose" a genome for all diseases already studied by previous genome wide studies.
I'd assume it's not that simple - if that was the case, every paper would reference it.
Thank you for your time
Technically, it is possible, by one doing the following:
Some extra points to consider:
Note, that, replacing 'predictive models' with 'AI' or 'machine learning algorithm' will likely increase your chance of funding for the work, if that is ultimately what you want.
Kevin
So, it's not as straightforward as simply calculating the PRS based on our genome's mapped SNPs, I see.
Thank you for the comprehensive answer!
Thank you for both of your answers
You can also look into our tutorial. However, I guess what you are asking is slightly different, in that you already got PRS associated with disease and you've got a new genome that you want to calculate the Score on. For that, you'll need to know what SNPs were used for the construction and what the weights (this are usually beta-coefficient from GWAS, either used as is (e.g. PRSice), or regularized / shrinked (e.g. LDpred, lassosum, PRS-CS etc). Once you've both information, you'll be able to re-calculate the score.
Thank you Sam. So, it seems that I can achieve that with GWAS catalog since a collection of different GWAS are present, and most of the SNPs have a beta-coefficient associated with them.
Yes, you can, but beware that using only the significant SNPs tends to generate underpowered PRS and if the study of interest use SNPs that are outside of the genome wide significance threshold, then it is likely that you won't have the information required to regenerate the score
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