Hello all,
My company has Whole exome sequencing (WES) data for individuals lying around and was wondering if this can be used to generate Polygenic Risk Scores (PRS)? From what I researched online, it seems to be more so used for GWAS and not WES.
Any advice is appreciated!
Roy
I wouldn't recommend to this. Most of the component variants in contemporary PRS are non-coding.
Good catch. I read right over that. Agree, perhaps with the caveat of "depending on the disease". For complex, autoimmune conditions, for example, it would appear that 90% of putatively "causal" variants are located in non-coding regions, with 60% found in enhancer regions alone.
Yes, as long as you have a GWAS that contain SNPs covered by your sequencing. On the other hand, if you are referring to only the rare variants. As far as I know, there isn't any method developed to account for rare variants just yet.
Yes there is, and as mathematics and logic dictate, it does not substantially differ from calculating PRS for common variants https://www.nature.com/articles/s41467-021-26114-0
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version 2.3.6
Quick note: It's Polygenic risk score, not "Polygenetic" risk score. I've changed your question to reflect this.
nature communications october 2021. sounds like your company needs a CGO