Polygenic Risk Score Analysis for an individual genome
1
1
Entering edit mode
8 weeks ago
Akshay Zawar ▴ 30

Hello,

I am developing a model for PRS calculation. For PRS, you need the base data and target data. I have got these datasets however, it is not clear how the model can be used to predict the susceptibility of a trait in a single genome.

Can you please help me understand how PRS calculation is done for an individual genome?

Thanks, Akshay

gwas wes prs • 265 views
ADD COMMENT
0
Entering edit mode

It is sort of difficult to explain without knowing what the equation is, but essentially you just plug the numbers corresponding to the individuals genetic profile into the general equation ...

ADD REPLY
0
Entering edit mode

Thanks, I am following PRS calculation from this paper: https://www.nature.com/articles/s41596-020-0353-1. From this article, it is clear how to develop a model. The fuzzy thing is regarding its application on an individual genome. That's where I need help.

ADD REPLY
2
Entering edit mode
8 weeks ago
Lemire ▴ 880

Once you have your model (which SNPs to include and their weights/betas) then get your individual genome in plink format and use the --score option.

https://www.cog-genomics.org/plink/1.9/score

But that will just give you a number which on its own is completely useless, because it doesn't translate to absolute risk (it's not clear from your post, but I can guess this is what you would like to get -- a risk estimate). You'll have to look at the literature of your trait/disease of interest to see if the conversion to absolute risk has ever been done and published.

ADD COMMENT

Login before adding your answer.

Traffic: 1244 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6