Question: Correcting the Negative beta coefficient (genetic risk score )
0
gravatar for Fadoua
6 weeks ago by
Fadoua 0
Fadoua 0 wrote:

Hi Dear all,

I am trying to create a weighted genetic risk score model.

However, The GWAS from where I got the SNP associated with the exposure factor, contained some SNPs that have a negative Beta coefficient; when I compare to my data the coded allele is reverse. how can I correct this before starting to establish my genetic score?
Any help is much appreciated.

Thank you,

Best regards,

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Fadoua 0

It's a known problem, especially if you're doing meta-analysis, you have to make sure your betas are in the same direction. Easiest way is to take the negative or make sure the major/minor alleles are the same.

ADD REPLYlink written 6 weeks ago by Asaf8.3k

Thank you for your reply. Actually I am willing to conduct an MR, using genetics variants as instrumental variables in order to infer causality between my exposure of interest and my target outcome. but first, I need to construct a PRS using summary data from a GWAS. the issue here is that in the original GWAS some betas of some SNPs are negative, when I have compared it to the target data I have found that the coded allele is reverse.so I am not sure how should I fix this problem? calculating the genetic risk score will be a mistake based on the revered allele? I am sorry I don't know if I am being clear.thank you in advance Regards

ADD REPLYlink written 6 weeks ago by Fadoua 0
1

There are software (e.g. PRSice) that takes care of this automatically.

ADD REPLYlink written 6 weeks ago by Lemire590
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