validation of probable SNPs
I recently got some significant SNPs from my GWAS analysis, many of these SNPs are imputed (I filtered Rsq>0.8 ). We are yet to do replication study for our findings, waiting for replication cohort samples and it might take a while for this. So now i have been told to validate these SNPs (especially the imputed ones) using PCR/Taqman. Can anyone please explain me or direct me towards papers/literature where it’s explained clearly how PCR/Taqman helps in validating the SNPs. Plus my understanding was that since I have filtered Rsq >0.8 for my imputation result (imputation done by Michigan server), and done additional QC based on maf, hwe, missingness and other parameters.(both pre and post imputation), so i thought the imputation quality would be quite good, So why again do i need to validate the imputed SNPs using lab experiments ?
Doing lots of reading at the moment, are there other ways to validate the imputed SNPs other than taqman/pcr (sorry my background is not lab).
Thank you all
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