Hi all, I recently got some significant SNPs from my GWAS analysis, many of these SNPs are imputed (I filtered Rsq>0.8 ). So now i have been told to validate these SNPs (the imputed ones) using PCR/Taqman. Can anyone please explain me or direct me towards papers/literature where it's explained clearly how/why 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 ? My only understanding of validation is to do a replication study (to validate my results) or do animal model study testing my original hypothesis, but why to do PCR is confusing me.
Sorry i am still learning bioinformatics and genetics, been few months i have started and thought i was making good progress in understanding genetics but seems still a looooong way to go :)
Thank you all