I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the weights were generated from a different cohort (d2), it appears that the original GWAS was based on the same dataset (d1) that I'm using. Does this method inflate the predictive qualities of the PRS for the cohort in d1? Or should we even use it in that case? (Still very new to the concept of PRS scores)
Unfortunately, if the same data set is used for the GWAS estimate, you can't include that in the PRS analysis, or you will get a highly inflated R2 and significance that cannot be replicate in other data set. 

Do you mean that d1 is part of d2? If d1 is a subset of d2, one method is to use the inverse meta-analysis approach. you should be able to find the equation here: https://www.biorxiv.org/content/10.1101/203257v1.full.pdf
