Base file of PRSice software

Question

[shubhamk.vit]

I am using PRSice software for Polygenic risk score calculation of complex diseases like Type 2 Diabetes, Coronary artery disease. Input files required for analysis are Base file (example: TOY_BASE_GWAS.assoc ) and target file (binary files from plink for your target data). I am able to create target files using plink plug in from genome studio .,but Don't know how to create gwas association file for my phenotype like Type 2 Diabetes

Answer 1

[Sam]

The base file is a GWAS association file. Usually you can obtain it from external data base (e.g. PGC). For Type 2 Diabetes, you might be able to get the summary statistics from WTCCC. Alternatively, if you have an independent data set (independent to your target data), you can also perform the GWAS analysis on it (with PLINK) to obtain the summary statistic