Our replication analysis occurred in three steps. In the first step, we took labels of genetic evidence directly from Nelson et al. 2015 and tested how these labels predict pipeline outcomes in the New Pipeline and Pipeline Progression validation sets. Second, we repeated the analysis using both updated pipeline data and updated genetic association datasets and determined whether genetic evidence labels constructed from associations reported after 2013 are positively associated with historical progression. This analysis uses the New Genetic validation set, defined as GWAS data added after May 2013 and OMIM data added after October 2013. Third, we determine whether genetic labels constructed from the full set of updated GWAS and OMIM genetic associations are linked to improved pipeline outcomes over the entire updated Pharmaprojects dataset (See Methods for more details). We refer to this analysis as Full Data.
