Across all three validation sets (Pipeline Progression, New Genetic, and New Pipeline), we consistently see a marked difference between the effect of genetic evidence derived from the OMIM database and genetic evidence derived from the GWAS Catalog. Estimated effects of OMIM genetic evidence are comparable to or greater than previously reported values [3], except for progressions from Phase I to Phase II, which are lower using new data. Notably, we see a positive and significant effect of OMIM genetic evidence on the probability of progression from Phase II to Phase III since 2013 (Pipeline Progression validation set). With the exception of progressing from Phase III to Approval, estimated effects from GWAS Catalog-derived genetic evidence are consistently lower than the originally reported values. Our estimated effects of GWAS genetic evidence in the New Genetic validation set are often significantly lower than the originally reported values. In validation sets, all estimates of the effect of GWAS evidence overlap one (no effect), except in the Pipeline Progression validation set, where we estimate a negative effect of GWAS evidence on Phase II to III progression (Fig 1B).
