Latent Unknown Clustering with Integrated Data (LUCID) is designed to leverage the omic data for identifying clusters of individuals with differences in the outcome and with similar profiles of risk factors and biomarkers. Rather than perform the analysis in a staged approach, latent cluster estimation and corresponding effect estimation is performed jointly. The model can be used to better identify disease associations or predict an individual’s potential risk, while also suggesting possible biological mechanisms defined by a combination of all factors.