A digital computer system stratifies in a set of patients, based on a set of observations. The observations can include physical, biochemical, histological, genetic, and gene-expression data, among other types of information. Adjustments can be made to account for the possibility that observations of several patients may begin at different points in the progression of their respective disease processes. Once these adjustments are made, the data are subjected to a statistical cluster analysis. Each cluster of patients potentially represents a different disease stratum, with its own underlying cause, optimum therapy, and prognosis. Once the strata are defined and patients are assigned to them, adjustments to the data can be refined. The cluster analysis then can be repeated, and so an iterative process of stratification and staging takes place.