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Tracking clonal evolution is critical to fully define the mechanisms of normal physiology and the disruptions of these processes in disease. In this issue of Cell Genomics, Pak and Saurty-Seerunghen et al. describe the development of Genotyping of Transcriptomes for multiple targets and sample types (GoT-Multi) and show how this new technology enables insights into cellular states that mediate clonal evolution in diseases, such as the Richter transformation of chronic lymphocytic leukemia, while also revealing convergence of cell states, even with distinct driver mutations.