Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.