Cancer is a heterogeneous collection of diseases with wild variation in etiology, pathogenesis, response to therapy, and prognosis. Sources of variation are frequently obscure. Current practice attempts to classify tumors by tissue of origin and extent of disease through staging such that more risky tumors can be managed with more aggressive treatments. Modest inroads have been made with biomarkers to further characterize groups of tumors with important characteristics such as response to selected drugs. However, biomarker-driven decisions are relatively few when examining the maze of clinical decisions in the care of cancer patients. Against this backdrop, waves of researchers have unleashed a vast array of new technologies, with the goal of better characterization of the inherent diversity of tumors. This review outlines the use of cancer biomarkers and emerging technologies to stratify patients with a focus on the challenges and opportunities of next-generation nucleic acid sequencing approaches in oncology.