Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for the disease, such as treatments that provide likely benefit or likely lack of benefit for the disease. The molecular profiling can include analysis of a sequence of a nucleic acid. The invention provides a method of identifying at least one treatment associated with a cancer in a subject. In still another related aspect, the invention provides use of a reagent in carrying out the methods of the invention, and/or use of a reagent in the manufacture of a reagent or kit for carrying out the methods of the invention. In an aspect, the invention provides a system for identifying at least one treatment associated with a cancer in a subject.
