Described herein is a chip-based apparatus for amplifying nucleic acids, a cartridge housing the apparatus, and methods of using the apparatus for amplification of nucleic acids. More specifically, this invention provides integrated semiconductor chip, manufactured with standard semiconductor manufacturing process, with on-chip circuitry to perform thermal management and optical sensing necessary for amplification of nucleic acids. The apparatus and methods embodied in this invention makes it possible to build a disease diagnosis and prognosis tool that is easy to use, portable and disposable.