A microfluidic device for analyzing a sample of interest is provided. The microfluidic device can comprise a microfluidic device body, wherein the microfluidic device body comprises a sample preparation area, a nucleic acid amplification area, a nucleic acid analysis area, and a network of fluid channels. Each of the sample preparation area, the nucleic acid amplification area and the nucleic acid analysis area are fluidly interconnected to at least one of the other two areas by at least one of the fluid channels. Using the microfluidic device, sample preparation can be combined with amplification of a biologically active molecule, and a suitable biological sample can be provided for analysis and/or detection of a molecule of interest. The small-scale apparatus and methods provided are easier, faster, less expensive, and equally efficacious compared to larger scale equipment for the preparation and analysis of a biological sample.