Breast cancer is one of the most common and fatal cancer diseases that affect women worldwide. As is true with most other cancer diseases, early detection of breast cancer is very crucial for proper medical treatment because treatment of advanced breast cancer will be much more difficult and inconsistent. Screening and testing of breast cancer biomarkers, either genetic or proteomic, are among techniques used for diagnosis of breast cancers. Nevertheless, none of the biomarkers is by itself sensitive and selective enough for diagnosis of breast cancer, and thus, multi-analyte assays towards detection of multiple breast cancer biomarkers from different classes are desired for accurate diagnosis of this disease. Described is a methodology with which both genetic and protein biomarkers of breast cancers are detected simultaneously on the same platform. This methodology consists of a novel hybrid biosensor system in a universal Zipcode DNA array format on the platform of polymer-based microfluidic devices. Detection of the genetic mutated material and the protein targeting material is through hybridization events between the arrayed universal Zipcode DNA sequences and the corresponding complementary Zipcode DNA sequences that are incorporated into both biomarkers during materials preparation. Signal generation and detection are through near-IR, laser-induced fluorescence imaging method. The hybrid biosensor system combines the strengths of microfluidic devices—high throughput, low sample consumption, and high kinetics—with that of the universal DNA array format, which uncouples detection from hybridization event, thereby increasing the sensitivity of detection. Near-IR laser-induced fluorescence detection method adds further sensitivity to this system. In this work, surface properties of the microfluidic device substrate, PMMA have been manipulated in surface functionalities, surface topography, and surface wettabilities. Biomolecules including both antibodies and DNA have been successfully immobilized onto the UV-modified PMMA surfaces. The targeting biomarker materials were prepared using distinct protocols: PCR/LDR combined assays were adopted to prepare the breast cancer gene marker BRCA1 mutated material, while the protein antigen CEA targeting complex was achieved by a semi-synthetic method. Monitoring and characterization of surface manipulation, bio-functionalization, and targeting materials preparation were accomplished by unique analytical tools
