Single molecule microarrays for the detection of mutant DNA in body fluids

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DESCRIPTION (provided by applicant): The formation of malignant tumors is associated with accumulation of genetic mutations that enhance cell proliferation. Detecting these mutations in body fluids can be used for cancer management and early cancer detection. However, current cancer diagnostic methods are not well suited for the detection of mutant DNA in body fluids which have prevented the development of effective, cost-efficient cancer screening strategies. Here, we propose the development of microarrays based on Twist-Biosensor technology to dramatically improve and simplify detection of biomarkers in body fluids for cancer screening. Twist-Biosensor is a novel microarray technique in which hybridization is detected with single molecule resolution. In addition, Twist-Biosensor applies disrupting torsional stress to DNA hybrids, a novel strategy uniquely designed to give microarrays high point mutation selectivity. Therefore, the technique is ideal for detection of mutated DNA at low concentration in the presence of a large proportion of wild-type DNA. The overall aim of this application is to demonstrate the capabilities of Twist-Biosensor microarrays for cancer screening. We will develop assays to detect mutations of the KRAS gene and test them with plasma and urine samples from pancreatic cancer patients. Each of the proposed aims of this application focuses on establishing two complementary properties of the microarrays: Detection of multiple cancer mutations (Aim 1) and ultra-sensitive detection of mutated DNA (Aim 2). In addition, both aims will demonstrate that Twist-Biosensor microarrays are faster and require fewer steps than alternative diagnostic techniques.