Novel microarrays for DNA genotyping in the presence of excess background DNA

DESCRIPTION provided by applicant DNA microarrays are a primary tool for DNA genotyping because of their capacity to detect multiple targets simultaneously However DNA microarrays require fluorescent labeling and long incubation steps which limit their applicability Furthermore DNA microarrays are not capable of detecting DNA targets in the presence of excess background DNA This capacity is essential in multiple biomedical applications such as tumor genotyping microbiology testing and non invasive prenatal genetic analysis Here we propose development of a novel microarray based on Twist Biosensor TBS technology that will be label free and more than times faster than standard microarrays Additionally the new technique will be capable of detecting DNA in the presence of fold excess background DNA making it ideal for difficult genotyping situations In this application we propose the development of novel microarrays to dramatically improve and simplify tumor genotyping for research and clinical applications Available techniques used to detect somatic mutations are either limited in their multiplexing capacity such as real time PCR and mass spectroscopy or time consuming and labor intensive such as Next Gen Sanger and Pyro sequencing 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 that gives the microarrays extremely high sequence selectivity Using these unique properties we will develop highly multiplexed microarrays to detect somatic mutations that will be accurate rapid and cost effective The overall aim of this proposal is to demonstrate the capabilities of Twist Biosensor microarrays for the detection of multiple mutations in the presence of excess background DNA We will develop prototype devices to detect mutations of the BRAF and KRAS genes and test them using tumor samples Aim focuses on demonstrating rapid hours and accurate detection of a single mutation in samples containing fold excess background DNA Aim focuses on improving TBS detection by integrating the biosensors in a digital sensor array The new system will have high multiplexing capability will use inexpensive equipment and will be easy to automate Our ultimate goal is to produce a flexible platform for biomedical research and clinical applications PUBLIC HEALTH RELEVANCE We propose development of DNA microarrays based on Twist Biosensor technology to dramatically simplify the genetic analysis of samples with excess background DNA such as tumors The new technology will facilitate the evaluation of new genetic makers and the application of personalized medicine