SNP Detection with Unlabeled, Unamplified Target DNA

DESCRIPTION (provided by applicant): The aim of the research project is to further develop the dual hybridization diagnostic genotyping method into a multiplex assay capable of using unlabeled, unamplified DNA as the target. The feasibility of the dual hybridization method was demonstrated in Phase I using amplified targets and single fluorophore labels. All results indicate that the method will transfer easily to a parallel, high sensitivity method using sheared genomic DNA and fluorescent microsphere labels. Current genetic diagnostic tests are expensive and usually only performed for a few specific mutations after adverse symptoms have occurred. The simplicity of this diagnostic test will remove the cost limitation, which currently exists for obtaining large amounts of genetic information, allowing routine diagnostics to be preventative medicine. Particular improvements include: 1) shorter manipulation time and less difficulty performing the procedure (no PCR, sample labeling, or multiple aliquoting is required), 2) reduction of patient sampling (blood, tissue, etc.), and 3) parallel genotyping of SNPs and larger mutations. The method uses a dual hybridization of target molecules. One hybridization event occurs between targeted fragments in the genomic DNA sample and long DNA probes immobilized in an array. The result of this hybridization is a sequence-specific immobilization of target nucleic acids. For example, all alleles of a gene would be localized to one array site. The other hybridization event occurs between the target nucleic acid and short probes of peptide nucleic acid (PNA, a nucleic acid analog) that form stable, highly sequence-specific hybrids with DNA. Each allelic variant has its own PNA probe with a unique label. The types of labels detected at the probe site indicate the alleles present in the patient's genome. This procedure is highly flexible since almost any label can be used. Pooled labeled PNA probes, DNA probe arrays, and possibly buffers and an automated flow cell (capable of maintaining correct temperature and liquid handling) will be sold to the consumer. For Phase II, an array for genotyping SNPs suspected of influencing susceptibility to colon cancer will be designed. This research tool and other custom arrays can be sold for research use until the method can be approved by the FDA for diagnostic use. A major research market for the device would be determining SNP patterns for diseases where massively parallel SNP genotyping must be performed on thousands of patients for each disease.