A -- Cooperative Research and Development Agreement to Further Develop DNA Melting Analysis for Detection of Single Nucleotide Polymorphism

The Laboratory of Neurogenetics (LNG), National Institute on Alcohol Abuse and Alcoholism (NIAAA) at the National Institutes of Health seeks a CRADA Collaborator. The principal goal of this CRADA is to increase the efficiency and sensitivity of identifying gene variants, including single nucleotide polymorphisms (SNPs). Because SNPs are present in large numbers in human populations (estimated at several million over the entire genome), they are likely to be retained because they are either genetically neutral or they confer survival advantages. However, when combined with other polymorphisms or environmental factors, SNPs may become low-level disease risk factors or disease modifiers. An understanding of functional variations among groups of people is important to medicine for many reasons, including the design of more effective therapeutic drugs and a better understanding of drug side effects, a concept known as pharmacogenetics. DNA melting analysis developed by LNG uses melting of DNA duplexes in solution to detect sequence variants. Potential Areas of Application: -rapid discovery of gene sequence variants -individualized drug therapeutics Main Advantages of Technology/Invention: -non-gel-based fluorescence, high throughput method -ability to detect previously undiscovered sequence variants -knowledge of the SNP (or other variant, such as an insertion or deletion) sequence is not required -expensive oligonucleotide hybridization probes is not required -modification of the primary sequence (i.e. introduction of a "GC clamp") to a PCR-generated amplicon to detect differences in melting behavior is not required -method is easily automated using available equipment -simultaneous analysis of a large number of samples -necessary reagents may be combined in a single step -melting analysis may be repeated multiple times on a single sample to reduce statistical data variation State of Development: -DNA melting analysis readily detects differences in the melting temperature between mixtures of DNAs having single base mismatches, deletions, or insertions and a perfectly based paired primary sequence -PCR-generated amplicons of 15-167 base pairs in length have been shown to be amenable to this technology/invention. Even larger longer DNAs can be potentially used to discover sequence variants -DNA amplicon concentrations are highly reproducible, with a coefficient of variation of 2.6% Further R&D Required: Under the present proposal, the overall goal of the CRADA collaboration will involve the following: 1.Further improvement of the technology/invention for high throughput applications including improved efficiency and sensitivity. 2.Developing improved melting parameters for larger PCR-generated DNAs for DNA melting analysis. 3.Developing software to improve variant detection by DNA melting analysis. References: Clinical Chemistry, March 2001 (Lipsky et al., volume 47, pages 635-644) Contact Information: Patricia Lake Technology Development Coordinator 6120 Executive Boulevard, Suite 450 Rockville, Maryland 20852-7181 +1 (555) 000-0000 FAX +1 (555) 000-0000 e-mail: contact@example.gov