A novel and highly innovative technology will be evaluated for high-throughput, low cost mRNA profiling. The technology has potential application in many areas of cancer research and drug discovery and development, as well as cancer diagnosis and prognosis and management of treatment. The proposal is based on the use of self-assembled arrays of beads on optical fibers. Self-assembly is rapid, which allows different arrays to be manufactured on demand. The arrays have 1-fold more elements per unit area than the most densely packed conventional arrays, and densities can be increased further. Small sample volumes are required by comparison to conventional arrays, allowing analysis of small amounts of material.
The specific aims relate to hybridization to oligonucleotide probes on beads in fiberoptic arrays. The feasibility of detecting a specific mRNA species present in total cellular mRNA at a level of 1 part in 100,000 will be assessed, in a sample having a total target RNA concentration of not more than 50 ug/ml. The feasibility of detecting 2-fold differences in gene expression will be assessed, for a range of mRNA concentrations from 1:100,000 to 1:1,000 in a total sample of 50 ug/ml.
Cellular functional profiling for cancer has application in drug target discovery, toxicology, functional genomics research, cancer diagnostics and management of patient treatment. Potential customers include pharmaceutical companies, genomics companies, research analytical suppliers, research laboratories, providers of screening services (e.g. clinical diagnostic labs), and point- of-care patient monitoring services (e.g. hospitals).
| Gunderson, Kevin L; Kruglyak, Semyon; Graige, Michael S et al. (2004) Decoding randomly ordered DNA arrays. Genome Res 14:870-7 |
| Fan, J B; Oliphant, A; Shen, R et al. (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69-78 |
