DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

156. Time-Resolved Sequence Analysis on High Density Fiberoptic DNA Probe Arrays

David R. Walt and Jane Ferguson

Tufts University, Department of Chemistry, 62 Talbot Avenue, Medford, 02155 Mark Chee, Illumina Inc.

david.walt@tufts.edu

An optical imaging fiber consists of a coherent bundle of individual fibers. Each individual fiber has a light conducting inner core that can be chemically etched at a different rate from its surrounding cladding. By treating the polished end of an optical fiber with acid, an array of microwells is generated. Using a simple, one step procedure, the individual wells in the etched fiber can be filled with microspheres slightly smaller in diameter than the well. To prepare a genosensor array, oligonucleotide probe sequences are attached to individual sets of microspheres. The resulting bead populations containing the sequences of interest are then pooled and randomly distributed into the etched fiber array. The position of each bead in the array is then ascertained in several ways. In the first method, each bead can be optically encoded with a unique combination of dyes to allow identification of the probe sequence contained on that bead. Alternatively, we can decode the probe by hybridizing the array to pools of labeled decoding sequences. In most array-based approaches to nucleic acid sequence analysis, each assay at each probe site aims to obtain information from a single sequence. Here, our aim is to develop more efficient methods of analyzing sequences for variation by using each site in the array to analyze multiple positions in a target sequence. We are investigating the simultaneous analysis of multiple positions in a target sequence. This approach has the potential to provide a new, highly parallel method of comparing a sample sequence to a previously determined reference sequence.