High-Throughput Array Instrument for DNA-Based Breast Cancer Diagnostics

The aim of this project is to develop improved methods for the production, processing, and analysis of microarrays (gene-chips) for breast-cancer diagnostics. These methods are based upon large numbers of discrete DNA spots placed on glass microscope slides typically, and hybridized to a probe derived from a tIssue or blood sample. %or breast- cancer diagnostics, there are two likely predominant modes of use. TIssue samples from suspect lesions, e.g., can be assessed for patterns of gene expression on cDNA arrays, indicative of a specific disease type or state. Additionally, analysis of known mutations can be performed on oligonucleotide-based arrays. We are optimizing cDNA microarray methods, and have achieved excellent limits of detection, although not good enough to detect the rarest transcripts. To improve this situation, we are redesigning our novel imaging (non-scanning) fluorescence microarray reader that currently performs four times better (with respect to limit of detection) than a commercial scanner, and does so about 300 times faster. Our next goal is to implement oligonucleotide arrays by various methods including both padlock probe-based ligation assays and allele-specific hybridization tests for specific known mutations. We are also actively improving direct covalent attachment of oligonucleotides to glass, and methods for printing oligonucleotide arrays much faster and cheaper.