Gene arrays and tissue microarrays are important new tools used for the discovery of new markers for improved diagnosis and classification of disease. This course will discuss practical issues related to the use of these technologies, either as individual or integrated approaches to determine patterns of gene expression in disease. With regard to gene arrays, several different platforms are available and this course will discuss relative merits of different cDNA and oligonucleotide array technologies.

In addition, we will discuss approaches to design and manufacture of custom cDNA arrays, techniques for fluorescent labeling and radiolabeling samples, data acquisition from hybridized arrays, and data management and data analysis issues, including decision-based analysis strategies used to recognize patterns in the large gene expression data sets commonly obtained in gene array analysis. Practical examples will be used to demonstrate steps of gene array analysis and common problems encountered. With regard to tissue arrays, we will discuss strategies to maximize the throughput of immunohistochemistry and in situ hybridization studies without sacrificing quality of assays. Topics in this part of the course will include computer-based image analysis and data management. This course is directed at academically oriented pathologists at all levels of training. Materials distributed to attendees will include protocols and links to software tools for array analysis.