Detection of novel gene expression in paraffin-embedded tissues by isotopic in situ hybridization in tissue microarrays

Correlating altered gene expression patterns with particular disease states is a critical step in understanding disease processes and developing treat ment strategies. Many thousands of novel gene sequences have recently been annotated in public and private databases and are now available for analysi s. Tissue-specific expression patterns of these sequences can be evaluated physically on DNA arrays and other high throughput assays, or virtually by bioinformatics mining of expressed sequence tag (EST) databases. As a secon dary screening tool, in situ hybridisation (ISH) not only confirms tissue s pecificity, but also reveals what is often valuable information about cell- type expression patterns of novel sequences. Due to their availability and long-term stability at room temperature, formalin-fixed paraffin-embedded c linical specimens provide an invaluable resource for evaluating expression patterns of novel human genes. We describe a high-throughput approach for i dentifying and quantifying the expression of novel genes in paraffin-em bed ded human tissues using isotopic in situ hybridisation and tissue micorarra ys (TMA). Copyright (C) 2001 John Wiley & Sons, Ltd.