Solid tissue-based DNA analysis by FISH in research and molecular diagnostics

Abstract

Molecular research in cancer has lead to the identification of many genomic alterations like single point mutations and deletions as well as gene locus amplifications, deletions, and translocations. Fluorescence in situ hybridization (FISH) is state of the art for high-resolution analysis of gene locus amplification, deletion, and translocation and has become of increasing importance in research and clinical diagnosis over the past years. In contrast to biochemical methods like DNA sequencing and PCR, FISH offers the advantage to analyze genomic alterations at cellular level in the context of tissue architecture and cell types. Therefore FISH can analyze intratumor heterogeneity of copy number variations and translocations with highest precision. Reliable and robust FISH data depend on several key steps including probe design, probe hybridization, FISH signal pattern evaluation, and data analysis, which is discussed in this chapter. Progresses in automated ISH, image scanning, and tissue image analysis promises further improvements and are waiting to be integrated into research and routine diagnosis. Despite the technological progress in FISH, tissue sample quality is still key and the most limiting factor for high-quality ISH data.