Interphase fluorescence in situ hybridization (I-FISH) beautifully exemplifies what a molecular cytogenetic technique can offer in contrast to conventional cytogenetic approaches: the analysis of chromosomal DNA at all stages of the cell cycle. It has made it possible to study chromosome numbers and structure in almost all tissues of an organism. Furthermore, it enables the delineation of new phenomena such as intercellular genomic variations and the detection of chromosomal mosaicism, which is a difficult task for cytogeneticists. The aim of this chapter is to present a comprehensive I-FISH protocol for the detection of intercellular genomic variations and low-level chromosomal mosaicism in somatic tissues. Special attention is paid to several issues encountered during I-FISH analysis, mainly the specificity of the cell suspension preparation, the selection of a benchmark for defining a cell population as mosaic, differentiation between I-FISH artifacts, the specificity of chromosome intranuclear organization, and variations in chromosome numbers.
