FISH Glossary: An Overview of the Fluorescence in Situ Hybridization Technique

Abstract

The introduction of FISH (fluorescence in situ hybridization) marked the beginning of a new era for the study of chromosome structure and function. As a combined molecular and cytological approach, the major advantage of this visually appealing technique resides in its unique ability to provide an intermediate degree of resolution between DNA analysis and chromosomal investigations while retaining information at the single-cell level. Used to support large-scale mapping and sequencing efforts related to the human genome project, FISH accuracy and versatility were subsequently capitalized on in biological and medical research, providing a wealth of diverse applications and FISH-based diagnostic assays. The diversification of the original FISH protocol into the impressive number of procedures available these days has been promoted throughout the years by a number of interconnected factors: the improvement in sensitivity, specificity and resolution, together with the advances in the fields of fluorescence microscopy and digital imaging, and the growing availability of genomic and bioinformatic resources. By assembling in a glossary format many of the "acronymed" FISH applications published so far, this review intends to celebrate the ability of FISH to re-invent itself and thus remain at the forefront of biomedical research.

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

“…Among these technologies are chromosome conformation capture (3C) (1) and its several iterations, such as Hi-C (2), which are applied to populations of nuclei to identify chromosomal regions that are in close proximity to each other (3,4). Another technology is fluorescence in situ hybridization (FISH), wherein nucleic acids are targeted by fluorescently labeled probes and then visualized via microscopy; this technology is an extension of methods that once used radioactive probes and autoradiography but have since been adapted to use nonradioactive labels (5)(6)(7)(8)(9)(10)(11). FISH is a single-cell assay, making it especially powerful for the detection of rare events that might otherwise be lost in mixed or asynchronous populations of cells.…”

“…Another limitation to clone-based probes is that the genomic regions that can be visualized with them are restricted by the availability of clones and the size of their genomic inserts, which typically range from 50 to 300 kb. Whereas it is possible to target larger regions and establish banding patterns by combining probes (9,(14)(15)(16)(17), this approach is often challenging, as each clone needs to be prepared and optimized for hybridization separately. The efficiency of these probes can also be variable, even among different preparations of the same probe.…”

Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration

“…In situ hybridization (ISH) consists of an array of methodologies that ultimately 53 allow the specific detection of nucleic acid sequences in biological samples (Jin and 54 Lloyd, 1997 (Cerqueira et al, 2008;Volpi and Bridger, 2008). FISH is widely used in the field of 60 microbiology (Amann and Fuchs, 2008), namely in the identification, quantification and 61 characterization of phylogenetically defined microbial populations in complex 62 environments (Wagner et al, 2003).…”

ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis

“…FISH involves the generation and hybridization of loci specific fluorescence‐labeled nucleic acid probes on to metaphase chromosomes or onto interphase nuclei 2. The use of this method made gene mapping possible at much higher resolution compared with other physical mapping technologies 3.…”