FISH
Definition
Fluorescence In Situ Hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes to detect and localize specific DNA or RNA sequences within fixed cells, tissue sections, or chromosomes. The method relies on complementary base pairing between the fluorescently-labeled probe and target nucleic acid sequences. FISH enables visualization of gene copy number variations, chromosomal abnormalities, gene expression patterns, and spatial organization of genetic material at subcellular resolution. It is crucial for cancer diagnostics, prenatal screening, and studying gene regulation, offering single-cell resolution that bulk sequencing methods cannot provide. FISH variants include multicolor FISH (mFISH), spectral karyotyping (SKY), and RNA-FISH for transcript localization.
Visualize FISH in Nodes Bio
Researchers can map FISH-validated gene targets and their regulatory networks in Nodes Bio to understand spatial expression patterns. Network visualization connects genes identified through FISH with their protein products, upstream transcription factors, and downstream pathways. This integration helps identify co-localized genes, predict functional relationships, and prioritize candidates for follow-up FISH experiments based on network proximity to known disease genes.
Visualization Ideas:
- Gene-chromosome location networks showing FISH-validated loci and their genomic neighbors
- Multi-gene FISH panel networks connecting co-expressed or co-amplified genes with shared regulatory pathways
- FISH biomarker-drug response networks linking chromosomal abnormalities to therapeutic targets and clinical outcomes
Example Use Case
A cancer research team uses FISH to detect HER2 gene amplification in breast tumor samples for treatment stratification. They identify 15 patients with HER2 amplification and 8 with chromosome 17 polysomy. To understand resistance mechanisms, they import FISH results into Nodes Bio, mapping HER2 alongside its signaling partners (PI3K, MAPK pathways) and resistance-associated genes (PTEN, PIK3CA). Network analysis reveals that patients with concurrent PTEN loss cluster together, suggesting combination therapy strategies targeting both HER2 and PI3K pathways.