Fluorescent in situ Hybridization (FISH)

SUBTYPE:Gene Expression
APPLICATION & SPECIALITY USES:Biomarker DiscoveryCell Therapy/ Regenerative MedicinePersonalized Medicine
Keywords:FISHFluorescent in situ HybridizationGene ExpressionMutation Analysis


Fluorescent in situ hybridization (FISH) is a powerful diagnostic and discovery tool for identifying the genomic status of samples, particularly oncology tissues. FISH involves the use of fluorescence probes to detect specific gene sequences within chromosomes and can be used to detect different kinds of mutations such as gene amplifications, deletions and translocations (fusions and breaks). Viral (RNA) sequences can also be detected. FISH can be applied to Formalin Fixed Paraffin Embedded (FFPE) and Flash Frozen (FF) samples, although FFPE is preferred due to superior morphology.

Using FISH to detect different types of mutations:

  • Gene Amplifications – In a fraction of patients with breast cancer, the HER2 protein is overexpressed. This is due to HER2 gene amplification.
  • Gene Deletions – Deletion of the AMT gene can be associated with mantle cell lymphoma, a subtype of non-Hodgkin’s lymphoma.
  • Gene Translocations – Translocations can fuse the coding sequences of two genes together to generate potent oncogenes. For example, the BCR-ABL fusion protein encoded by the chimeric gene is associated with chronic myelogenous leukemia (CML). Gene translocations can also be detected using break-apart probes. Abnormalities in the ROS1 gene can lead to non-small cell lung carcinoma.
  • FISH can also be used to detect viral sequences within cells – e.g. HPV (human papillomavirus).

Custom FISH Probe Design and Validation

If probes to the target gene are not available, a custom-made probe can be designed in house and validated by our expert scientists.

For example, probes can be designed to bind to two regions in close proximity that span a break-apart mutation. Thus, overlapping signals indicate a wild-type gene, and non-overlapping signals indicate the presence of a translocation mutation. Additonally, custom-made break-apart probes can be validated in positive and negative control cell lines.

Features & Benefits

  • Custom assay development and testing for commercially-available ISH probes
  • Ease of design for custom target probes versus creation of specific, selective antibody
  • Localization of mulitple mRNA targets in the same tissue section
  • Localization of mRNA and protein expression in the same tissue section
  • Precise location of mRNA in tissue section
  • Comparison of mRNA and protein localization for the same target
  • Useful for antibody validation