In situ hybridization (ISH)


In situ hybridization (often abbreviated as ISH) is a specialized laboratory test that enables pathologists to detect specific pieces of genetic material (DNA or RNA) directly within the cells of a tissue sample. The phrase “in situ” means “in its original place,” and “hybridization” refers to the way a probe (a small piece of complementary genetic material) attaches to its matching sequence inside the cell. When the probe binds, it can be seen under the microscope as a colored signal. This allows pathologists to see exactly which cells contain the genetic material of interest and where in the tissue it is located.

Why is in situ hybridization performed?

Pathologists use in situ hybridization to answer important diagnostic questions, such as:

  • Detecting viruses: ISH can find viral DNA or RNA in cells, which helps confirm infections such as human papillomavirus (HPV), Epstein–Barr virus (EBV), or cytomegalovirus (CMV).

  • Looking for genetic changes in cancer: ISH can identify changes in specific genes that may guide treatment. For example, it can test whether the HER2 gene is amplified in breast or stomach cancer, or whether specific chromosomal rearrangements are present in lymphomas or sarcomas.

  • Prognosis and treatment: The presence or absence of specific genetic signals can help doctors predict how a tumor might behave and whether it will respond to targeted therapies.

How is in situ hybridization reported?

In your pathology report, in situ hybridization results are usually described as either positive (the genetic material was detected) or negative (it was not detected). Sometimes, the report includes more detailed information, such as whether a gene is amplified (present in extra copies), deleted (missing), or rearranged (altered in structure). Pathologists may also comment on whether the abnormality was found in all of the cells or only in some of them.

What are the types of in situ hybridization?

Different methods of ISH may be mentioned in your report:

  • Fluorescence in situ hybridization (FISH): Uses fluorescent signals that glow under a special microscope. This is commonly used to look for chromosomal abnormalities and gene amplifications.

  • Chromogenic in situ hybridization (CISH): Produces colored signals visible with a standard microscope. This method is commonly employed in routine pathology laboratories.

  • RNA in situ hybridization: Detects messenger RNA (mRNA) to show whether a gene is actively being expressed in cells.

Why is in situ hybridization important?

In situ hybridization provides very specific information that cannot be seen with routine stains. It enables pathologists to confirm infections, identify genetic alterations, and inform treatment decisions. For example, a positive HER2 ISH result in breast cancer may mean the cancer can be treated with HER2-targeted therapy. Similarly, finding EBV by ISH in a tumor may confirm a diagnosis of nasopharyngeal carcinoma.

Questions to ask your doctor

  • Why was in situ hybridization performed on my sample?

  • Which virus, gene, or genetic change was the test looking for?

  • What do the results (positive, negative, amplified, deleted, or rearranged) mean for my diagnosis?

  • Will these results affect my treatment options?

  • Are there any additional tests I may need based on this result?

A+ A A-