CISH, or chromogenic in situ hybridization, is a process in which a labeled complementary DNA or RNA strand is used to localize a specific DNA or RNA sequence in a tissue specimen. CISH methodology may be used to evaluate gene amplification, gene deletion, chromosome translocation, and chromosome number. CISH utilizes conventional peroxidase or alkaline phosphatase reactions visualized under a standard bright-field microscope, and is applicable to formalin-fixed, paraffin-embedded (FFPE) tissues, blood or bone marrow smears, metaphase chromosome spreads, and fixed cells.

What CISH offers:

  • Evaluation of gene status simultaneously with tissue morphology
  • Use of existing bright-field microscopy and techniques similar to IHC
  • Archivable and quantitative results

About the Technology



Invitrogen's CISH probes are created with Subtraction Probe Technology (SPT™), a proprietary technology that produces highly specific probes by significantly reducing the repetitive sequences found in human DNA. Consequently, our probes do not require the repetitive sequence blocking that is common for traditional cytogenetic DNA probes.



On Day 1, major steps include tissue preparation, heat pretreatment, pepsin digestion, probe addition, and denaturation/hybridization. Following an overnight hybridization step, Day 2 begins with a stringent wash before proceeding with the immunodetection steps. After using a standard tissue mounting procedure, the specimens are ready for interpretation on a bright-field microscope.



CISH detection of non-amplified HER2 gene status (A) and amplified HER2 gene status (B) in different breast cancer tissue samples at 40X magnification.

How does CISH compare to IHC and FISH?

  CISH FISH IHC
Signal stabilityArchivableFades over timeArchivable
MicroscopeBright-fieldFluorescenceBright-field
Magnification40x60–100x20–40x
CProtocol lengthOvernight + 3 hr, 55 minOvernight + 3 hr, 12 min3 hr, 2 min
MorphologyGoodLimitedGood
Amount of training requiredMediumHighLow
Internal controlYesYesNo
InterpretationObjective/quantitativeObjective/quantitativeSubjective/qualitative
Overall costMediumHighLow