Choose a FISH probe by the biological question, not by gene name alone. Use a break-apart probe when one gene may rearrange with multiple possible partners; a dual-fusion probe when the two fusion partners are known; an enumeration/centromeric probe for chromosome copy number; a deletion/locus-control probe for loss of a defined region; and an amplification/copy-number design for gain relative to a reference locus.
Fluorescence in situ hybridisation is only as informative as the probe design. Two products targeting the same gene can answer different biological questions because one may be a break-apart design, another a fusion probe, and another a copy-number assay.
1. Break-apart FISH probes
A break-apart probe uses two differently labelled probe regions flanking or spanning opposite sides of a target gene. In a non-rearranged locus, the colours are adjacent or overlapping. When the locus is rearranged, the signals separate according to the probe-specific scoring definition.
Best used when
- You need to detect whether a gene is rearranged.
- The target can fuse with multiple different partners.
- The identity of the fusion partner is not required for the first-pass question.
What it does not automatically tell you
A break-apart result shows rearrangement of the interrogated locus; it does not necessarily identify the partner gene. Follow-up testing may be needed when partner identity matters.
2. Dual-fusion FISH probes
Dual-fusion designs use differently coloured probes targeting two known loci. A rearrangement bringing the loci together creates fusion or co-localised signal patterns. These probes are useful when a specific translocation/fusion pair is the biological question.
Best used when
- Both partner genes are known.
- You want direct evidence consistent with a specific fusion event.
- The probe design includes signal logic that distinguishes normal homologues from the rearranged chromosomes.
3. Enumeration and centromeric probes
Centromeric enumeration probes commonly target repetitive alpha-satellite sequences near the centromere of a specific chromosome. They are used to assess chromosome copy number or as a reference signal in locus/centromere ratio analyses.
Best used when
- The question is aneuploidy or chromosome copy number.
- A locus-specific target requires a chromosome/reference control.
- You need a reference probe for amplification or deletion interpretation.
4. Deletion / locus-control probes
A deletion design compares a target locus with a separate reference locus, often on the same chromosome or at a centromeric region. Loss of target signal relative to the control can indicate deletion, subject to specimen quality and probe-specific cut-offs.
Why the control matters
FFPE sections can truncate nuclei. A missing target signal alone may reflect sectioning artefact rather than true deletion. A matched reference signal and validated scoring criteria reduce this risk.
5. Amplification and copy-number probes
Amplification assays compare the target gene/locus signal with a reference signal. Increased target copies, clustered signals or an increased target-to-reference ratio may support amplification depending on the probe and assay-specific scoring rules.
Do not apply one universal ratio threshold across different genes, products or disease contexts. Use the specific IFU and laboratory validation.
6. Locus-specific and subtelomeric probes
Locus-specific probes target a defined chromosomal region without necessarily being configured as break-apart, fusion or ratio assays. Subtelomeric probes target regions near chromosome ends and are useful for selected structural chromosome questions.
7. Whole-chromosome painting probes
Chromosome painting uses a complex probe pool spanning much of a chromosome to visualise chromosome territories and structural rearrangements, particularly in metaphase analysis and research applications.
Which FISH probe should I choose?
| Research question | Most likely probe design | Key interpretation |
|---|---|---|
| Is this gene rearranged, regardless of partner? | Break-apart | Separation pattern consistent with rearrangement |
| Are these two specific genes fused? | Dual-fusion / fusion probe | Co-localised or fusion signal pattern |
| Is chromosome copy number abnormal? | Enumeration / centromeric | Number of chromosome-specific signals |
| Is this locus deleted? | Deletion + control locus | Target loss relative to control |
| Is this gene amplified? | Target + reference copy-number probe | Target copy increase relative to reference |
| Where is chromosome material located? | Chromosome paint / region-specific paint | Chromosome or chromosomal region visualisation |
Signal interpretation: the common mistakes
- Assuming every separated red/green signal is positive: break-apart scoring distances are product-specific.
- Ignoring section truncation: FFPE nuclei can lose signal because only part of the nucleus is present.
- Scoring overlapping nuclei: can create false copy-number or fusion patterns.
- Using the wrong control locus: copy-number interpretation depends on the actual probe design.
- Assuming colours are standardised across manufacturers: fluorophore assignments vary. Always review the probe map.
ABMIUM FISH probe access
ABMIUM currently lists 444 active research-use FISH Probe Reagents from Wuhan HealthCare Biotechnology. The catalogue includes break-apart, fusion, deletion, amplification, enumeration/centromeric and locus-specific configurations, alongside additional FISH products from other manufacturers in the wider FISH collection.
If you send us the gene/locus, biological question, specimen type and desired signal design, we can help narrow the shortlist rather than asking you to search hundreds of catalogue entries manually. Contact ABMIUM or use Find your MATCH.
Frequently asked questions
Is a break-apart probe better than a fusion probe?
Neither is universally better. Break-apart probes are useful when one gene can rearrange with multiple partners. Fusion probes are more specific to a known partner pair.
Can a centromeric probe detect gene amplification?
A centromeric probe is usually a chromosome copy-number/reference probe. Amplification assessment generally requires a locus-specific target probe and an interpretation method appropriate to the target/reference design.
Can I identify the fusion partner with a break-apart probe?
Not usually. A break-apart assay shows that the target locus is rearranged. Additional testing may be needed to identify the partner.
Why can normal cells show imperfectly fused signals?
Three-dimensional nuclear geometry, sectioning, probe footprint and optical resolution can create small separations. That is why scoring thresholds are probe-specific and should be established from the IFU and local validation.