FISH

Decision Support & AI

Fluorescent in situ hybridization (FISH) is a molecular technique commonly used to detect chromosomal abnormalities and gene mutations such as translocation, amplification, and deletion. The desired gene regions are made visible with fluorescent labeled DNA probes, which is the complement of the gene region that needs to be detected [1].

Automatic FISH analysis detects amplification, break apart, fusion, deletion of target sequence and performs quantitative analysis in digital slides. It enables detection of very low signals and visualizes the DAPI and signals. The algorithm categorizes the nuclei into normal, abnormal and artifact groups.

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Keywords

Gene mutations, molecular pathology, fluorescent probes, image analysis

Methods

First, signal sizes and their locations are analyzed by using several filter algorithms. Second, detected cell nuclei are classified as positive, negative and artifact according to given probe type.

Quantitative output variables

1. Amplification for HER2 Gene

Total green signal count
Total red signal count
Average HER2/CEP17
HER2 copy count
cep17 copy count
ISH status
Total positive ROI
List of all dapi with signal counts

2. Amplification for other specific genes

Total green signal count
Total red signal count
Total specific genes amplification
Total negative ROI
Positivity Index
List of all dapi with signal counts

3. Deletion

Total green signal count
Total red signal count
Total specific genes deletion
Total negative ROI
Positivity Index
List of all dapi with signal counts

4. Break Apart

Total positive ROI
Total negative ROI
Positivity Index
List of all dapi with signal counts, break apart and fusion status

5. Fusion

Total positive ROI
Total negative ROI
Positivity Index
List of all dapi with signal numbers, break apart and fusion status

Workflows

View the FISH whole slide digital image on ViraPath.
Select FISH analysis according to probe and calibrate the parameters.
Run the related FISH analysis.

References

[1] Ratan, Z. A., Zaman, S. B., Mehta, V., Haidere, M. F., Runa, N. J., & Akter, N. (2017). Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science. Cureus.