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Decision Support & AI

FISH

Fluorescent in situ hybridization (FISH) is a molecular technique commonly used to detect chromosomal abnormalities and gene mutations such as translocation, amplification, 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 signal and visualizes the DAPI and signals. The algorithm categorizes the nuclei to normal, abnormal and artifact groups.

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Keywords

Gene mutations, molecular pathology, fluorescent probes, image analysis

Methods

Firstly, signals size and their locations are analysed by using several filter algorithms. Secondly, detected cell nuclei are classified as positive, negative and artefact 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
Workflow
  1. View the FISH whole slide digital image on ViraPath.
  2. Select FISH analysis according to probe and calibrate the parameters.
  3. 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

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