Optimized workflow for digitalized FISH analysis in pathology

Chea, Vira; Pleiner, Valerie; Schweizer, Viviane; Herzog, Benjamin; Bode, Beata; Tinguely, Marianne

doi:10.1186/s13000-021-01103-5

Cited by 5 publications

(3 citation statements)

References 9 publications

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“…According to in‐house standard operating procedures, a minimum of four images per FISH analysis were stored allowing retrospective re‐evaluation of the results. Digital pathology measures were not used in this setting as validation of the various FISH probes for sarcomas, including tumour entities with densely packed cells, has proven challenging [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours

Zago Baltazar,

Claerhout,

Vander Borght

et al. 2024

The Journal of Pathology CR

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The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA‐based sequencing (targeted RNA‐seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA‐seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA‐seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA‐seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA‐seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH‐positive analyses showed a lower percentage of rearrangement‐positive nuclei (range 15–41%) compared to the concordant FISH‐positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA‐seq findings. For the EWSR1 FISH probe, we observed a gene‐dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA‐seq (22.9%). This study demonstrates an added value of targeted RNA‐seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA‐seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.

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Section: Methodsmentioning

confidence: 99%

Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours

Zago Baltazar,

Claerhout,

Vander Borght

et al. 2024

The Journal of Pathology CR

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“…Computation cytology bears important role in molecular study. Chea et al 15 showed that WSI of the fluorescent in situ hybridization (FISH) technique scanning had equal performance compared with manual interpretation. The digital slides is of good image quality, and takes significantly less time for analysis.…”

Section: Computational Cytology In the Precise Diagnosis Over The Man...mentioning

confidence: 99%

An emerging era of computational cytology

Dey

Bansal

Saini

2023

Diagnostic Cytopathology

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Background The significant advancement in digital imaging, data management, advanced computational power, and artificial neural network have an immense impact on the field of cytology. The amalgamation of these areas has generated a newer discipline known as computational cytology. Aims and objective In To discuss the various important aspects of computational cytology. Materials and methods We reviewed the different studies published in English during the last few years on computational cytology. Result Computational cytology is a newer and emerging discipline in pathology that deals with the patient's meta‐data and digital image data to make a mathematical model to produce diagnostic interpretations and predictions. The role of the cytologist is now changing from a simple observational scientist and slide interpreter to a dynamic and integrated multi‐parametric prediction‐based scientist. Conclusion In the current stage, the cytologist must understand the situation and should have a vision of the complete scenario on computational cytology.

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“…It’s worth highlighting that visualizing in situ hybridization results enables the application of diverse microscopic techniques for 3D signal visualization within tissues ( 35 ). Modern technologies such as FISHQuant, coupled with optimizations in analysis steps utilizing novel buffering systems to enhance tissue sample stability, are gaining widespread adoption ( 36 ).…”

Section: Introductionmentioning

confidence: 99%

Insights into brain tumor diagnosis: exploring in situ hybridization techniques

Namiot,

Zembatov,

Tregub

2024

Front. Neurol.

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ObjectivesDiagnosing brain tumors is critical due to their complex nature. This review explores the potential of in situ hybridization for diagnosing brain neoplasms, examining their attributes and applications in neurology and oncology.MethodsThe review surveys literature and cross-references findings with the OMIM database, examining 513 records. It pinpoints mutations suitable for in situ hybridization and identifies common chromosomal and gene anomalies in brain tumors. Emphasis is placed on mutations’ clinical implications, including prognosis and drug sensitivity.ResultsAmplifications in EGFR, MDM2, and MDM4, along with Y chromosome loss, chromosome 7 polysomy, and deletions of PTEN, CDKN2/p16, TP53, and DMBT1, correlate with poor prognosis in glioma patients. Protective genetic changes in glioma include increased expression of ADGRB3/1, IL12B, DYRKA1, VEGFC, LRRC4, and BMP4. Elevated MMP24 expression worsens prognosis in glioma, oligodendroglioma, and meningioma patients. Meningioma exhibits common chromosomal anomalies like loss of chromosomes 1, 9, 17, and 22, with specific genes implicated in their development. Main occurrences in medulloblastoma include the formation of isochromosome 17q and SHH signaling pathway disruption. Increased expression of BARHL1 is associated with prolonged survival. Adenomas mutations were reviewed with a focus on adenoma-carcinoma transition and different subtypes, with MMP9 identified as the main metalloprotease implicated in tumor progression.DiscussionMolecular-genetic diagnostics for common brain tumors involve diverse genetic anomalies. In situ hybridization shows promise for diagnosing and prognosticating tumors. Detecting tumor-specific alterations is vital for prognosis and treatment. However, many mutations require other methods, hindering in situ hybridization from becoming the primary diagnostic method.

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Optimized workflow for digitalized FISH analysis in pathology

Cited by 5 publications

References 9 publications

Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours

Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours

An emerging era of computational cytology

Insights into brain tumor diagnosis: exploring in situ hybridization techniques

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