Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors

Sun, Lulu; McNulty, Samantha N.; Evenson, Michael; Zhu, Xiaopei; Robinson, Joshua A.; Mann, Patrick R.; Duncavage, Eric J.; Pfeifer, John D.

doi:10.1016/j.jmoldx.2021.08.009

Cited by 6 publications

(3 citation statements)

References 38 publications

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“…This means that FISH pointed in a different diagnostic direction in almost one of three cases. A similar concordance of 73.0% between targeted RNA-seq and conventional methods has been described by Sun et al [19]. In terms of probe concordance rate, 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.…”

Section: Methods Performancesupporting

confidence: 82%

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: Methods Performancesupporting

confidence: 82%

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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“…We analyzed a total of 210 NSCLC samples by FISH, and we succeeded in characterizing 200 of these samples (95%) by targeted RNA NGS and 198 samples (94%) by RT-PCR. The results of our analyses, together with already published data [ 17 , 18 , 19 , 20 ], showed an excellent concordance rate (91%) of the targeted RNA NGS results with the so-far considered gold standard FISH technique, underlining the essential role of the NGS testing approach in the molecular pathology diagnostics laboratory.…”

Section: Discussionsupporting

confidence: 74%

Gene Fusion Detection in NSCLC Routine Clinical Practice: Targeted-NGS or FISH?

Pecciarini

Brunetto

Grassini

et al. 2023

Cells

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The ability to identify the broadest range of targetable gene fusions is crucial to facilitate personalized therapy selection for advanced lung adenocarcinoma (LuADs) patients harboring targetable receptor tyrosine kinase (RTK) genomic alterations. In order to evaluate the most effective testing approach for LuAD targetable gene fusion detection, we analyzed 210 NSCLC selected clinical samples, comparing in situ (Fluorescence In Situ Hybridization, FISH, and ImmunoHistoChemistry, IHC) and molecular (targeted RNA Next-Generation Sequencing, NGS, and RealTime-PCR, RT-PCR) approaches. The overall concordance among these methods was high (>90%), and targeted RNA NGS was confirmed to be the most efficient technique for gene fusion identification in clinical practice, allowing the simultaneous analysis of a large set of genomic rearrangements at the RNA level. However, we observed that FISH was useful to detect targetable fusions in those samples with inadequate tissue material for molecular testing as well as in those few cases whose fusions were not identified by the RNA NGS panel. We conclude that the targeted RNA NGS analysis of LuADs allows accurate RTK fusion detection; nevertheless, standard methods such as FISH should not be dismissed, as they can crucially contribute to the completion of the molecular characterization of LuADs and, most importantly, the identification of patients as candidates for targeted therapies.

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“…Several publications have addressed the topic of diagnostic test algorithms for detecting NTRK gene fusions or TRK fusion proteins, using methods such as immunohistochemistry, fluorescence in situ hybridization, reverse transcriptase-polymerase chain reaction (RT-PCR), and DNA or RNA-based NGS [ 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ]. Other publications have described the validation or the clinical implementation of NGS panels capable of detecting gene fusions in solid tumors or hematologic malignancies, providing useful information on defining quality metrics, performance characteristic assessment, verification of novel fusions and troubleshooting [ 11 , 12 , 13 , 14 , 15 , 16 ]. However, testing for gene fusions using RNA-based NGS is based on different principles than for DNA-based NGS.…”

Section: Introductionmentioning

confidence: 99%

Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing

Stockley

Box³

et al. 2023

Current Oncology

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The detection of gene fusions by RNA-based next-generation sequencing (NGS) is an emerging method in clinical genetic laboratories for oncology biomarker testing to direct targeted therapy selections. A recent Canadian study (CANTRK study) comparing the detection of NTRK gene fusions on different NGS assays to determine subjects’ eligibility for tyrosine kinase TRK inhibitor therapy identified the need for recommendations for best practices for laboratory testing to optimize RNA-based NGS gene fusion detection. To develop consensus recommendations, representatives from 17 Canadian genetic laboratories participated in working group discussions and the completion of survey questions about RNA-based NGS. Consensus recommendations are presented for pre-analytic, analytic and reporting aspects of gene fusion detection by RNA-based NGS.

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Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors

Cited by 6 publications

References 38 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

Gene Fusion Detection in NSCLC Routine Clinical Practice: Targeted-NGS or FISH?

Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing

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