Sarcoma Subgrouping by Detection of Fusion Transcripts Using NanoString nCounter Technology

Sheth, Javal; Arnoldo, Anthony; Zhong, Yunan; Marrano, Paula; Pereira, Carlos Augusto; Ryall, Scott; Thorner, Paul; Hawkins, Cynthia; Somers, Gino R.

doi:10.1177/1093526618790747

Cited by 14 publications

(12 citation statements)

References 36 publications

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“…In conclusion, the NanoString nCounter FusionPlex assay is a screening tool with high sensitivity and specificity [5][6][7]12,13 for the detection of sarcoma-defining fusion gene transcripts in Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumors. Its diagnostic yield for rare soft tissue tumors is limited and might require additional or alternative testing.…”

Section: Estimated Diagnostic Coverage Of Nanostring In Stb Tumorsmentioning

confidence: 99%

“…At present, the two novel molecular multiplex methods commonly used in Dutch sarcoma centers are the anchored multiplex PCR (AMP)‐based NGS (Archer FusionPlex Sarcoma assay) and the NanoString nCounter platform . The Archer AMP PCR method targets exons of 26 genes commonly involved in fusion genes of soft tissue tumors, whereas the NanoString assay is a high‐throughput hybridization technique, which uses specific probes that target 174 unique gene fusion junctions in 22 soft tissue tumor types …”

Section: Introductionmentioning

confidence: 99%

“…5 The Archer AMP PCR method targets exons of 26 genes commonly involved in fusion genes of soft tissue tumors, whereas the NanoString assay is a high-throughput hybridization technique, which uses specific probes that target 174 unique gene fusion junctions in 22 soft tissue tumor types. 6 In this quality control study, we evaluated the sensitivity and specificity of the NanoString nCounter platform for gene fusion detection in 22 different soft tissue tumors, adding our results to the initial report on this method. 7 2 | MATERIALS AND METHODS The study was approved by the UMCG institutional ethical review board (P18-116) and performed in accordance with the code of conduct for responsible use of human tissue that is used in the Netherlands (Dutch Federation of Biomedical Scientific Societies; http://www.federa.org).…”

Section: Introductionmentioning

confidence: 99%

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Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors

Song

Platteel

Suurmeijer

et al. 2020

Genes Chromosomes & Cancer

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Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. For other sarcomas, additional molecular testing may be required when a translocation transcript is not identified with the current 174 gene fusion panel.

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Section: Estimated Diagnostic Coverage Of Nanostring In Stb Tumorsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors

Song

Platteel

Suurmeijer

et al. 2020

Genes Chromosomes & Cancer

View full text Add to dashboard Cite

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“…NGS-based approaches are recommended for classifying small round cell sarcomas where a diagnosis consistent with ES cannot be made following classic immunohistochemistry, FISH, or RT-PCR. Several NGS assays, such as the Archer FusionPlex sarcoma assay, or different NanoString assays are available, but cost is still an issue [36][37][38][39]. Although CD99 is an extremely sensitive marker for ES, CD99 staining is very unspecific as it stains positive in a variety of other tumors [40].…”

Section: Molecular Diagnosticsmentioning

confidence: 99%

Current Status of Management and Outcome for Patients with Ewing Sarcoma

Hesla

Papakonstantinou

Tsagozis

2021

Cancers

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Ewing sarcoma is the second most common bone sarcoma in children after osteosarcoma. It is a very aggressive malignancy for which systemic treatment has greatly improved outcome for patients with localized disease, who now see survival rates of over 70%. However, for the quarter of patients presenting with metastatic disease, survival is still dismal with less than 30% of patients surviving past 5 years. Patients with disease relapse, local or distant, face an even poorer prognosis with an event-free 5-year survival rate of only 10%. Unfortunately, Ewing sarcoma patients have not yet seen the benefit of recent years’ technical achievements such as next-generation sequencing, which have enabled researchers to study biological systems at a level never seen before. In spite of large multinational studies, treatment of Ewing sarcoma relies entirely on chemotherapeutic agents that have been largely unchanged for decades. As many promising modern therapies, including monoclonal antibodies, small molecules, and immunotherapy, have been disappointing to date, there is no clear candidate as to which drug should be investigated in the next large-scale clinical trial. However, the mechanisms driving tumor development in Ewing sarcoma are slowly unfolding. New entities of Ewing-like tumors, with fusion transcripts that are related to the oncogenic EWSR1-FLI1 fusion seen in the majority of Ewing tumors, are being mapped. These tumors, although sharing much of the same morphologic features as classic Ewing sarcoma, behave differently and may require a different treatment. There are also controversies regarding local treatment of Ewing sarcoma. The radiosensitive nature of the disease and the tendency for Ewing sarcoma to arise in the axial skeleton make local treatment very challenging. Surgical treatment and radiotherapy have their pros and cons, which may give rise to different treatment strategies in different centers around the world. This review article discusses some of these controversies and reproduces the highlights from recent publications with regard to diagnostics, systemic treatment, and surgical treatment of Ewing sarcoma.

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“…There were no false-positive results; nevertheless, four cases were false negative when compared with FISH or RT-PCR. Another NanoString assay for testing 22 fusion transcripts associated with the most prevalent pediatric sarcomas was developed by Javal Sheth et al [25]. The results showed that NanoString assay was 100% concordant with RT-PCR.…”

Section: Improvement In the Diagnosis And Discovery Of New Entities Using Next-generation Techniquesmentioning

confidence: 99%

Breakthrough Technologies Reshape the Ewing Sarcoma Molecular Landscape

Salguero-Aranda

Amaral

Olmedo-Pelayo

et al. 2020

Cells

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Ewing sarcoma is a highly aggressive round cell mesenchymal neoplasm, most often occurring in children and young adults. At the molecular level, it is characterized by the presence of recurrent chromosomal translocations. In the last years, next-generation technologies have contributed to a more accurate diagnosis and a refined classification. Moreover, the application of these novel technologies has highlighted the relevance of intertumoral and intratumoral molecular heterogeneity and secondary genetic alterations. Furthermore, they have shown evidence that genomic features can change as the tumor disseminates and are influenced by treatment as well. Similarly, next-generation technologies applied to liquid biopsies will significantly impact patient management by allowing the early detection of relapse and monitoring response to treatment. Finally, the use of these novel technologies has provided data of great value in order to discover new druggable pathways. Thus, this review provides concise updates on the latest progress of these breakthrough technologies, underscoring their importance in the generation of key knowledge, prognosis, and potential treatment of Ewing Sarcoma.

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Sarcoma Subgrouping by Detection of Fusion Transcripts Using NanoString nCounter Technology

Cited by 14 publications

References 36 publications

Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors

Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors

Current Status of Management and Outcome for Patients with Ewing Sarcoma

Breakthrough Technologies Reshape the Ewing Sarcoma Molecular Landscape

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