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Gastier-Foster JM, Lutwama F, Mbabazi O, Mlenga S, Ulaya K, Namazzi R, Hollingsworth EF, Lopez-Terrada D, Fisher KE, Roy A, Allen CE, Poplack DG, Mzikamanda R, Ozuah N, Wasswa P. Rapid gene fusion testing using the NanoString nCounter platform to improve pediatric leukemia diagnoses in Sub-Saharan Africa. Front Oncol 2024; 14:1426638. [PMID: 38939333 PMCID: PMC11208450 DOI: 10.3389/fonc.2024.1426638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Risk stratification and molecular targeting have been key to increasing cure rates for pediatric cancers in high-income countries. In contrast, precise diagnosis in low-resource settings is hindered by insufficient pathology infrastructure. The Global HOPE program aims to improve outcomes for pediatric cancer in Sub-Saharan Africa (SSA) by building local clinical care and diagnostic capacity. This study aimed to assess the feasibility of implementing molecular assays to improve leukemia diagnoses in SSA. Custom NanoString nCounter gene fusion assays, previously validated in the US, were used to test samples from suspected leukemia patients. The NanoString platform was chosen due to relatively low cost, minimal technical and bioinformatics expertise required, ability to test sub-optimal RNA, and rapid turnaround time. Fusion results were analyzed blindly, then compared to morphology and flow cytometry results. Of 117 leukemia samples, 74 were fusion-positive, 30 were negative, 7 were not interpretable, and 6 failed RNA quality. Nine additional samples were negative for leukemia by flow cytometry and negative for gene fusions. All 74 gene fusions aligned with the immunophenotype determined by flow cytometry. Fourteen samples had additional information available to further confirm the accuracy of the gene fusion results. The testing provided a more precise diagnosis in >60% of cases, and 9 cases were identified that could be treated with an available tyrosine kinase inhibitor, if detected at diagnosis. As risk-stratified and targeted therapies become more available in SSA, implementing this testing in real-time will enable the treatment of pediatric cancer to move toward incorporating risk stratification for optimized therapy.
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Affiliation(s)
- Julie M. Gastier-Foster
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Fredrick Lutwama
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Olive Mbabazi
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Steven Mlenga
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Kennedy Ulaya
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Ruth Namazzi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - E. Faith Hollingsworth
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Dolores Lopez-Terrada
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Kevin E. Fisher
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Angshumoy Roy
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Carl E. Allen
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - David G. Poplack
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Rizine Mzikamanda
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Nmazuo Ozuah
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Peter Wasswa
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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2
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Berger A, Rennie S, Aijaz J, Johnson LM, Antillon F, Roberts MC, Chitsike I, Kambugu J, Saha V, Bhakta N, Davis AM, Alexander TB. The role of relative advantage for development of sequencing-based diagnostics for pediatric cancer in low- and middle-income countries. Cancer 2024; 130:173-178. [PMID: 37843081 DOI: 10.1002/cncr.35065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Efforts to address limitations in cancer diagnostics in low‐ and middle‐income countries should follow an approach that avoids two extremes: unproductive attempts to require implementation of high‐income country gold standards or acquiescence to the diagnostic status quo. The relative advantage of implementing new diagnostic tests (including sequencing‐based approaches) should be determined through comparison to local standards of care, with context‐specific clinical utility determined using locally available therapeutic options.
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Affiliation(s)
- Anissa Berger
- Department of Social Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Stuart Rennie
- Department of Social Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Javeria Aijaz
- Department of Pathology, Indus Health and Hospital Network, Karachi, Pakistan
| | - Liza-Marie Johnson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Megan C Roberts
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Vaskar Saha
- Tata Translational Cancer Research Center, Kolkata, India
| | - Nickhill Bhakta
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Arlene M Davis
- Department of Social Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thomas B Alexander
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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3
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de Oliveira Cavagna R, de Andrade ES, Tadin Reis M, de Paula FE, Noriz Berardinelli G, Bonatelli M, Ramos Teixeira G, Garbe Zaniolo B, Mourão Dias J, da Silva FAF, Baston Silva CE, Xavier Reis M, Lopes Maia E, de Alencar TS, Jacinto AA, da Nóbrega Oliveira REN, Molina-Vila MA, Ferro Leal L, Reis RM. Detection of NTRK fusions by RNA-based nCounter is a feasible diagnostic methodology in a real-world scenario for non-small cell lung cancer assessment. Sci Rep 2023; 13:21168. [PMID: 38036758 PMCID: PMC10689426 DOI: 10.1038/s41598-023-48613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
NTRK1, 2, and 3 fusions are important therapeutic targets for NSCLC patients, but their prevalence in South American admixed populations needs to be better explored. NTRK fusion detection in small biopsies is a challenge, and distinct methodologies are used, such as RNA-based next-generation sequencing (NGS), immunohistochemistry, and RNA-based nCounter. This study aimed to evaluate the frequency and concordance of positive samples for NTRK fusions using a custom nCounter assay in a real-world scenario of a single institution in Brazil. Out of 147 NSCLC patients, 12 (8.2%) cases depicted pan-NTRK positivity by IHC. Due to the absence of biological material, RNA-based NGS and/or nCounter could be performed in six of the 12 IHC-positive cases (50%). We found one case exhibiting an NTRK1 fusion and another an NTRK3 gene fusion by both RNA-based NGS and nCounter techniques. Both NTRK fusions were detected in patients diagnosed with lung adenocarcinoma, with no history of tobacco consumption. Moreover, no concomitant EGFR, KRAS, and ALK gene alterations were detected in NTRK-positive patients. The concordance rate between IHC and RNA-based NGS was 33.4%, and between immunohistochemistry and nCounter was 40%. Our findings indicate that NTRK fusions in Brazilian NSCLC patients are relatively rare (1.3%), and RNA-based nCounter methodology is a suitable approach for NRTK fusion identification in small biopsies.
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Affiliation(s)
- Rodrigo de Oliveira Cavagna
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Murilo Bonatelli
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | - Gustavo Ramos Teixeira
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | - Beatriz Garbe Zaniolo
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | | | | | | | - Marina Xavier Reis
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | - Erika Lopes Maia
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Miguel A Molina-Vila
- Laboratory of Oncology/Pangaea Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela, Barretos, São Paulo, 14784-400, Brazil.
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil.
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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4
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Stelloo E, Meijers RWJ, Swennenhuis JF, Allahyar A, Hajo K, Cangiano M, de Leng WWJ, van Helvert S, Van der Meulen J, Creytens D, van Kempen LC, Cleton-Jansen AM, Bovee JVMG, de Laat W, Splinter E, Feitsma H. Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors. J Mol Diagn 2023; 25:758-770. [PMID: 37517473 DOI: 10.1016/j.jmoldx.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded-targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.
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Affiliation(s)
| | - Ruud W J Meijers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Amin Allahyar
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd van Helvert
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Léon C van Kempen
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Judith V M G Bovee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
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5
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Diagnosis of Fusion-Associated Sarcomas by Exon Expression Imbalance and Gene Expression. J Mol Diagn 2023; 25:121-131. [PMID: 36503147 DOI: 10.1016/j.jmoldx.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Sarcomas are a diverse group of tumors, with >70 subtypes in the current World Health Organization classification, each with distinct biological behavior requiring specific clinical management. A significant portion of sarcomas are molecularly defined by expression of a driver fusion gene; identification of such fusions is the basis of molecular diagnostics in sarcomas, which is of increasing complexity due to the ongoing discovery of new gene fusions. Recently, a multiplex NanoString platform-based assay was developed and clinically implemented, with fusion junction-spanning probes that detect the majority of sarcoma fusion types, with high sensitivity and specificity, and with lower cost and shorter turnaround time than those of targeted next-generation sequencing-based alternatives. Despite the effectiveness of this assay, there are several entities for which fusion-junction probes are not suitable due to multiple possible gene partners or excessive variability at the exon junctions. Here, the development and evaluation of a companion assay are described that uses NanoString-based gene expression analysis to detect aberrant 3'/5' exon expression imbalance and/or total gene overexpression as a surrogate marker for fusion gene rearrangement. This assay evaluates exon imbalance in 23 genes involved in over 25 mesenchymal tumor types and five genes specific to sarcomas with CIC rearrangements. Based on evaluation of 115 retrospectively and 91 prospectively collected cases, an assay sensitivity of 92.8% and specificity of 93.5% are demonstrated.
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6
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Wang J, Bhakta N, Ayer Miller V, Revsine M, Litzow MR, Paietta E, Fedoriw Y, Roberts KG, Gu Z, Mullighan CG, Jones CD, Alexander TB. Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing. JCO Precis Oncol 2022; 6:e2100326. [PMID: 35442720 PMCID: PMC9200386 DOI: 10.1200/po.21.00326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. MATERIALS AND METHODS We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. RESULTS We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. CONCLUSION Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.
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Affiliation(s)
- Jeremy Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Nickhill Bhakta
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN
| | - Vanessa Ayer Miller
- Office of Clinical Translational Research, University of North Carolina, Chapel Hill, NC
| | - Mahler Revsine
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Mark R. Litzow
- Division of Hematology and Transplant Center, Mayo Clinic Rochester, Rochester, MN
| | | | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Kathryn G. Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | | | - Corbin D. Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Thomas B. Alexander
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC,Department of Pediatrics, University of North Carolina, Chapel Hill, NC,Thomas B. Alexander, MD, MPH, Department of Pediatrics and Department of Pathology and Laboratory Medicine, University of North Carolina Chapel Hill, 170 Manning Dr, 1185A Houpt Building, CB#7236, Chapel Hill, NC 27599;e-mail:
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7
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Chen J, Liu X, Lan J, Li T, She C, Zhang Q, Yang W. Rhabdomyosarcoma in Adults: Case Series and Literature Review. Int J Womens Health 2022; 14:405-414. [PMID: 35370426 PMCID: PMC8973688 DOI: 10.2147/ijwh.s352143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/03/2022] [Indexed: 12/31/2022] Open
Abstract
Rhabdomyosarcoma, a common soft tissue malignant tumor in children and adolescents, is exceedingly rare in adults. Nevertheless, The outcome in adults is very poor, especially when compared to outcomes in children in whom significant improvements in treatment has been achieved. The first case was of a 24-year-old pregnant Chinese woman with a rare primary site of rhabdomyosarcoma in the perineal body. She presented with a perineal mass and was diagnosed during the second trimester of pregnancy, which is a very rare occurrence. The second case was a 70-year-old Chinese woman who suffered from right lower abdominal pain for 1 month and was misdiagnosed with an epithelial ovarian carcinoma. Mesenteric pleomorphic rhabdomyosarcoma was later confirmed by postoperative pathology. Both cases had undergone preoperative examination with chest and abdominal computed tomography (CT) and pelvic magnetic resonance imaging (MRI) examinations, as well as examination of complete blood count, liver panel, renal panel, and serum tumor markers. Diagnosis was based on histopathology and immunohistochemistry. The patient in the first case received chemotherapy after which the mass decreased in size; however, the patient was lost to follow-up. The second case underwent tumor resection and received chemotherapy and radiotherapy.
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Affiliation(s)
- Jian Chen
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Xiaoyun Liu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Jian Lan
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Tingchao Li
- Pathology Department, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Chaokun She
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Qingyun Zhang
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
| | - Wei Yang
- Imaging Department, The Third Affiliated Hospital of Zunyi Medical University (The First People’s Hospital of Zunyi), Zunyi City, Guizhou Province, People’s Republic of China
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8
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Wang XQ, Goytain A, Dickson BC, Nielsen TO. Advances in Sarcoma Molecular Diagnostics. Genes Chromosomes Cancer 2022; 61:332-345. [DOI: 10.1002/gcc.23025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xue Qi Wang
- Faculty of Medicine University of British Columbia Vancouver Canada
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Angela Goytain
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Torsten Owen Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
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9
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Haley L, Parimi V, Jiang L, Pallavajjala A, Hardy M, Yonescu R, Morsberger L, Stinnett V, Long P, Zou YS, Gocke CD. Diagnostic Utility of Gene Fusion Panel to Detect Gene Fusions in Fresh and Formalin-Fixed, Paraffin-Embedded Cancer Specimens. J Mol Diagn 2021; 23:1343-1358. [PMID: 34358677 DOI: 10.1016/j.jmoldx.2021.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/04/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
Somatic gene fusions are common in leukemias/lymphomas and solid tumors. The detection of gene fusions is crucial for diagnosis. NanoString fusion technology is a multiplexed hybridization method that interrogates hundreds of gene fusions in a single reaction. This study's objective was to determine the performance characteristics and diagnostic utility of NanoString fusion assay in a clinical diagnostics laboratory. Validation using 100 positive specimens and 15 negative specimens by a combined reference standard of fluorescence in situ hybridization (FISH)/RT-PCR/next-generation sequencing (NGS) assays achieved 100% sensitivity in leukemias/lymphomas and 95.0% sensitivity and 100% specificity in solid tumors. Subsequently, 214 consecutive clinical cases, including 73 leukemia/lymphoma specimens and 141 formalin-fixed, paraffin-embedded solid tumor specimens, were analyzed by gene fusion panels across 638 unique gene fusion transcripts. A variety of comparator tests, including FISH panels, conventional karyotyping, a DNA-based targeted NGS assay, and custom RT-PCR testing, were performed in parallel. The gene fusion assay detected 31 gene fusions, including 16 in leukemia/lymphoma specimens and 15 in solid tumor specimens. The overall sensitivity, specificity, and accuracy of gene fusions detected by the gene fusion panel in all 329 specimens (validation and consecutive clinical specimens) tested in this study were 94.8%, 100%, and 97.9%, respectively, compared with FISH/RT-PCR/NGS assays. The gene fusion panel is a reliable approach that maximizes molecular detection of fusions among both fresh and formalin-fixed, paraffin-embedded cancer specimens.
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Affiliation(s)
- Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Raluca Yonescu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Laura Morsberger
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Victoria Stinnett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Patty Long
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland.
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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10
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Hesla AC, Papakonstantinou A, Tsagkozis P. Current Status of Management and Outcome for Patients with Ewing Sarcoma. Cancers (Basel) 2021; 13:1202. [PMID: 33801953 PMCID: PMC7998375 DOI: 10.3390/cancers13061202] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/16/2022] Open
Abstract
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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RNA-Based Multiplexing Assay for Routine Testing of Fusion and Splicing Variants in Cytological Samples of NSCLC Patients. Diagnostics (Basel) 2020; 11:diagnostics11010015. [PMID: 33374879 PMCID: PMC7824402 DOI: 10.3390/diagnostics11010015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
The detection of ALK receptor tyrosine kinase (ALK), ROS proto-oncogen1, receptor tyrosine kinase (ROS1), ret proto-oncogen (RET), and MET proto-oncogen exon 14 skipping (METΔex14) allows for the selection of specific kinase inhibitor treatment in patients with non-small cell lung cancer (NSCLC). Multiplex technologies are recommended in this setting. We used nCounter, a multiplexed technology based on RNA hybridization, to detect ALK, ROS1, RET, and METΔex14 in RNA purified from cytological specimens (n = 16) and biopsies (n = 132). Twelve of the 16 cytological samples (75.0%) were evaluable by nCounter compared to 120 out of 132 (90.9%) biopsies. The geometrical mean (geomean) of the housekeeping genes of the nCounter panel, but not the total amount of RNA purified, was significantly higher in biopsies vs. cytological samples. Among cytological samples, we detected ALK (n = 3), METΔex14 (n = 1) and very high MET expression (n = 1) positive cases. The patient with METΔex14 had a partial response to tepotinib, one of the patients with ALK fusions was treated with crizotinib with a complete response. Cell blocks and cytological extensions can be successfully used for the detection of fusions and splicing variants using RNA-based methods such as nCounter.
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Breakthrough Technologies Reshape the Ewing Sarcoma Molecular Landscape. Cells 2020; 9:cells9040804. [PMID: 32225029 PMCID: PMC7226764 DOI: 10.3390/cells9040804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
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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Song W, Platteel I, Suurmeijer AJH, van Kempen LC. Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors. Genes Chromosomes Cancer 2020; 59:318-324. [PMID: 31965673 PMCID: PMC7079105 DOI: 10.1002/gcc.22834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/11/2022] Open
Abstract
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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Affiliation(s)
- Wangzhao Song
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Inge Platteel
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Albert J H Suurmeijer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Léon C van Kempen
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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