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Hasegawa N, Hayashi T, Niizuma H, Kikuta K, Imanishi J, Endo M, Ikeuchi H, Sasa K, Sano K, Hirabayashi K, Takagi T, Ishijima M, Kato S, Kohsaka S, Saito T, Suehara Y. Detection of Novel Tyrosine Kinase Fusion Genes as Potential Therapeutic Targets in Bone and Soft Tissue Sarcomas Using DNA/RNA-based Clinical Sequencing. Clin Orthop Relat Res 2024; 482:549-563. [PMID: 38014853 PMCID: PMC10871756 DOI: 10.1097/corr.0000000000002901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Approximately 1% of clinically treatable tyrosine kinase fusions, including anaplastic lymphoma kinase, neurotrophic tyrosine receptor kinase, RET proto-oncogene, and ROS proto-oncogene 1, have been identified in soft tissue sarcomas via comprehensive genome profiling based on DNA sequencing. Histologic tumor-specific fusion genes have been reported in approximately 20% of soft tissue sarcomas; however, unlike tyrosine kinase fusion genes, these fusions cannot be directly targeted in therapy. Approximately 80% of tumor-specific fusion-negative sarcomas, including myxofibrosarcoma and leiomyosarcoma, that are defined in complex karyotype sarcomas remain genetically uncharacterized; this mutually exclusive pattern of mutations suggests that other mutually exclusive driver oncogenes are yet to be discovered. Tumor-specific, fusion-negative sarcomas may be associated with unique translocations, and oncogenic fusion genes, including tyrosine kinase fusions, may have been overlooked in these sarcomas. QUESTIONS/PURPOSES (1) Can DNA- or RNA-based analysis reveal any characteristic gene alterations in bone and soft tissue sarcomas? (2) Can useful and potential tyrosine kinase fusions in tumors from tumor-specific, fusion-negative sarcomas be detected using an RNA-based screening system? (3) Do the identified potential fusion tumors, especially in neurotrophic tyrosine receptor kinase gene fusions in bone sarcoma, transform cells and respond to targeted drug treatment in in vitro assays? (4) Can the identified tyrosine kinase fusion genes in sarcomas be useful therapeutic targets? METHODS Between 2017 and 2020, we treated 100 patients for bone and soft tissue sarcomas at five institutions. Any biopsy or surgery from which a specimen could be obtained was included as potentially eligible. Ninety percent (90 patients) of patients were eligible; a further 8% (8 patients) were excluded because they were either lost to follow-up or their diagnosis was changed, leaving 82% (82 patients) for analysis here. To answer our first and second questions regarding gene alterations and potential tyrosine kinase fusions in eight bone and 74 soft tissue sarcomas, we used the TruSight Tumor 170 assay to detect mutations, copy number variations, and gene fusions in the samples. To answer our third question, we performed functional analyses involving in vitro assays to determine whether the identified tyrosine kinase fusions were associated with oncogenic abilities and drug responses. Finally, to determine usefulness as therapeutic targets, two pediatric patients harboring an NTRK fusion and an ALK fusion were treated with tyrosine kinase inhibitors in clinical trials. RESULTS DNA/RNA-based analysis demonstrated characteristic alterations in bone and soft tissue sarcomas; DNA-based analyses detected TP53 and copy number alterations of MDM2 and CDK4 . These single-nucleotide variants and copy number variations were enriched in specific fusion-negative sarcomas. RNA-based screening detected fusion genes in 24% (20 of 82) of patients. Useful potential fusions were detected in 19% (11 of 58) of tumor-specific fusion-negative sarcomas, with nine of these patients harboring tyrosine kinase fusion genes; five of these patients had in-frame tyrosine kinase fusion genes ( STRN3-NTRK3, VWC2-EGFR, ICK-KDR, FOXP2-MET , and CEP290-MET ) with unknown pathologic significance. The functional analysis revealed that STRN3-NTRK3 rearrangement that was identified in bone had a strong transforming potential in 3T3 cells, and that STRN3-NTRK3 -positive cells were sensitive to larotrectinib in vitro. To confirm the usefulness of identified tyrosine kinase fusion genes as therapeutic targets, patients with well-characterized LMNA-NTRK1 and CLTC-ALK fusions were treated with tyrosine kinase inhibitors in clinical trials, and a complete response was achieved. CONCLUSION We identified useful potential therapeutic targets for tyrosine kinase fusions in bone and soft tissue sarcomas using RNA-based analysis. We successfully identified STRN3-NTRK3 fusion in a patient with leiomyosarcoma of bone and determined the malignant potential of this fusion gene via functional analyses and drug effects. In light of these discoveries, comprehensive genome profiling should be considered even if the sarcoma is a bone sarcoma. There seem to be some limitations regarding current DNA-based comprehensive genome profiling tests, and it is important to use RNA testing for proper diagnosis and accurate identification of fusion genes. Studies on more patients, validation of results, and further functional analysis of unknown tyrosine kinase fusion genes are required to establish future treatments. CLINICAL RELEVANCE DNA- and RNA-based screening systems may be useful for detecting tyrosine kinase fusion genes in specific fusion-negative sarcomas and identifying key therapeutic targets, leading to possible breakthroughs in the treatment of bone and soft tissue sarcomas. Given that current DNA sequencing misses fusion genes, RNA-based screening systems should be widely considered as a worldwide test for sarcoma. If standard treatments such as chemotherapy are not effective, or even if the sarcoma is of bone, RNA sequencing should be considered to identify as many therapeutic targets as possible.
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Affiliation(s)
- Nobuhiko Hasegawa
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hidetaka Niizuma
- Department of Pediatrics, Tohoku University School of Medicine, Miyagi, Japan
| | - Kazutaka Kikuta
- Division of Musculoskeletal Oncology and Orthopaedic Surgery, Tochigi Cancer Center, Tochigi, Japan
| | - Jungo Imanishi
- Department of Orthopaedic Surgery, Teikyo University School of Medicine, Tokyo, Japan
- Department of Orthopaedic Oncology and Surgery, Saitama Medical University International Medical Center, Saitama, Japan
| | - Makoto Endo
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Ikeuchi
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Keita Sasa
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kei Sano
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaoru Hirabayashi
- Division of Diagnostic Pathology, Tochigi Cancer Center, Tochigi, Japan
| | - Tatsuya Takagi
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Muneaki Ishijima
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shunsuke Kato
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Al Shihabi A, Tebon PJ, Nguyen HTL, Chantharasamee J, Sartini S, Davarifar A, Jensen AY, Diaz-Infante M, Cox H, Gonzalez AE, Swearingen S, Tavanaie N, Dry S, Singh A, Chmielowski B, Crompton JG, Kalbasi A, Eilber FC, Hornicek F, Bernthal N, Nelson SD, Boutros PC, Federman N, Yanagawa J, Soragni A. The landscape of drug sensitivity and resistance in sarcoma. bioRxiv 2023:2023.05.25.542375. [PMID: 37292676 PMCID: PMC10245988 DOI: 10.1101/2023.05.25.542375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sarcomas are a family of rare malignancies composed of over 100 distinct histological subtypes. The rarity of sarcoma poses significant challenges in conducting clinical trials to identify effective therapies, to the point that many rarer subtypes of sarcoma do not have standard-of-care treatment. Even for established regimens, there can be substantial heterogeneity in responses. Overall, novel, personalized approaches for identifying effective treatments are needed to improve patient out-comes. Patient-derived tumor organoids (PDTOs) are clinically relevant models representative of the physiological behavior of tumors across an array of malignancies. Here, we use PDTOs as a tool to better understand the biology of individual tumors and characterize the landscape of drug resistance and sensitivity in sarcoma. We collected n=194 specimens from n=126 sarcoma patients, spanning 24 distinct subtypes. We characterized PDTOs established from over 120 biopsy, resection, and metastasectomy samples. We leveraged our organoid high-throughput drug screening pipeline to test the efficacy of chemotherapeutics, targeted agents, and combination therapies, with results available within a week from tissue collection. Sarcoma PDTOs showed patient-specific growth characteristics and subtype-specific histopathology. Organoid sensitivity correlated with diagnostic subtype, patient age at diagnosis, lesion type, prior treatment history, and disease trajectory for a subset of the compounds screened. We found 90 biological pathways that were implicated in response to treatment of bone and soft tissue sarcoma organoids. By comparing functional responses of organoids and genetic features of the tumors, we show how PDTO drug screening can provide an orthogonal set of information to facilitate optimal drug selection, avoid ineffective therapies, and mirror patient outcomes in sarcoma. In aggregate, we were able to identify at least one effective FDA-approved or NCCN-recommended regimen for 59% of the specimens tested, providing an estimate of the proportion of immediately actionable information identified through our pipeline. Highlights Standardized organoid culture preserve unique sarcoma histopathological featuresDrug screening on patient-derived sarcoma organoids provides sensitivity information that correlates with clinical features and yields actionable information for treatment guidanceHigh-throughput screenings provide orthogonal information to genetic sequencingSarcoma organoid response to treatment correlates with patient response to therapyLarge scale, functional precision medicine programs for rare cancers are feasible within a single institution.
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Badran A, Steele C, Alquaydheb H, Ba Theeb A, Bawazir A, Elshenawy MA, Atallah JP. The Use of Crizotinib in Sclerosing Epithelioid Fibrosarcoma with ALK Mutation: A Case Report. Case Rep Oncol 2023; 16:746-752. [PMID: 37900840 PMCID: PMC10601707 DOI: 10.1159/000532099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/12/2023] [Indexed: 10/31/2023] Open
Abstract
Sclerosing epithelioid fibrosarcoma is an ultra-rare and aggressive high-grade fibrosarcoma that was originally described in 1995. More than 100 cases are documented worldwide, with the most extensive case series reporting a high rate of recurrence and metastasis. ALK mutations are commonly seen in soft-tissue sarcomas; however, this is the first known case of an ALK V757M mutation. Here, we present a case using crizotinib in treating an ALK-positive sclerosing epithelioid fibrosarcoma refractory to all traditional treatment options.
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Affiliation(s)
- Ahmed Badran
- Department of Medical Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Clara Steele
- School of Medicine, Brookfield Health Sciences Complex, University College Cork, Cork, Ireland
| | - Hisham Alquaydheb
- Department of Internal Medicine, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ahmed Ba Theeb
- Faculty of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Mahmoud A. Elshenawy
- Department of Medical Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt
| | - Jean Paul Atallah
- Department of Medical Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Lopes-Brás R, Lopez-Presa D, Esperança-Martins M, Melo-Alvim C, Gallego L, Costa L, Fernandes I. Genomic Profiling of Sarcomas: A Promising Weapon in the Therapeutic Arsenal. Int J Mol Sci 2022; 23. [PMID: 36430703 DOI: 10.3390/ijms232214227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Sarcomas are rare malignant mesenchymal neoplasms, and the knowledge of tumor biology and genomics is scarce. Chemotherapy is the standard of care in advanced disease, with poor outcomes. Identifying actionable genomic alterations may offer effective salvage therapeutic options when previous lines have failed. Here, we report a retrospective cohort study of sarcoma patients followed at our center and submitted to comprehensive genomic profiling between January 2020 and June 2021. Thirty patients were included, most (96.7%) with reportable genomic alterations. The most common alterations were linked to cell cycle regulation (TP53, CDKN2A/B, and RB1 deletions and CDK4, MDM2, and MYC amplifications). Most patients (96.7%) had microsatellite stability and low tumor mutational burden (≤10 muts/megabase (Mb); median 2 Muts/Mb). Two-thirds of patients had actionable mutations for targeted treatments, including five cases with alterations amenable to targeted therapies with clinical benefit within the patient's tumor type, ten cases with targetable alterations with clinical benefit in other tumor types, and five cases with alterations amenable to targeting with drugs under investigation in a clinical trial setting. A significant proportion of cases in this study had actionable genomic alterations with available targeted drugs. Next-generation sequencing is a feasible option for identifying molecular drivers that can provide therapeutic options for individual patients. Molecular Tumor Boards should be implemented in the clinical practice to discuss genomic findings and inform clinically relevant targeted therapies.
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Fujii T, Takeda M, Uchiyama T, Nitta Y, Maebou K, Terada C, Okada F, Matsuoka M, Sugimoto S, Sasaki S, Morita K, Itami H, Miyake M, Takeda M, Sawabata N, Fujimoto K, Ohbayashi C. Identification of fusion transcripts in sarcoma from archival formalin-fixed paraffin-embedded tissues: A next-generation sequencing approach. Pathol Int 2022; 72:444-456. [PMID: 35975909 DOI: 10.1111/pin.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Most sarcomas are highly aggressive, and cause necrosis and hemorrhage. The diagnosis of sarcoma is challenging because of the lack of specificity of immunohistochemical staining; however, molecular biological approaches, such as genetic mutation, chromosomal translocation, and gene amplification, are promising. In this study, we extracted RNA from formalin-fixed paraffin-embedded (FFPE) tissue derived from surgically resected specimens of sarcoma stored for various periods and performed next-generation sequencing (NGS) analysis by MiniSeq using the Archer Fusion-Plex Sarcoma Panel. RNA was extracted from 63 FFPE tissue samples, and the degree of RNA degradation was assessed. The number of reads and fragment lengths were evaluated by NGS analysis. RNA extraction and cDNA synthesis were successful in 56 cases and library preparation was possible. Fusion genes were detected in 16 of 63 archived FFPE tissue samples in this study. However, in 18 cases, fragmentation was strong, and high-quality libraries could not be obtained. Nevertheless, comprehensive analysis of fusion genes with high sequence specificity by NGS can be a powerful alternative to reverse transcription-polymerase chain reaction and fluorescence in situ hybridization methods.
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Affiliation(s)
- Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Maiko Takeda
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tomoko Uchiyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Yuji Nitta
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Katsuya Maebou
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Chiyoko Terada
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Fumi Okada
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Minami Matsuoka
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Sumire Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Shoh Sasaki
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Kohei Morita
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Hiroe Itami
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Makito Miyake
- Department of Urology, Nara Medical University School of Medicine, Nara, Japan
| | - Masayuki Takeda
- Department of Cancer Genomics and Medical Oncology, Nara Medical University School of Medicine, Nara, Japan
| | - Noriyoshi Sawabata
- Department of Thoracic and Cardiovascular Surgery, Nara Medical University School of Medicine, Nara, Japan
| | - Kiyohide Fujimoto
- Department of Urology, Nara Medical University School of Medicine, Nara, Japan
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Reimers MA, Sehn JK, Van Tine BA, Smith ZL. Primary Prostatic Synovial Sarcoma With Pulmonary Metastases Identified by Routine Next-Generation Sequencing. JCO Precis Oncol 2022; 5:1133-1140. [PMID: 34994631 DOI: 10.1200/po.21.00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Melissa A Reimers
- Division of Oncology, Department of Internal Medicine, Section of Medical Oncology, Washington University in St Louis, St Louis, MO.,Siteman Cancer Center, Washington University in St Louis, St Louis, MO
| | - Jennifer K Sehn
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO
| | - Brian A Van Tine
- Division of Oncology, Department of Internal Medicine, Section of Medical Oncology, Washington University in St Louis, St Louis, MO.,Siteman Cancer Center, Washington University in St Louis, St Louis, MO.,Department of Pediatric Hematology and Oncology, St Louis Children's Hospital, St Louis, MO
| | - Zachary L Smith
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO.,Division of Urologic Surgery, Department of Surgery, Washington University in St Louis, St Louis, MO
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9
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Osinski BL, BenTaieb A, Ho I, Jones RD, Joshi RP, Westley A, Carlson M, Willis C, Schleicher L, Mahon BM, Stumpe MC. Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides. Mod Pathol 2022; 35:1791-803. [PMID: 36198869 DOI: 10.1038/s41379-022-01161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022]
Abstract
To achieve minimum DNA input requirements for next-generation sequencing (NGS), pathologists visually estimate macrodissection and slide count decisions. Unfortunately, misestimation may cause tissue waste and increased laboratory costs. We developed an artificial intelligence (AI)-augmented smart pathology review system (SmartPath) to empower pathologists with quantitative metrics for accurately determining tissue extraction parameters. SmartPath uses two deep learning architectures, a U-Net based network for cell segmentation and a multi-field-of-view convolutional network for tumor area segmentation, to extract features from digitized H&E-stained formalin-fixed paraffin-embedded slides. From the segmented tumor area, SmartPath suggests a macrodissection area. To predict DNA yield per slide, the extracted features from within the macrodissection area are correlated with known DNA yields to fit a regularized linear model (R = 0.85). Then, a pathologist-defined target yield divided by the predicted DNA yield per slide gives the number of slides to scrape. Following model development, an internal validation trial was conducted within the Tempus Labs molecular sequencing laboratory. We evaluated our system on 501 clinical colorectal cancer slides, where half received SmartPath-augmented review and half traditional pathologist review. The SmartPath cohort had 25% more DNA yields within a desired target range of 100-2000 ng. The number of extraction attempts was statistically unchanged between cohorts. The SmartPath system recommended fewer slides to scrape for large tissue sections, saving tissue in these cases. Conversely, SmartPath recommended more slides to scrape for samples with scant tissue sections, especially those with degraded DNA, helping prevent costly re-extraction due to insufficient extraction yield. A statistical analysis was performed to measure the impact of covariates on the results, offering insights on how to improve future applications of SmartPath. With these improvements, AI-augmented histopathologic review has the potential to decrease tissue waste, sequencing time, and laboratory costs by optimizing DNA yields, especially for samples with scant tissue and/or degraded DNA.
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10
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Sun L, McNulty SN, Evenson MJ, Zhu X, Robinson J, Mann PR, Duncavage EJ, Pfeifer JD. Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors. J Mol Diagn 2021; 23:1749-1760. [PMID: 34562614 DOI: 10.1016/j.jmoldx.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/09/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
The detection of recurrent gene fusions can help confirm diagnoses in solid tumors, particularly when the morphology and staining are unusual or nonspecific, and can guide therapeutic decisions. Although fluorescence in situ hybridization and PCR are often used to identify fusions, the rearrangement must be suspected, with only a few prioritized probes run. We hypothesized that the Illumina TruSight RNA Fusion Panel, which detects fusions of 507 genes and their partners, would uncover fusions with greater sensitivity than other approaches, leading to changes in diagnosis, prognosis, or therapy. Targeted RNA sequencing was performed on formalin-fixed, paraffin-embedded sarcoma and carcinoma cases in which fluorescence in situ hybridization, RT-PCR, or DNA-based sequencing was conducted during the diagnostic workup. Of 153 cases, 138 (90%) were sequenced with adequate quality control metrics. A total of 101 of 138 (73%) cases were concordant by RNA sequencing and the prior test method. RNA sequencing identified an additional 30 cases (22%) with fusions that were not detected by conventional methods. In seven cases (5%), the additional fusion information provided by RNA sequencing would have altered the diagnosis and management. A total of 19 novel fusion pairs (not previously described in the literature) were discovered (14%). Overall, the findings show that a targeted RNA-sequencing method can detect gene fusions in formalin-fixed, paraffin-embedded specimens with high sensitivity.
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Affiliation(s)
- Lulu Sun
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Samantha N McNulty
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Evenson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Xiaopei Zhu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Joshua Robinson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Patrick R Mann
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
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Stewart JP, Gazdova J, Darzentas N, Wren D, Proszek P, Fazio G, Songia S, Alcoceba M, Sarasquete ME, Villarese P, van der Klift MY, Heezen KC, McCafferty N, Pal K, Catherwood M, Kim CS, Srivastava S, Kroeze LI, Hodges E, Stamatopoulos K, Klapper W, Genuardi E, Ferrero S, van den Brand M, Cazzaniga G, Davi F, Sutton LA, Garcia-Sanz R, Groenen PJTA, Macintyre EA, Brüggemann M, Pott C, Langerak AW, Gonzalez D; EuroClonality-NGS Working Group. Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-98. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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Allahyar A, Pieterse M, Swennenhuis J, Los-de Vries GT, Yilmaz M, Leguit R, Meijers RWJ, van der Geize R, Vermaat J, Cleven A, van Wezel T, Diepstra A, van Kempen LC, Hijmering NJ, Stathi P, Sharma M, Melquiond ASJ, de Vree PJP, Verstegen MJAM, Krijger PHL, Hajo K, Simonis M, Rakszewska A, van Min M, de Jong D, Ylstra B, Feitsma H, Splinter E, de Laat W. Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing. Nat Commun 2021; 12:3361. [PMID: 34099699 PMCID: PMC8184748 DOI: 10.1038/s41467-021-23695-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/10/2021] [Indexed: 12/03/2022] Open
Abstract
In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.
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Affiliation(s)
- Amin Allahyar
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark Pieterse
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - G Tjitske Los-de Vries
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | - Roos Leguit
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | - Ruud W J Meijers
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | | | - Joost Vermaat
- Leiden University Medical Centre, Department of Hematology, Leiden, the Netherlands
| | - Arjen Cleven
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Tom van Wezel
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Arjan Diepstra
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Léon C van Kempen
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Nathalie J Hijmering
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Phylicia Stathi
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Milan Sharma
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Adrien S J Melquiond
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paula J P de Vree
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | | | - Daphne de Jong
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Wouter de Laat
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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Hynst J, Navrkalova V, Pal K, Pospisilova S. Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application. PeerJ 2021; 9:e10897. [PMID: 33850640 PMCID: PMC8019320 DOI: 10.7717/peerj.10897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/13/2021] [Indexed: 01/21/2023] Open
Abstract
Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders.
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Affiliation(s)
- Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Veronika Navrkalova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics, Faculty of Medicine and University Hospital Brno, Masaryk University, Brno, Czech Republic
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Mc Connell L, Gazdova J, Beck K, Srivastava S, Harewood L, Stewart JP, Hübschmann D, Stenzinger A, Glimm H, Heilig CE, Fröhling S, Gonzalez D. Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing. Cancers (Basel) 2020; 12:E3627. [PMID: 33287361 PMCID: PMC7761870 DOI: 10.3390/cancers12123627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
Circulating tumour DNA (ctDNA) analysis using next generation sequencing (NGS) is being implemented in clinical practice for treatment stratification and disease monitoring. However, using ctDNA to detect structural variants, a common occurrence in sarcoma, can be challenging. Here, we use a sarcoma-specific targeted NGS panel to identify translocations and copy number variants in a cohort of 12 tissue specimens and matched circulating cell-free DNA (cfDNA) from soft tissue sarcoma patients, including alveolar rhabdomyosarcoma (n = 2), Ewing's Sarcoma (n = 2), synovial sarcoma (n = 2), extraskeletal myxoid chondrosarcoma (n = 1), clear cell sarcoma (n = 1), undifferentiated round cell sarcoma (n = 1), myxoid liposarcoma (n = 1), alveolar soft part cell sarcoma (n = 1) and dedifferentiated liposarcoma (n = 1). Structural variants were detected in 11/12 (91.6%) and 6/12 (50%) of tissue and plasma samples, respectively. Structural variants were detected in cfDNA at variant allele frequencies >0.2% with an average sequencing depth of 1026×. The results from this cohort show clinical potential for using NGS in ctDNA to aid in the diagnosis and clinical monitoring of sarcomas and warrant additional studies in larger cohorts.
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Affiliation(s)
- Lauren Mc Connell
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
| | - Jana Gazdova
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
| | - Katja Beck
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (K.B.); (C.E.H.); (S.F.)
- German Cancer Research Center, 69120 Heidelberg, Germany;
| | - Shambhavi Srivastava
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
| | - Louise Harewood
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
| | - JP Stewart
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
| | - Daniel Hübschmann
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, 69120 Heidelberg, Germany;
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- German Cancer Research Center, 69120 Heidelberg, Germany;
- Institute of Pathology, University Hospital Heidelberg Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany;
- Center for Personalized Oncology, National Center for Tumour Diseases (NCT) Dresden and University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 01307 Dresden, Germany
| | - Christoph E. Heilig
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (K.B.); (C.E.H.); (S.F.)
- German Cancer Research Center, 69120 Heidelberg, Germany;
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (K.B.); (C.E.H.); (S.F.)
- German Cancer Research Center, 69120 Heidelberg, Germany;
| | - David Gonzalez
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK; (L.M.C.); (J.G.); (S.S.); (L.H.); (J.S.)
- Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
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15
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Wakely PE. Extraskeletal myxoid chondrosarcoma: combining cytopathology with molecular testing to achieve diagnostic accuracy. J Am Soc Cytopathol 2020; 10:293-299. [PMID: 32828707 DOI: 10.1016/j.jasc.2020.07.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Advances in the genetics of soft tissue neoplasia have allowed for the diagnostic recognition of specific tumor types from small biopsy specimens, including those procured using the fine needle aspiration (FNA) biopsy technique. Extraskeletal myxoid chondrosarcoma (EMC) is a malignant mesenchymal neoplasm characterized by NR4A3 and, less specifically, by EWSR1 gene rearrangements. A series of EMC cytologic specimens was examined to demonstrate the diagnostic value of incorporating fluorescence in situ hybridization (FISH) testing in cytologic cases of suspected EMC. MATERIALS AND METHODS A search was made of our cytopathology and surgical pathology databases for cases diagnosed as EMC. FNA biopsy cytology, exfoliative cytology, imprint cytology, and FISH analysis were performed and examined using standard techniques. RESULTS A total of 16 cases of EMC were retrieved from 15 patients (male/female ratio, 2.8:1; mean age, 62 years). Of the 15 patients, 10 were new patients with primary tumors, 2 had locally recurrent tumors, and 4 had metastases. The sites included the extremities in 10 cases, the trunk in 4, serous effusion in 1, and a mediastinal lymph node in 1 case. The specific cytologic diagnoses were EMC (14 cases; 88%), suspicious for EMC (n = 1), and malignant cells (n = 1). All cases for which FISH testing was successfully used were specifically recognized as EMC. Aspirates and imprint smears consisted of uniformly rounded cells set in an opaque myxoid/chondromyxoid stroma (less abundant and more diaphanous in the effusion sample), sometimes arranged in short anastomosing cords. FNA of 1 case of an EMC cellular variant mimicked a malignant small rounded cell tumor. CONCLUSION EMC can be added to the growing list of soft tissue neoplasms that are specifically recognizable using cytopathology, coupled with judicious application of ancillary molecular testing.
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Affiliation(s)
- Paul E Wakely
- Department of Pathology, James Cancer Hospital and Solove Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio.
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16
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Agrawal T, Monaco SE. Musculoskeletal small biopsies from small patients: current status in 2 academic hospitals. J Am Soc Cytopathol 2020; 9:442-449. [PMID: 32654990 DOI: 10.1016/j.jasc.2020.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Pediatric bone and soft tissue (BST) lesions typically undergo biopsy prior to treatment, which commonly involves core needle biopsy (CNB) and/or fine-needle aspiration biopsy (FNAB). This study looks at the utility of small biopsies in the current diagnosis of pediatric BST lesions from 2 institutions. MATERIALS AND METHODS A retrospective search of BST small biopsies obtained during a 2-year time period (2018-2019) at 2 academic institutions was performed to look at clinicopathologic features, biopsy diagnoses, and correlation with follow-up. RESULTS A total of 96 pediatric patients (average age 11.2 years, range: 10 months-19 years) with BST lesions underwent a small biopsy, which represents 5% of the total BST lesions biopsied. The results show that the majority of lesions were benign (65%), and diagnosed by CNB alone (73%); a combination of FNAB and CNB (16%), and FNAB alone (11%), were less frequent. The CNB was effective in making a definitive diagnosis in 93% of cases and overall small biopsy was effective in 91% of the cases. Cases with definitive diagnoses on small biopsy were more likely to have concurrent CNB or characteristic ancillary studies performed. CONCLUSIONS Although pediatric BST lesions constitute only 5% of all BST lesions biopsied, minimally invasive small biopsies with cytologic evaluation for triage and appropriate ancillary study utilization can help render specific diagnoses that help to determine the appropriate treatment for young patients with BST lesions. The current diagnostic approach frequently involves CNB with intraprocedural evaluation or concurrent FNAB, with fewer biopsied by FNAB alone.
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Affiliation(s)
- Tanupriya Agrawal
- Department of Pathology, University of Rochester Medical Center (URMC), Rochester, New York
| | - Sara E Monaco
- Department of Pathology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, Pennsylvania.
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