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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [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] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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2
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Giacomini P, Ciliberto G. Molecular Tumor Boards: On the evolution of species. Eur J Cancer 2024; 201:113910. [PMID: 38382152 DOI: 10.1016/j.ejca.2024.113910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Patrizio Giacomini
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCSS Regina Elena National Cancer Institute, Rome, Italy.
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3
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Gong J, Dong L, Wang C, Luo N, Han T, Li M, Sun T, Ding R, Han B, Li G. Molecular genomic landscape of pediatric solid tumors in Chinese patients: implications for clinical significance. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04756-5. [PMID: 37140698 DOI: 10.1007/s00432-023-04756-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/08/2023] [Indexed: 05/05/2023]
Abstract
PURPOSE Pediatric solid tumors are significantly different from adult tumors. Studies have revealed genomic aberrations in pediatric solid tumors, but these analyses were based on Western populations. Currently, it is not known to what extent the existing genomic findings represent differences in ethnic backgrounds. EXPERIMENTAL DESIGN: We retrospectively analyzed the basic clinical characteristics of the patients, including age, cancer type, and sex distribution, and further analyzed the somatic and germline mutations of cancer-related genes in a Chinese pediatric cohort. In addition, we investigated the clinical significance of genomic mutations on therapeutic, prognostic, diagnostic, and preventive actions. RESULTS Our study enrolled 318 pediatric patients, including 234 patients with CNS tumors and 84 patients with non-CNS tumors. Somatic mutation analysis showed that there were significant differences in mutation types between CNS tumors and non-CNS tumors. P/LP germline variants were identified in 8.49% of patients. In total, 42.8% patients prompted diagnostic, 37.7% patients prompted prognostic, 58.2% patients prompted therapeutic, and 8.5% patients prompted tumor-predisposing and preventive, and we found that genomic findings might improve clinical management. CONCLUSIONS Our study is the first large-scale study to analyze the landscape of genetic mutations in pediatric patients with solid tumors in China. Genomic findings in CNS and non-CNS solid pediatric tumors provide evidence for the clinical classification and individualized treatment of pediatric tumors, and they will facilitate improvement of clinical management. Data presented in this study should serve as a reference to guide the future design of clinical trials.
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Affiliation(s)
- Jie Gong
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Liujian Dong
- Department of Neurosurgery, Children's Hospital Affiliated to Zhengzhou University; Henan Children's Hospital; Zhengzhou Children's Hospital, Zhengzhou, 450000, Henan, China
| | - Chuanwei Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Ningning Luo
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Tiantian Han
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Mengmeng Li
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Tingting Sun
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Ran Ding
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210000, Jiangsu, China
| | - Bo Han
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Department of Pathology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012, Shandong, China.
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Liu A, Vicenzi P, Sharma I, Orr K, Teller C, Koentz M, Trinkman H, Vallance K, Ray A. Molecular Tumor Boards: The Next Step towards Precision Therapy in Cancer Care. Hematol Rep 2023; 15:244-255. [PMID: 37092519 PMCID: PMC10123678 DOI: 10.3390/hematolrep15020025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/05/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
The application of molecular tumor profiles in clinical decision making remains a challenge. To aid in the interpretation of complex biomarkers, molecular tumor boards (MTBs) have been established worldwide. In the present study, we show that a multidisciplinary approach is essential to the success of MTBs. Our MTB, consisting of pediatric oncologists, pathologists, and pharmacists, evaluated 115 cases diagnosed between March 2016 and September 2021. If targetable mutations were identified, pharmacists aided in the evaluation of treatment options based on drug accessibility. Treatable genetic alterations detected through molecular testing most frequently involved the cell cycle. For 85% of the cases evaluated, our MTB provided treatment recommendations based on the patient’s history and results of molecular tumor testing. Only three patients, however, received MTB-recommended targeted therapy, and only one of these patients demonstrated an improved clinical outcome. For the remaining patients, MTB-recommended treatment often was not administered because molecular tumor profiling was not performed until late in the disease course. For the three patients who did receive MTB-recommended therapy, such treatment was not administered until months after diagnosis due to physician preference. Thus, the education of healthcare providers regarding the benefits of targeted therapy may increase acceptance of these novel agents and subsequently improve patient survival.
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Affiliation(s)
- Angela Liu
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Paige Vicenzi
- Department of Pediatrics, Dell Children’s Medical Center, Austin, TX 78723, USA
| | - Ishna Sharma
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Kaci Orr
- Texas A&M Health Science Center School of Medicine, Bryan, TX 77807, USA
| | - Christa Teller
- Department of Pediatric Hematology/Oncology, Cook Children’s Medical Center, Fort Worth, TX 76104, USA
| | - Micha Koentz
- Department of Pharmacy, Cook Children’s Medical Center, Fort Worth, TX 76104, USA
| | - Heidi Trinkman
- Department of Pharmacy, Cook Children’s Medical Center, Fort Worth, TX 76104, USA
| | - Kelly Vallance
- Department of Pediatric Hematology/Oncology, Cook Children’s Medical Center, Fort Worth, TX 76104, USA
| | - Anish Ray
- Department of Pediatric Hematology/Oncology, Cook Children’s Medical Center, Fort Worth, TX 76104, USA
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Schapranow MP, Borchert F, Bougatf N, Hund H, Eils R. Software-Tool Support for Collaborative, Virtual, Multi-Site Molecular Tumor Boards. SN COMPUTER SCIENCE 2023; 4:358. [PMID: 37131499 PMCID: PMC10136394 DOI: 10.1007/s42979-023-01771-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/03/2023] [Indexed: 05/04/2023]
Abstract
The availability of high-throughput molecular diagnostics builds the foundation for Molecular Tumor Boards (MTBs). Although more fine-grained data is expected to support decision making of oncologists, assessment of data is complex and time-consuming slowing down the implementation of MTBs, e.g., due to retrieval of the latest medical publications, assessment of clinical evidence, or linkage to the latest clinical guidelines. We share our findings from analysis of existing tumor board processes and defininion of clinical processes for the adoption of MTBs. Building on our findings, we have developed a real-world software prototype together with oncologists and medical professionals, which supports the preparation and conduct of MTBs and enables collaboration between medical experts by sharing medical knowledge even across the hospital locations. We worked in interdisciplinary teams of clinicians, oncologists, medical experts, medical informaticians, and software engineers using design thinking methodology. With their input, we identified challenges and limitations of the current MTB approaches, derived clinical process models using Business Process and Modeling Notation (BMPN), and defined personas, functional and non-functional requirements for software tool support. Based on it, we developed software prototypes and evaluated them with clinical experts from major university hospitals across Germany. We extended the Kanban methodology enabling holistic tracking of patient cases from "backlog" to "follow-up" in our app. The feedback from interviewed medical professionals showed that our clinical process models and software prototype provide suitable process support for the preparation and conduction of molecular tumor boards. The combination of oncology knowledge across hospitals and the documentation of treatment decision can be used to form a unique medical knowledge base by oncologists for oncologists. Due to the high heterogeneity of tumor diseases and the spread of the latest medical knowledge, a cooperative decision-making process including insights from similar patient cases was considered as a very valuable feature. The ability to transform prepared case data into a screen presentation was recognized as an essential feature speeding up the preparation process. Oncologists require special software tool support to incorporate and assess molecular data for the decision-making process. In particular, the need for linkage to the latest medical knowledge, clinical evidence, and collaborative tools to discuss individual cases were named to be of importance. With the experiences from the COVID-19 pandemic, the acceptance of online tools and collaborative working is expected to grow. Our virtual multi-site approach proved to allow a collaborative decision-making process for the first time, which we consider to have a positive impact on the overall treatment quality.
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Affiliation(s)
- Matthieu-P. Schapranow
- Hasso Plattner Institute for Digital Engineering, University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| | - Florian Borchert
- Hasso Plattner Institute for Digital Engineering, University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| | - Nina Bougatf
- Department of Radiation Oncology, Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
| | - Hauke Hund
- GECKO Institute, Heilbronn University of Applied Sciences, Max-Planck-Straße 39, 74081 Heilbronn, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany
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6
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O'Regan P, Hoskins R, Grave C, Stevenson JA, Frost H, Graham DM, Krebs MG, Freitas A, Landers D. Digital ECMT Cancer Trial Matching Tool: an Open Source Research Application to Support Oncologists in the Identification of Precision Medicine Clinical Trials. JCO Clin Cancer Inform 2023; 7:e2200137. [PMID: 36657092 DOI: 10.1200/cci.22.00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
PURPOSE Matching patients with cancer to precision medicine clinical trials on the basis of their tumor genotype has the potential to improve outcomes for patients who have exhausted standard-of-care treatment options. However, the matching process presents a substantial challenge because of the number of clinical trials available. We describe a free, open source research tool designed to extract relevant trial information to support oncologists in the matching process, and we illustrate its utility with recent case studies of patients who were matched to trials using this tool. METHODS Trial records are sourced from ClinicalTrials.gov and indexed using natural language processing techniques, including named entity recognition, term normalization, and relationship extraction. Relationships between trials and genetic alterations are assigned scores on the basis of a rule-based system. All data are updated daily. A user interface is provided via R Shiny app. RESULTS An instance of the trial match tool, configured for UK clinical trials, is hosted by the digital Experimental Cancer Medicine Team (see link in Data Sharing Statement). Users select the relevant cancer type and genetic alteration(s). Matching studies are ranked according to the score assigned for the selected genetic alterations. Results may be downloaded and attached to the patient's health record if desired. The tool is currently being used to support the ongoing TARGET National study, which aims to match up to 6,000 patients to early phase clinical trials. We present three case studies that exemplify relationships between genetic alterations and studies. CONCLUSION With increasing numbers of precision medicine treatments and as comprehensive molecular profiling of tumor samples becomes more common, decision support tools are likely to become increasingly important. This work represents an important step toward the development and wider implementation of such systems.
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Affiliation(s)
- Paul O'Regan
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
| | - Richard Hoskins
- Research IT, The University of Manchester, Manchester, United Kingdom
| | - Christopher Grave
- Research IT, The University of Manchester, Manchester, United Kingdom
| | - Julie-Anne Stevenson
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
| | - Hannah Frost
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
- Department of Computer Science, Kilburn Building, The University of Manchester, Manchester, United Kingdom
| | - Donna M Graham
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Matthew G Krebs
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Andre Freitas
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
- Department of Computer Science, Kilburn Building, The University of Manchester, Manchester, United Kingdom
- Idiap Research Institute, Martigny, Switzerland
| | - Dónal Landers
- Digital Experimental Cancer Medicine Team, Cancer Research UK Manchester Institute, The Oglesby Cancer Research Building, The University of Manchester, Manchester, United Kingdom
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7
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Hamamoto R, Koyama T, Kouno N, Yasuda T, Yui S, Sudo K, Hirata M, Sunami K, Kubo T, Takasawa K, Takahashi S, Machino H, Kobayashi K, Asada K, Komatsu M, Kaneko S, Yatabe Y, Yamamoto N. Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information. Exp Hematol Oncol 2022; 11:82. [PMID: 36316731 PMCID: PMC9620610 DOI: 10.1186/s40164-022-00333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year's State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
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Affiliation(s)
- Ryuji Hamamoto
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Takafumi Koyama
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Nobuji Kouno
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.258799.80000 0004 0372 2033Department of Surgery, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8303 Japan
| | - Tomohiro Yasuda
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Shuntaro Yui
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Kazuki Sudo
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Department of Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Makoto Hirata
- grid.272242.30000 0001 2168 5385Department of Genetic Medicine and Services, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Kuniko Sunami
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Takashi Kubo
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Ken Takasawa
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Satoshi Takahashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Hidenori Machino
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Kazuma Kobayashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Ken Asada
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Masaaki Komatsu
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Syuzo Kaneko
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Yasushi Yatabe
- grid.272242.30000 0001 2168 5385Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Noboru Yamamoto
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
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Cahn F, Revon-Riviere G, Min V, Rome A, Filaine P, Pelletier A, Abed S, Gentet JC, Verschuur A, André N. Blood-Derived Liquid Biopsies Using Foundation One ® Liquid CDx for Children and Adolescents with High-Risk Malignancies: A Monocentric Experience. Cancers (Basel) 2022; 14:cancers14112774. [PMID: 35681754 PMCID: PMC9179410 DOI: 10.3390/cancers14112774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/15/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Precision oncology requires tumor molecular profiling to identify actionable targets. Blood-derived liquid biopsy (LB) is a potential alternative that is not yet documented in real-world settings, especially in pediatric oncology. Analyzing, retrospectively, the use of LB in children with refractory relapsing diseases, we were able to show that this is a feasible alternative to tissue biopsy, resulting in successful analysis in a subset of patients. Abstract Precision oncology requires tumor molecular profiling to identify actionable targets. Tumor biopsies are considered as the gold standard, but their indications are limited by the burden of procedures in children. Blood-derived liquid biopsy (LB) is a potential alternative that is not yet documented in real-world settings, especially in pediatric oncology. We performed a retrospective analysis of children and teenagers with a relapsing or refractory disease, upon whom LB was performed using the Foundation One® liquid CDx from 1 January 2020 to 31 December 2021 in a single center. Forty-five patients (27 boys) were included, with a median age of 9 years of age (range: 1.5–17 years old). Underlying malignancies were neuroblastoma (12 patients), bone sarcoma (12), soft tissue sarcoma (9), brain tumors (7), and miscellaneous tumors (5). Forty-three patients had metastatic disease. Six patients had more than one biopsy because of a failure in first LB. Median time to obtain results was 13 days. Overall, analysis was successful for 33/45 patients. Eight patients did not present any molecular abnormalities. Molecular alterations were identified in 25 samples with a mean of 2.1 alterations per sample. The most common alterations concerned TP53 (7 pts), EWS-FLI1 (5), ALK (3), MYC (3), and CREBBP (2). TMB was low in all cases. Six patients received treatment based on the results from LB analysis and all were treated off-trial. Three additional patients were included in early phase clinical trials. Mean duration of treatment was 85 days, with one patient with stable disease after eight months. Molecular profiling using Foundation One® Liquid CDx was feasible in pediatric patients with high-risk solid tumors and lead to identification of targetable mutations in a subset of patients.
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Affiliation(s)
- Fanny Cahn
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Gabriel Revon-Riviere
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Victoria Min
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Angélique Rome
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Pauline Filaine
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Annick Pelletier
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Sylvie Abed
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Jean-Claude Gentet
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Arnauld Verschuur
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Nicolas André
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
- SMARTc Unit, CRCM Inserm 1068, CNRS UMR 7258, Aix-Marseille University, 13005 Marseille, France
- Correspondence:
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9
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Summers RJ, Castellino SM, Porter CC, MacDonald TJ, Basu GD, Szelinger S, Bhasin MK, Cash T, Carter AB, Castellino RC, Fangusaro JR, Mitchell SG, Pauly MG, Pencheva B, Wechsler DS, Graham DK, Goldsmith KC. Comprehensive Genomic Profiling of High-Risk Pediatric Cancer Patients Has a Measurable Impact on Clinical Care. JCO Precis Oncol 2022; 6:e2100451. [PMID: 35544730 DOI: 10.1200/po.21.00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Profiling of pediatric cancers through deep sequencing of large gene panels and whole exomes is rapidly being adopted in many clinical settings. However, the most impactful approach to genomic profiling of pediatric cancers remains to be defined. METHODS We conducted a prospective precision medicine trial, using whole-exome sequencing of tumor and germline tissue and whole-transcriptome sequencing (RNA Seq) of tumor tissue to characterize the mutational landscape of 127 tumors from 126 unique patients across the spectrum of pediatric brain tumors, hematologic malignancies, and extracranial solid tumors. RESULTS We identified somatic tumor alterations in 121/127 (95.3%) tumor samples and identified cancer predisposition syndromes on the basis of known pathogenic or likely pathogenic germline mutations in cancer predisposition genes in 9/126 patients (7.1%). Additionally, we developed a novel scoring system for measuring the impact of tumor and germline sequencing, encompassing therapeutically relevant genomic alterations, cancer-related germline findings, recommendations for treatment, and refinement of risk stratification or prognosis. At least one impactful finding from the genomic results was identified in 108/127 (85%) samples sequenced. A recommendation to consider a targeted agent was provided for 82/126 (65.1%) patients. Twenty patients ultimately received therapy with a molecularly targeted agent, representing 24% of those who received a targeted agent recommendation and 16% of the total cohort. CONCLUSION Paired tumor/normal whole-exome sequencing and tumor RNA Seq of de novo or relapsed/refractory tumors was feasible and clinically impactful in high-risk pediatric cancer patients.
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Affiliation(s)
- Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Sharon M Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Christopher C Porter
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Tobey J MacDonald
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | | | | | - Manoj K Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA
| | - Thomas Cash
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Alexis B Carter
- Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, GA
| | - Robert Craig Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Jason R Fangusaro
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Sarah G Mitchell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Melinda G Pauly
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Bojana Pencheva
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Daniel S Wechsler
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
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10
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Borchert F, Mock A, Tomczak A, Hügel J, Alkarkoukly S, Knurr A, Volckmar AL, Stenzinger A, Schirmacher P, Debus J, Jäger D, Longerich T, Fröhling S, Eils R, Bougatf N, Sax U, Schapranow MP. Knowledge bases and software support for variant interpretation in precision oncology. Brief Bioinform 2021; 22:bbab134. [PMID: 33971666 PMCID: PMC8574624 DOI: 10.1093/bib/bbab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.
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Affiliation(s)
- Florian Borchert
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| | - Andreas Mock
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Aurelie Tomczak
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jonas Hügel
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Samer Alkarkoukly
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne
| | - Alexander Knurr
- Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Coorporation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Roland Eils
- Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitötsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany
| | - Nina Bougatf
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Ulrich Sax
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Matthieu-P Schapranow
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
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11
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Langenberg KPS, Looze EJ, Molenaar JJ. The Landscape of Pediatric Precision Oncology: Program Design, Actionable Alterations, and Clinical Trial Development. Cancers (Basel) 2021; 13:4324. [PMID: 34503139 PMCID: PMC8431194 DOI: 10.3390/cancers13174324] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Over the last years, various precision medicine programs have been developed for pediatric patients with high-risk, relapsed, or refractory malignancies, selecting patients for targeted treatment through comprehensive molecular profiling. In this review, we describe characteristics of these initiatives, demonstrating the feasibility and potential of molecular-driven precision medicine. Actionable events are identified in a significant subset of patients, although comparing results is complicated due to the lack of a standardized definition of actionable alterations and the different molecular profiling strategies used. The first biomarker-driven trials for childhood cancer have been initiated, but until now the effect of precision medicine on clinical outcome has only been reported for a small number of patients, demonstrating clinical benefit in some. Future perspectives include the incorporation of novel approaches such as liquid biopsies and immune monitoring as well as innovative collaborative trial design including combination strategies, and the development of agents specifically targeting aberrations in childhood malignancies.
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Affiliation(s)
- Karin P. S. Langenberg
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
| | - Eleonora J. Looze
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
- Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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12
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Koopman B, Groen HJ, Ligtenberg MJ, Grünberg K, Monkhorst K, de Langen AJ, Boelens MC, Paats MS, von der Thüsen JH, Dinjens WN, Solleveld N, van Wezel T, Gelderblom H, Hendriks LE, Speel EM, Theunissen TE, Kroeze LI, Mehra N, Piet B, van der Wekken AJ, ter Elst A, Timens W, Willems SM, Meijers RW, de Leng WW, van Lindert AS, Radonic T, Hashemi SM, Heideman DA, Schuuring E, van Kempen LC. Multicenter Comparison of Molecular Tumor Boards in The Netherlands: Definition, Composition, Methods, and Targeted Therapy Recommendations. Oncologist 2021; 26:e1347-e1358. [PMID: 33111480 PMCID: PMC8342588 DOI: 10.1002/onco.13580] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Molecular tumor boards (MTBs) provide rational, genomics-driven, patient-tailored treatment recommendations. Worldwide, MTBs differ in terms of scope, composition, methods, and recommendations. This study aimed to assess differences in methods and agreement in treatment recommendations among MTBs from tertiary cancer referral centers in The Netherlands. MATERIALS AND METHODS MTBs from all tertiary cancer referral centers in The Netherlands were invited to participate. A survey assessing scope, value, logistics, composition, decision-making method, reporting, and registration of the MTBs was completed through on-site interviews with members from each MTB. Targeted therapy recommendations were compared using 10 anonymized cases. Participating MTBs were asked to provide a treatment recommendation in accordance with their own methods. Agreement was based on which molecular alteration(s) was considered actionable with the next line of targeted therapy. RESULTS Interviews with 24 members of eight MTBs revealed that all participating MTBs focused on rare or complex mutational cancer profiles, operated independently of cancer type-specific multidisciplinary teams, and consisted of at least (thoracic and/or medical) oncologists, pathologists, and clinical scientists in molecular pathology. Differences were the types of cancer discussed and the methods used to achieve a recommendation. Nevertheless, agreement among MTB recommendations, based on identified actionable molecular alteration(s), was high for the 10 evaluated cases (86%). CONCLUSION MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational cancer profiles. We propose a "Dutch MTB model" for an optimal, collaborative, and nationally aligned MTB workflow. IMPLICATIONS FOR PRACTICE Interpretation of genomic analyses for optimal choice of target therapy for patients with cancer is becoming increasingly complex. A molecular tumor board (MTB) supports oncologists in rationalizing therapy options. However, there is no consensus on the most optimal setup for an MTB, which can affect the quality of recommendations. This study reveals that the eight MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational profiles. The Dutch MTB model is based on a collaborative and nationally aligned workflow with interinstitutional collaboration and data sharing.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Harry J.M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marjolijn J.L. Ligtenberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
- Department of Human Genetics, Radboud University Medical CenterNijmegenThe Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Adrianus J. de Langen
- Department of Thoracic Oncology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mirjam C. Boelens
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Marthe S. Paats
- Department of Pulmonary Medicine, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Jan H. von der Thüsen
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Winand N.M. Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Nienke Solleveld
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Tom van Wezel
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical CenterLeidenThe Netherlands
| | - Lizza E. Hendriks
- Department of Pulmonary Diseases, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Ernst‐Jan M. Speel
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Tom E. Theunissen
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical CenterNijmegenThe Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Ruud W.J. Meijers
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Wendy W.J. de Leng
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | | | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sayed M.S. Hashemi
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Daniëlle A.M. Heideman
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
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13
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Bot N, Waelli M. Implementing a clinical cutting-edge and decision-making activity: an ethnographic teamwork approach to a molecular tumorboard. BMC Health Serv Res 2020; 20:922. [PMID: 33028316 PMCID: PMC7542871 DOI: 10.1186/s12913-020-05786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/30/2020] [Indexed: 11/29/2022] Open
Abstract
Background New technology implementation in healthcare must address important challenges such as interdisciplinary approaches. In oncology, molecular tumorboard (MTB) settings require biomedical researchers and clinical practitioners to collaborate and work together. While acknowledging that MTBs have been primarily investigated from a clinical rather than an organizational perspective, this article analyzes team processes and dynamics in a newly implemented MTB. Methods A systemic case study of a newly implemented MTB in a Swiss teaching hospital was conducted between July 2017 and February 2018, with in situ work observations, six exploratory interviews and six semi-structured interviews. Results An MTB workflow is progressively stabilized in four steps: 1) patient case submissions, 2) molecular analyses and results validation, 3) co-elaboration of therapeutic proposals, and 4) reporting during formal MTB sessions. The elaboration of a therapeutic proposal requires a framework for discussion that departs from the formality of institutional relationships, which was gradually incepted in this MTB. Conclusions Firstly, our research showed that an MTB organizational process requires the five teaming components that characterizes a learning organization. It showed that at the organizational level, procedures can be stabilized without limiting practice flexibility. Secondly, this research highlighted the importance of non-clinical outcomes from an MTB, e.g. an important support network for the oncologist community.
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Affiliation(s)
- Nathalie Bot
- Institute of Global Health, University of Geneva, Geneva, Switzerland.
| | - Mathias Waelli
- Institute of Global Health, University of Geneva, Geneva, Switzerland.,EHESP, French School of Public Health, EA7348 MOS, Rennes, France
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14
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Ball J, Thompson J, Wulff-Burchfield E, Ellerbeck E, Kimminau K, Brooks JV, Petersen S, Rotich D, Kinney AY, Ellis SD. Precision community: a mixed methods study to identify determinants of adoption and implementation of targeted cancer therapy in community oncology. Implement Sci Commun 2020. [DOI: 10.1186/s43058-020-00064-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Background
Precision medicine has enormous potential to improve cancer outcomes. Over one third of the 1.5 million Americans diagnosed with cancer each year have genetic mutations that could be targeted with an FDA-approved drug to treat their disease more effectively. However, the current uptake of targeted cancer therapy in clinical practice is suboptimal. Tumor testing is not widely used, and treatments based on molecular and genomic profiling are often not prescribed when indicated. Challenges with the uptake of precision medicine may disproportionately impact cancer patients in rural communities and other underserved populations. The objective of this study is to identify the determinants of adoption and implementation of precision cancer therapy to design an implementation strategy for community oncology practices, including those in rural areas.
Methods
This study is an explanatory sequential mixed methods study to identify factors associated with the use of targeted cancer therapy. Levels of targeted therapy use will be ascertained by secondary analysis of medical records to identify concordance with 18 national guideline recommendations for use of precision medicine in the treatment of breast, colorectal, lung, and melanoma skin cancer. Concurrently, facilitators and barriers associated with the use of precision cancer therapy will be elicited from interviews with up to a total of 40 oncologists, administrators, pathology, and pharmacy staff across the participating sites. Qualitative analysis will be a template analysis based on the Theoretical Domains Framework. Quantitative data aggregated at the practice level will be used to rank oncology practices’ adherence to targeted cancer therapy guidelines. Determinants will be compared among high and low users to isolate factors likely to facilitate targeted therapy use. The study will be conducted in eight community oncology practices, with an estimated 4121 targeted therapy treatment decision-making opportunities over a 3-year period.
Discussion
Despite unprecedented investment in precision medicine, translation into practice is suboptimal. Our study will identify factors associated with the uptake of precision medicine in community settings. These findings will inform future interventions to increase equitable uptake of evidence-based targeted cancer treatment.
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15
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Vashistha V, Poonnen PJ, Snowdon JL, Skinner HG, McCaffrey V, Spector NL, Hintze B, Duffy JE, Weeraratne D, Jackson GP, Kelley MJ, Patel VL. Medical oncologists' perspectives of the Veterans Affairs National Precision Oncology Program. PLoS One 2020; 15:e0235861. [PMID: 32706774 PMCID: PMC7380614 DOI: 10.1371/journal.pone.0235861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND To support the rising need for testing and to standardize tumor DNA sequencing practices within the U.S. Department of Veterans Affairs (VA)'s Veterans Health Administration (VHA), the National Precision Oncology Program (NPOP) was launched in 2016. We sought to assess oncologists' practices, concerns, and perceptions regarding Next-Generation Sequencing (NGS) and the NPOP. MATERIALS AND METHODS Using a purposive total sampling approach, oncologists who had previously ordered NGS for at least one tumor sample through the NPOP were invited to participate in semi-structured interviews. Questions assessed the following: expectations for the NPOP, procedural requirements, applicability of testing results, and the summative utility of the NPOP. Interviews were assessed using an open coding approach. Thematic analysis was conducted to evaluate the completed codebook. Themes were defined deductively by reviewing the direct responses to interview questions as well as inductively by identifying emerging patterns of data. RESULTS Of the 105 medical oncologists who were invited to participate, 20 (19%) were interviewed from 19 different VA medical centers in 14 states. Five recurrent themes were observed: (1) Educational Efforts Regarding Tumor DNA Sequencing Should be Undertaken, (2) Pathology Departments Share a Critical Role in Facilitating Test Completion, (3) Tumor DNA Sequencing via NGS Serves as the Most Comprehensive Testing Modality within Precision Oncology, (4) The Availability of the NPOP Has Expanded Options for Select Patients, and (5) The Completion of Tumor DNA Sequencing through the NPOP Could Help Improve Research Efforts within VHA Oncology Practices. CONCLUSION Medical oncologists believe that the availability of tumor DNA sequencing through the NPOP could potentially lead to an improvement in outcomes for veterans with metastatic solid tumors. Efforts should be directed toward improving oncologists' understanding of sequencing, strengthening collaborative relationships between oncologists and pathologists, and assessing the role of comprehensive NGS panels within the battery of precision tests.
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Affiliation(s)
- Vishal Vashistha
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
- Duke Cancer Institute, Durham, NC, United states of America
- Department of Hematology and Oncology, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | - Pradeep J. Poonnen
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
- Duke Cancer Institute, Durham, NC, United states of America
- Department of Hematology and Oncology, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | | | - Halcyon G. Skinner
- College of Health, Lehigh University, Bethlehem, PA, United States of America
| | | | - Neil L. Spector
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
- Duke Cancer Institute, Durham, NC, United states of America
- Department of Hematology and Oncology, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | - Bradley Hintze
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
| | - Jill E. Duffy
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
| | | | - Gretchen P. Jackson
- Watson Health, IBM, Cambridge, MA, United States of America
- Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Michael J. Kelley
- Department of Veterans Affairs, National Precision Oncology Program, Durham, NC, United States of America
- Duke Cancer Institute, Durham, NC, United states of America
- Department of Hematology and Oncology, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | - Vimla L. Patel
- Center for Cognitive Sciences in Medicine and Public Health, The New York Academy of Medicine, New York City, NY, United States of America
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16
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Jones SF, McKenzie AJ. Molecular Profiling in Drug Development: Paving a Way Forward. Am Soc Clin Oncol Educ Book 2020; 40:309-318. [PMID: 32463698 DOI: 10.1200/edbk_100024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As researchers learn more about tumor biology and the molecular mechanisms involved in tumorigenesis, metastasis, and tumor evolution, clinical trials are growing more complex and patient selection for clinical trials is becoming more specific. Rather than exploit certain phenotypic characteristics of tumor cells (e.g., rapid cell division and uncontrolled cell growth), pharmaceuticals targeting the genotypic causes of tumorigenesis are emerging. The sequencing of the human genome, advances in chemical techniques, and increased efficiency in drug target identification have changed the way drugs are developed. Now, more precise drugs targeting specific mutations within individual genes are being used to treat narrow patient populations harboring these specific driver mutations, often with greater efficacy and lower toxicity than traditional chemotherapeutic agents. This precision in drug development relies not only on the ability to design exquisitely specific pharmaceuticals but also to identify (with the same level of precision) the patients who are most likely to respond to those therapies. Robust screening techniques and adequate molecular oncology education are required to match the appropriate patient to precision therapies, and these same screening techniques provide the data necessary to advance to the next generation of drug development.
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17
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Bourien H, Lespagnol A, Campillo-Gimenez B, Felten-Vinot I, Metges JP, Corre R, Lesimple T, le Marechal C, Boussemart L, Kammerer-Jacquet SF, le Gall E, Denoual F, de Tayrac M, Galibert MD, Mosser J, Edeline J. Implementation of a molecular tumor board at a regional level to improve access to targeted therapy. Int J Clin Oncol 2020; 25:1234-1241. [PMID: 32215806 DOI: 10.1007/s10147-020-01661-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/08/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND With the development of precision oncology, Molecular Tumor Boards (MTB) are developing in many institutions. However, the implementation of MTB in routine clinical practice has still not been thoroughly studied. MATERIAL AND METHODS Since the first drugs approved for targeted therapies, patient tumor samples were centralized to genomic testing platforms. In our institution, all tumor samples have been analyzed since 2014 by Next Generation Sequencing (NGS). In 2015, we established a regional MTB to discuss patient cases with 1 or more alterations identified by NGS, in genes different from those related to drug approval. We conducted a retrospective comparative analysis to study whether our MTB increased the prescriptions of Molecular Targeted Therapies (MTT) and the inclusions of patients in clinical trials with MTT, in comparison with patients with available NGS data but no MTB discussion. RESULTS In 2014, 86 patients had UGA, but the results were not available to clinicians and not discussed in MTB. During the years 2015 and 2016, 113 patients with an UGA (unreferenced genomic alteration) were discussed in MTB. No patients with an UGA were included in 2014 in a clinical trial, versus 2 (2%) in 2015-2016. 13 patients with an UGA (12%) were treated in 2015-2016 with a MTT whereas in 2014, no patient (p = 0.001). CONCLUSIONS In this retrospective analysis, we showed that the association of large-scale genomic testing and MTB was feasible, and could increase the prescription of MTT. However, in routine clinical practice, the majority of patients with UGA still do not have access to MTT.
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Affiliation(s)
| | | | | | | | - Jean-Philippe Metges
- Pôle Régionale de Cancérologie de Bretagne, Rennes, France.,CHU Brest, Brest, France.,ARPEGO (Accès à La Recherche Précoce Dans Le Grand-Ouest) Network, Rennes, France
| | - Romain Corre
- CHU Pontchaillou, Rennes, France.,ARPEGO (Accès à La Recherche Précoce Dans Le Grand-Ouest) Network, Rennes, France
| | - Thierry Lesimple
- Centre Eugene Marquis, Unicancer, Rennes, France.,ARPEGO (Accès à La Recherche Précoce Dans Le Grand-Ouest) Network, Rennes, France
| | | | - Lise Boussemart
- CHU Pontchaillou, Rennes, France.,Université Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | | | | | | | | | | | - Jean Mosser
- CHU Pontchaillou, Rennes, France.,Université Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Julien Edeline
- Centre Eugene Marquis, Unicancer, Rennes, France.,ARPEGO (Accès à La Recherche Précoce Dans Le Grand-Ouest) Network, Rennes, France
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18
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Barsan V, Paul M, Gorsi H, Malicki D, Elster J, Kuo DJ, Crawford J. Clinical Impact of Next-generation Sequencing in Pediatric Neuro-Oncology Patients: A Single-institutional Experience. Cureus 2019; 11:e6281. [PMID: 31827999 PMCID: PMC6892579 DOI: 10.7759/cureus.6281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The implementation of next-generation sequencing (NGS) in pediatric neuro-oncology may impact diagnosis, prognosis, therapeutic strategies, clinical trial enrollment, and germline risk. We retrospectively analyzed 58 neuro-oncology patients (31 boys, 27 girls, average age 7.4 years) who underwent NGS tumor profiling using a single commercially available platform on paraffin-embedded tissue obtained at diagnosis (20 low-grade gliomas, 12 high-grade gliomas, 11 embryonal tumors, four ependymal tumors, three meningeal tumors, and eight other CNS tumors) from May 2014 to December 2016. NGS results were analyzed for actionable mutations, variants of unknown significance and clinical impact. Seventy-four percent of patients (43 of 57) had actionable mutations; 26% had only variants of uncertain significance (VUS). NGS findings impacted treatment decisions in 55% of patients; 24% were given a targeted treatment based on NGS findings. Seven of eight patients with low-grade tumors treated with targeted therapy (everolimus, trametinib, or vemurafenib) experienced partial response or stable disease. All high-grade tumors had progressive disease on targeted therapy. Forty percent of patients had a revision or refinement of their diagnosis, and nine percent of patients were diagnosed with a previously unconfirmed cancer predisposition syndrome. Turnaround time between sample shipment and report generation averaged 13.4 ± 6.4 days. One sample failed due to insufficient DNA quantity. Our experience highlights the feasibility and clinical utility of NGS in the management of pediatric neuro-oncology patients. Future prospective clinical trials using NGS are needed to establish efficacy.
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Affiliation(s)
- Valentin Barsan
- Pediatric Hematology/Oncology, Stanford University School of Medicine, Palo Alto, USA
| | - Megan Paul
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Hamza Gorsi
- Pediatric Hematology/Oncology, Children's Hospital of Michigan, Michigan, USA
| | - Denise Malicki
- Pathology, University of California San Diego, La Jolla, USA
| | - Jennifer Elster
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Dennis J Kuo
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - John Crawford
- Neurosciences and Pediatrics, University of California San Diego, La Jolla, USA
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19
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Lee JW, Kim NKD, Lee SH, Cho HW, Ma Y, Ju HY, Yoo KH, Sung KW, Koo HH, Park WY. Discovery of actionable genetic alterations with targeted panel sequencing in children with relapsed or refractory solid tumors. PLoS One 2019; 14:e0224227. [PMID: 31747416 PMCID: PMC6867621 DOI: 10.1371/journal.pone.0224227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/08/2019] [Indexed: 11/18/2022] Open
Abstract
Advances in genomic technologies and the development of targeted therapeutics are making the use of precision medicine increasingly possible. In this study, we explored whether precision medicine can be applied for the management of refractory/relapsed pediatric solid tumors by discovering actionable alterations using targeted panel sequencing. Samples of refractory/relapsed pediatric solid tumors were tested using a targeted sequencing panel covering the exonic DNA sequences of 381 cancer genes and introns across 22 genes to detect clinically significant genomic aberrations in tumors. The molecular targets were tiered from 1 to 5 based on the presence of actionable genetic alterations, strength of supporting evidence, and drug availability in the Republic of Korea. From January 2016 to October 2018, 55 patients were enrolled. The median time from tissue acquisition to drug selection was 29 d (range 14–39), and tumor profiling was successful in 53 (96.4%) patients. A total of 27 actionable alterations in tiers 1–4 were detected in 20 patients (36.4%), and the majority of actionable alterations were copy number variations. The tiers of molecular alterations were tier 1 (clinical evidence) in 4 variants, tier 2 (preclinical evidence) in 8 variants, tier 3 (consensus opinion) in 2 variants, and tier 4 (actionable variants with a drug that is available in other countries but not in the Republic of Korea) in 9 variants. In one patient with relapsed neuroblastoma with ALK F1174L mutation and ALK amplification, lorlatinib was used in a compassionate use program, and it showed some efficacy. In conclusion, using a targeted sequencing panel to discover actionable alterations in relapsed/refractory pediatric solid tumors was practical and feasible.
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Affiliation(s)
- Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nayoung K. D. Kim
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Geninus Inc., Seoul, Korea
| | - Soo Hyun Lee
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
| | - Hee Won Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Youngeun Ma
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Young Ju
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail: (KWS); (WYP)
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Geninus Inc., Seoul, Korea
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail: (KWS); (WYP)
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20
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George SL, Izquierdo E, Campbell J, Koutroumanidou E, Proszek P, Jamal S, Hughes D, Yuan L, Marshall LV, Carceller F, Chisholm JC, Vaidya S, Mandeville H, Angelini P, Wasti A, Bexelius T, Thway K, Gatz SA, Clarke M, Al-Lazikani B, Barone G, Anderson J, Tweddle DA, Gonzalez D, Walker BA, Barton J, Depani S, Eze J, Ahmed SW, Moreno L, Pearson A, Shipley J, Jones C, Hargrave D, Jacques TS, Hubank M, Chesler L. A tailored molecular profiling programme for children with cancer to identify clinically actionable genetic alterations. Eur J Cancer 2019; 121:224-235. [PMID: 31543384 PMCID: PMC6839402 DOI: 10.1016/j.ejca.2019.07.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND For children with cancer, the clinical integration of precision medicine to enable predictive biomarker-based therapeutic stratification is urgently needed. METHODS We have developed a hybrid-capture next-generation sequencing (NGS) panel, specifically designed to detect genetic alterations in paediatric solid tumours, which gives reliable results from as little as 50 ng of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue. In this study, we offered an NGS panel, with clinical reporting via a molecular tumour board for children with solid tumours. Furthermore, for a cohort of 12 patients, we used a circulating tumour DNA (ctDNA)-specific panel to sequence ctDNA from matched plasma samples and compared plasma and tumour findings. RESULTS A total of 255 samples were submitted from 223 patients for the NGS panel. Using FFPE tissue, 82% of all submitted samples passed quality control for clinical reporting. At least one genetic alteration was detected in 70% of sequenced samples. The overall detection rate of clinically actionable alterations, defined by modified OncoKB criteria, for all sequenced samples was 51%. A total of 8 patients were sequenced at different stages of treatment. In 6 of these, there were differences in the genetic alterations detected between time points. Sequencing of matched ctDNA in a cohort of extracranial paediatric solid tumours also identified a high detection rate of somatic alterations in plasma. CONCLUSION We demonstrate that tailored clinical molecular profiling of both tumour DNA and plasma-derived ctDNA is feasible for children with solid tumours. Furthermore, we show that a targeted NGS panel-based approach can identify actionable genetic alterations in a high proportion of patients.
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Affiliation(s)
- Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Elisa Izquierdo
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - James Campbell
- Bioinformatics Core Facility, The Institute of Cancer Research, London, UK
| | - Eleni Koutroumanidou
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Paula Proszek
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Sabri Jamal
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Deborah Hughes
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Lina Yuan
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Lynley V Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Julia C Chisholm
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Sucheta Vaidya
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Henry Mandeville
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Ajla Wasti
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Tomas Bexelius
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Khin Thway
- Pathology Department, Royal Marsden NHS Foundation Trust, London, UK
| | - Susanne A Gatz
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK; Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Matthew Clarke
- Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Bissan Al-Lazikani
- Bioinformatics Core Facility, The Institute of Cancer Research, London, UK
| | - Giuseppe Barone
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John Anderson
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
| | - Deborah A Tweddle
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - David Gonzalez
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
| | - Brian A Walker
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jack Barton
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
| | - Sarita Depani
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jessica Eze
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Saira W Ahmed
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lucas Moreno
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; HNJ-CNIO Clinical Research Unit, Hospital Universitario Nino Jesus, Madrid, Spain; Paediatric Oncology & Haematology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Andrew Pearson
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Chris Jones
- Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Darren Hargrave
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael Hubank
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
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21
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Itahashi K, Kondo S, Kubo T, Fujiwara Y, Kato M, Ichikawa H, Koyama T, Tokumasu R, Xu J, Huettner CS, Michelini VV, Parida L, Kohno T, Yamamoto N. Evaluating Clinical Genome Sequence Analysis by Watson for Genomics. Front Med (Lausanne) 2018; 5:305. [PMID: 30474028 PMCID: PMC6237914 DOI: 10.3389/fmed.2018.00305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Background: Oncologists increasingly rely on clinical genome sequencing to pursue effective, molecularly targeted therapies. This study assesses the validity and utility of the artificial intelligence Watson for Genomics (WfG) for analyzing clinical sequencing results. Methods: This study identified patients with solid tumors who participated in in-house genome sequencing projects at a single cancer specialty hospital between April 2013 and October 2016. Targeted genome sequencing results of these patients' tumors, previously analyzed by multidisciplinary specialists at the hospital, were reanalyzed by WfG. This study measures the concordance between the two evaluations. Results: In 198 patients, in-house genome sequencing detected 785 gene mutations, 40 amplifications, and 22 fusions after eliminating single nucleotide polymorphisms. Breast cancer (n = 40) was the most frequent diagnosis in this analysis, followed by gastric cancer (n = 31), and lung cancer (n = 30). Frequently detected single nucleotide variants were found in TP53 (n = 107), BRCA2 (n = 24), and NOTCH2 (n = 23). MYC (n = 10) was the most frequently detected gene amplification, followed by ERBB2 (n = 9) and CCND1 (n = 6). Concordant pathogenic classifications (i.e., pathogenic, benign, or variant of unknown significance) between in-house specialists and WfG included 705 mutations (89.8%; 95% CI, 87.5%−91.8%), 39 amplifications (97.5%; 95% CI, 86.8–99.9%), and 17 fusions (77.3%; 95% CI, 54.6–92.2%). After about 12 months, reanalysis using a more recent version of WfG demonstrated a better concordance rate of 94.5% (95% CI, 92.7–96.0%) for gene mutations. Across the 249 gene alterations determined to be pathogenic by both methods, including mutations, amplifications, and fusions, WfG covered 84.6% (88 of 104) of all targeted therapies that experts proposed and offered an additional 225 therapeutic options. Conclusions: WfG was able to scour large volumes of data from scientific studies and databases to analyze in-house clinical genome sequencing results and demonstrated the potential for application to clinical practice; however, we must train WfG in clinical trial settings.
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Affiliation(s)
- Kota Itahashi
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Shunsuke Kondo
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan.,Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kubo
- Division of Translational Genomics, National Cancer Center-Exploratory Oncology Research and Clinical Trial Center, Tokyo, Japan
| | - Yutaka Fujiwara
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Ichikawa
- Division of Translational Genomics, National Cancer Center-Exploratory Oncology Research and Clinical Trial Center, Tokyo, Japan.,Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takahiko Koyama
- IBM T. J. Watson Research Center, Yorktown Heights, NY, United States
| | - Reitaro Tokumasu
- Tokyo Software & Systems Development Laboratory, IBM Japan, Tokyo, Japan
| | - Jia Xu
- IBM Watson Health, Cambridge, MA, United States
| | | | | | - Laxmi Parida
- IBM T. J. Watson Research Center, Yorktown Heights, NY, United States
| | - Takashi Kohno
- Division of Translational Genomics, National Cancer Center-Exploratory Oncology Research and Clinical Trial Center, Tokyo, Japan.,Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Noboru Yamamoto
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
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22
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van der Velden DL, van Herpen CML, van Laarhoven HWM, Smit EF, Groen HJM, Willems SM, Nederlof PM, Langenberg MHG, Cuppen E, Sleijfer S, Steeghs N, Voest EE. Molecular Tumor Boards: current practice and future needs. Ann Oncol 2018; 28:3070-3075. [PMID: 29045504 DOI: 10.1093/annonc/mdx528] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Due to rapid technical advances, steeply declining sequencing costs, and the ever-increasing number of targeted therapies, it can be expected that extensive tumor sequencing such as whole-exome and whole-genome sequencing will soon be applied in standard care. Clinicians will thus be confronted with increasingly complex genetic information and multiple test-platforms to choose from. General medical training, meanwhile, can hardly keep up with the pace of innovation. Consequently, there is a rapidly growing gap between clinical knowledge and genetic potential in cancer care. Multidisciplinary Molecular Tumor Boards (MTBs) have been suggested as a means to address this disparity, but shared experiences are scarce in literature and no quality requirements or guidelines have been published to date. Methods Based on literature review, a survey among hospitals in The Netherlands, and our own experience with the establishment of a nationally operating MTB, this article evaluates current knowledge and unmet needs and lays out a strategy for successful MTB implementation. Results Having access to an MTB can improve and increase the application of genetics-guided cancer care. In our survey, however, <50% of hospitals and only 5% of nonacademic hospitals had access to an MTB. In addition, current MTBs vary widely in terms of composition, tasks, tools, and workflow. This may not only lead to variation in quality of care but also hinders data sharing and thus creation of an effective learning community. Conclusions This article acknowledges a leading role for MTBs to govern (extensive) tumor sequencing into daily practice and proposes three basic necessities for successful MTB implementation: (i) global harmonization in cancer sequencing practices and procedures, (ii) minimal member and operational requirements, and (iii) an appropriate unsolicited findings policy. Meeting these prerequisites would not only optimize MTB functioning but also improve general interpretation and application of genomics-guided cancer care.
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Affiliation(s)
| | - C M L van Herpen
- Division of Medical Oncology, Radboud University Medical Center, Nijmegen
| | | | - E F Smit
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam
| | - H J M Groen
- Division of Medical Oncology, University Medical Center Groningen, Groningen
| | - S M Willems
- Division of Pathology, University Medical Center Utrecht, Utrecht
| | - P M Nederlof
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam
| | | | - E Cuppen
- Human Genetics, University Medical Center Utrecht, Utrecht
| | - S Sleijfer
- Division of Medical Oncology, Erasmus University Medical Center, Rotterdam
| | - N Steeghs
- Division of Medical Oncology and Clinical Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E E Voest
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam
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Haynes HR, Killick-Cole CL, Hares KM, Redondo J, Kemp KC, Moutasim KA, Faulkner C, Wilkins A, Kurian KM. Evaluation of the quality of RNA extracted from archival FFPE glioblastoma and epilepsy surgical samples for gene expression assays. J Clin Pathol 2018; 71:695-701. [DOI: 10.1136/jclinpath-2017-204969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023]
Abstract
AimsHistopathological tissue samples are being increasingly used as sources of nucleic acids in molecular pathology translational research. This study investigated the suitability of glioblastoma and control central nervous system (CNS) formalin-fixed paraffin embedded (FFPE) tissue-derived RNA for gene expression analyses.MethodsTotal RNA was extracted from control (temporal lobe resection tissue) and glioblastoma FFPE tissue samples. RNA purity (260/280 ratios) was determined and RNA integrity number (RIN) analysis was performed. RNA was subsequently used for RT-qPCR for two reference genes,18SandGAPDH.ResultsReference gene expression was equivalent between control and glioblastoma tissue when using RNA extracted from FFPE tissue, which has key implications for biological normalisation for CNS gene expression studies. There was a significant difference between the mean RIN values of control and glioblastoma FFPE tissue. There was no significant correlation between 260/280 or RIN values versus total RNA yield. The age of the tissue blocks did not influence RNA yield, fragmentation or purity. There was no significant correlation between RIN or 260/280 ratios and mean qPCR cycle threshold for either reference gene.ConclusionsThis study showed that routinely available CNS FFPE tissue is suitable for RNA extraction and downstream gene expression studies, even after 60 months of storage. Substantial RNA fragmentation associated with glioblastoma and control FFPE tissue blocks did not preclude downstream RT-qPCR gene expression analyses. Cross validation with both archival and prospectively collated FFPE specimens is required to further demonstrate that CNS tissue blocks can be used in novel translational molecular biomarker studies.
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Abstract
PURPOSE OF REVIEW The current review will focus on the current knowledge of the contribution of both germline and somatic mutations to the development and management of cancer in pediatric patients. RECENT FINDINGS It has long been thought that genetic mutations in both germline and somatic cells can contribute to the development of cancer in pediatric patients. With the recent advances in genomic technologies, there are now over 500 known cancer predisposition genes. Recent studies have confirmed an 8.5-14% germline mutation rate in cancer predisposition genes in pediatric cancer patients. SUMMARY The discovery of both germline and somatic cells mutation(s) in pediatric cancer patients not only aids in the management of current disease, but can also have direct implications for future management as well as the medical management of family members.
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25
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Burkard ME, Deming DA, Parsons BM, Kenny PA, Schuh MR, Leal T, Uboha N, Lang JM, Thompson MA, Warren R, Bauman J, Mably MS, Laffin J, Paschal CR, Lager AM, Lee K, Matkowskyj KA, Buehler DG, Rehrauer WM, Kolesar J. Implementation and Clinical Utility of an Integrated Academic-Community Regional Molecular Tumor Board. JCO Precis Oncol 2017; 1:1600022. [PMID: 32913980 DOI: 10.1200/po.16.00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Precision oncology develops and implements evidence-based personalized therapies that are based on specific genetic targets within each tumor. However, a major challenge that remains is the provision of a standardized, up-to-date, and evidenced-based precision medicine initiative across a geographic region. Materials and Methods We developed a statewide molecular tumor board that integrates academic and community oncology practices. The Precision Medicine Molecular Tumor Board (PMMTB) has three components: a biweekly Web-based teleconference tumor board meeting provided as a free clinical service, an observational research registry, and a monthly journal club to establish and revise evidence-based guidelines for off-label therapies. The PMMTB allows for flexible and rapid implementation of treatment, uniformity in practice, and the ability to track outcomes. Results We describe the implementation of the PMMTB and its first year of activity. Seventy-seven patient cases were presented, 48 were enrolled in a registry, and 38 had recommendations and clinical follow-up. The 38 subjects had diverse solid tumors (lung, 45%; GI, 21%; breast, 13%; other, 21%). Of these subjects, targeted therapy was recommended for 32 (84%). Clinical trials were identified for 24 subjects (63%), and nontrial targeted medicines for 16 (42%). Nine subjects (28%) received recommended therapy with a response rate of 17% (one of six) and a clinical benefit rate (partial response + stable disease) of 38% (three of eight). Although clinical trials often were identified, patients rarely enrolled. Conclusion The PMMTB provides a model for a regional molecular tumor board with clinical utility. This work highlights the need for outcome registries and improved access to clinical trials to pragmatically implement precision oncology.
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Affiliation(s)
- Mark E Burkard
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Dustin A Deming
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Benjamin M Parsons
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Paraic A Kenny
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Marissa R Schuh
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Ticiana Leal
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Nataliya Uboha
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Joshua M Lang
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Michael A Thompson
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Ruth Warren
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jordan Bauman
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Mary S Mably
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jennifer Laffin
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Catherine R Paschal
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Angela M Lager
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Kristy Lee
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Kristina A Matkowskyj
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Darya G Buehler
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - William M Rehrauer
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jill Kolesar
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
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Tsui PC, Lee YF, Liu ZWY, Ip LRH, Piao W, Chiang AKS, Lui VWY. An update on genomic-guided therapies for pediatric solid tumors. Future Oncol 2017; 13:1345-1358. [PMID: 28589766 DOI: 10.2217/fon-2017-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Currently, out of the 82 US FDA-approved targeted therapies for adult cancer treatments, only three are approved for use in children irrespective of their genomic status. Apart from leukemia, only a handful of genomic-based trials involving children with solid tumors are ongoing. Emerging genomic data for pediatric solid tumors may facilitate the development of precision medicine in pediatric patients. Here, we provide an up-to-date review of all reported genomic aberrations in the eight most common pediatric solid tumors with whole-exome sequencing or whole-genome sequencing data (from cBioPortal database, Pediatric Cancer Genome Project, Therapeutically Applicable Research to Generate Effective Treatments) and additional non-whole-exome sequencing studies. Potential druggable events are highlighted and discussed so as to facilitate preclinical and clinical research in this area.
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Affiliation(s)
- Pui Chi Tsui
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yin-Fai Lee
- School of Pharmacy & Medical Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Zoey Wing Yee Liu
- Department of Anatomical & Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Laura Ren Huey Ip
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenying Piao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Alan Kwok Shing Chiang
- Department of Pediatrics & Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Vivian Wai Yan Lui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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27
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Siniard RC, Harada S. Immunogenomics: using genomics to personalize cancer immunotherapy. Virchows Arch 2017; 471:209-219. [DOI: 10.1007/s00428-017-2140-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 01/06/2023]
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28
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Johnson LM, Valdez JM, Quinn EA, Sykes AD, McGee RB, Nuccio R, Hines-Dowell SJ, Baker JN, Kesserwan C, Nichols KE, Mandrell BN. Integrating next-generation sequencing into pediatric oncology practice: An assessment of physician confidence and understanding of clinical genomics. Cancer 2017; 123:2352-2359. [PMID: 28192596 DOI: 10.1002/cncr.30581] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/02/2016] [Accepted: 01/01/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND The incorporation of genomic testing to identify targetable somatic alterations and predisposing germline mutations into the clinical setting is becoming increasingly more common. Despite its potential usefulness, to the authors' knowledge physician confidence with regard to understanding and applying genomic testing remains unclear, particularly within the realm of pediatric oncology. METHODS Before initiating an institutional feasibility study regarding the integration of clinical genomic testing, the authors surveyed pediatric oncologists regarding their confidence around understanding of genomic testing, perceived usefulness of test results, preferences around the disclosure of germline test results, and possible risks and benefits of testing. RESULTS Among survey respondents (52 of 88 contacted; response rate of 59%), only a minority were confident in interpreting, using, and discussing somatic (35%) or germline (27%) genomic test results. Providers who were confident in interpreting somatic results were significantly more likely to anticipate using the results to plan the treatment of patients with relapsed or refractory cancers (P = .009). Similarly, providers who reported confidence in interpreting germline results were significantly more likely to discuss and use these results as part of clinical care (P<.0001). The majority of physicians (93%), regardless of their level of confidence, wanted to speak to a genetic counselor before disclosing germline test results. CONCLUSIONS Among physicians at a comprehensive pediatric cancer center, confidence in the interpretation, use, and discussion of oncology-based genomic test results appears to be low, both in terms of somatic and germline testing. To optimize the integration of genomic sequencing into cancer care, methods must be developed to improve basic competencies around cancer-based genomic testing. Given the complexities surrounding variant interpretation and genotype-phenotype relationships, interdisciplinary collaborations are warranted. Cancer 2017;123:2352-2359. © 2017 American Cancer Society.
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Affiliation(s)
- Liza-Marie Johnson
- Division of Hospitalist Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jessica M Valdez
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Emily A Quinn
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - April D Sykes
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rose B McGee
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Regina Nuccio
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stacy J Hines-Dowell
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Justin N Baker
- Division of Quality of Life and Palliative Care, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chimene Kesserwan
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim E Nichols
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Belinda N Mandrell
- Division of Nursing Research, St. Jude Children's Research Hospital, Memphis, Tennessee
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29
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Marks LJ, Oberg JA, Pendrick D, Sireci AN, Glasser C, Coval C, Zylber RJ, Chung WK, Pang J, Turk AT, Hsiao SJ, Mansukhani MM, Glade Bender JL, Kung AL, Sulis ML. Precision Medicine in Children and Young Adults with Hematologic Malignancies and Blood Disorders: The Columbia University Experience. Front Pediatr 2017; 5:265. [PMID: 29312904 PMCID: PMC5732960 DOI: 10.3389/fped.2017.00265] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/28/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The advent of comprehensive genomic profiling has markedly advanced the understanding of the biology of pediatric hematological malignancies, however, its application to clinical care is still unclear. We present our experience integrating genomic data into the clinical management of children with high-risk hematologic malignancies and blood disorders and describe the broad impact that genomic profiling has in multiple aspects of patient care. METHODS The Precision in Pediatric Sequencing Program at Columbia University Medical Center instituted prospective clinical next-generation sequencing (NGS) for high-risk malignancies and blood disorders. Testing included cancer whole exome sequencing (WES) of matched tumor-normal samples or targeted sequencing of 467 cancer-associated genes, when sample adequacy was a concern, and tumor transcriptome (RNA-seq). A multidisciplinary molecular tumor board conducted interpretation of results and final tiered reports were transmitted to the electronic medical record according to patient preferences. RESULTS Sixty-nine samples from 56 patients with high-risk hematologic malignancies and blood disorders were sequenced. Patients carried diagnoses of myeloid malignancy (n = 25), lymphoid malignancy (n = 25), or histiocytic disorder (n = 6). Six patients had only constitutional WES, performed for a suspicion of an inherited predisposition for their disease. For the remaining 50 patients, tumor was sequenced with matched normal tissue when available. The mean number of somatic variants per sample was low across the different disease categories (2.85 variants/sample). Interestingly, a gene fusion was identified by RNA-seq in 58% of samples who had adequate RNA available for testing. Molecular profiling of tumor tissue led to clinically impactful findings in 90% of patients. Forty patients (80%) had at least one targetable gene variant or fusion identified in their tumor tissue; however, only seven received targeted therapy. Importantly, NGS findings contributed to the refinement of diagnosis and prognosis for 34% of patients. Known or likely pathogenic germline alterations were discovered in 24% of patients involving cancer predisposition genes in 12% of cases. CONCLUSION Incorporating whole exome and transcriptome profiling of tumor and normal tissue into clinical practice is feasible, and the value that comprehensive testing provides extends beyond the ability to target-specific mutations.
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Affiliation(s)
- Lianna J Marks
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jennifer A Oberg
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Danielle Pendrick
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Anthony N Sireci
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Chana Glasser
- Department of Pediatric Hematology/Oncology, NYU Winthrop University Medical Center, Mineola, NY, United States
| | - Carrie Coval
- Department of Pediatrics, Columbia University Medical Center, New York, NY, United States
| | - Rebecca J Zylber
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Jiuhong Pang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Andrew T Turk
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Julia L Glade Bender
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Andrew L Kung
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria Luisa Sulis
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
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30
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Oberg JA, Glade Bender JL, Sulis ML, Pendrick D, Sireci AN, Hsiao SJ, Turk AT, Dela Cruz FS, Hibshoosh H, Remotti H, Zylber RJ, Pang J, Diolaiti D, Koval C, Andrews SJ, Garvin JH, Yamashiro DJ, Chung WK, Emerson SG, Nagy PL, Mansukhani MM, Kung AL. Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations. Genome Med 2016; 8:133. [PMID: 28007021 PMCID: PMC5180407 DOI: 10.1186/s13073-016-0389-6] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. METHODS The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient's electronic medical record. RESULTS NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. CONCLUSIONS Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.
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Affiliation(s)
- Jennifer A. Oberg
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Julia L. Glade Bender
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Maria Luisa Sulis
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Danielle Pendrick
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Anthony N. Sireci
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Susan J. Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Andrew T. Turk
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Helen Remotti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Rebecca J. Zylber
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Jiuhong Pang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Daniel Diolaiti
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Carrie Koval
- Department of Clinical Genetics, Columbia University Medical Center, New York, NY 10032 USA
| | - Stuart J. Andrews
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - James H. Garvin
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Darrell J. Yamashiro
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Stephen G. Emerson
- Department of Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Peter L. Nagy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Present address: MNG Laboratories, 5424 Glenridge Drive, Atlanta, GA 30342 USA
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Andrew L. Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
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31
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Harris G, O'Toole S, George P, Browett P, Print C. Massive parallel sequencing of solid tumours - challenges and opportunities for pathologists. Histopathology 2016; 70:123-133. [DOI: 10.1111/his.13067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Gavin Harris
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
- Canterbury Health Laboratories; Christchurch New Zealand
| | - Sandra O'Toole
- Department of Tissue Pathology and Diagnostic Oncology; Royal Prince Alfred Hospital; Camperdown NSW Australia
- Sydney Medical School; Sydney University; Sydney Australia
- The Kinghorn Cancer Centre; Garvan Institute of Medical Research; Darlinghurst NSW Australia
| | - Peter George
- Canterbury Health Laboratories; Christchurch New Zealand
| | - Peter Browett
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre; c/o University of Auckland; Auckland New Zealand
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32
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Ganesan S, Rodriguez-Rodriguez L, DiPaola RS. Precision Medicine: Implications for Science and Practice. J Am Coll Surg 2016; 223:433-439.e1. [PMID: 27321387 DOI: 10.1016/j.jamcollsurg.2016.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Shridar Ganesan
- Precision Medicine Initiative, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | | | - Robert S DiPaola
- Office of the Dean, University of Kentucky, College of Medicine, Lexington, KY
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