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      Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (edition 2.1)

      research-article
      1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 33 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 18 , 32 , , Japanese Society of Medical Oncology, Japan Society of Clinical Oncology, Japanese Cancer Association
      International Journal of Clinical Oncology
      Springer Singapore
      Clinical practice guidance, Cancer genomic profiling test, Next-generation sequencing, Solid cancer

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          To promote precision oncology in clinical practice, the Japanese Society of Medical Oncology, the Japanese Society of Clinical Oncology, and the Japanese Cancer Association, jointly published “Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment” in 2017. Since new information on cancer genomic medicine has emerged since the 1st edition of the guidance was released, including reimbursement for NGS-based multiplex gene panel tests in 2019, the guidance revision was made.

          Methods

          A working group was organized with 33 researchers from cancer genomic medicine designated core hospitals and other academic institutions. For an impartial evaluation of the draft version, eight committee members from each society conducted an external evaluation. Public comments were also made on the draft. The finalized Japanese version was published on the websites of the three societies in March 2020.

          Results

          The revised edition consists of two parts: an explanation of the cancer genomic profiling test (General Discussion) and clinical questions (CQs) that are of concern in clinical practice. Particularly, patient selection should be based on the expectation that the patient's post-test general condition and organ function will be able to tolerate drug therapy, and the optimal timing of test should be considered in consideration of subsequent treatment plans, not limited to treatment lines.

          Conclusion

          We expect that the revised version will be used by healthcare professionals and will also need to be continually reviewed in line with future developments in cancer genome medicine.

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          Most cited references51

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          Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

          The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1 In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next generation sequencing. By adopting and leveraging next generation sequencing, clinical laboratories are now performing an ever increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes and epigenetic assays for genetic disorders. By virtue of increased complexity, this paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP and CAP stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories including genotyping, single genes, panels, exomes and genomes. This report recommends the use of specific standard terminology: ‘pathogenic’, ‘likely pathogenic’, ‘uncertain significance’, ‘likely benign’, and ‘benign’ to describe variants identified in Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a CLIA-approved laboratory with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or equivalent.
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            Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients

            Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically-defined tumor types, coupled with an expanding portfolio of molecularly-targeted therapies, demands flexible and comprehensive approaches to profile clinically significant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative utilizing a comprehensive assay, MSK-IMPACT, through which we have compiled matched tumor and normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel non-coding alterations, and mutational signatures that were shared among common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.
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              Alpelisib for PIK3CA-Mutated, Hormone Receptor–Positive Advanced Breast Cancer

              PIK3CA mutations occur in approximately 40% of patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer. The PI3Kα-specific inhibitor alpelisib has shown antitumor activity in early studies.
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                Author and article information

                Contributors
                ktsuchih@east.ncc.go.jp
                Journal
                Int J Clin Oncol
                Int J Clin Oncol
                International Journal of Clinical Oncology
                Springer Singapore (Singapore )
                1341-9625
                1437-7772
                29 November 2020
                29 November 2020
                2021
                : 26
                : 2
                : 233-283
                Affiliations
                [1 ]GRID grid.497282.2, Department of General Internal Medicine/Breast and Medical Oncology/Experimental Therapeutics, , National Cancer Center Hospital East, ; Kashiwa, Japan
                [2 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, Genome Science Division, Research Center for Advanced Science and Technology, , University of Tokyo, ; Tokyo, Japan
                [3 ]GRID grid.412167.7, ISNI 0000 0004 0378 6088, Clinical Research and Medical Innovation Center, , Hokkaido University Hospital, ; Sapporo, Japan
                [4 ]GRID grid.177174.3, ISNI 0000 0001 2242 4849, Department of Oncology and Social Medicine, Graduate School of Medical Sciences, , Kyushu University, ; Fukuoka, Japan
                [5 ]GRID grid.69566.3a, ISNI 0000 0001 2248 6943, Department of Investigative Pathology, , Tohoku University Graduate School of Medicine, ; Sendai, Japan
                [6 ]GRID grid.26091.3c, ISNI 0000 0004 1936 9959, Department of Surgery, , Keio University School of Medicine, ; Tokyo, Japan
                [7 ]GRID grid.257022.0, ISNI 0000 0000 8711 3200, Natural Science Center for Basic Research and Development, , Hiroshima University, ; Hiroshima, Japan
                [8 ]GRID grid.265073.5, ISNI 0000 0001 1014 9130, Cancer Center, , Tokyo Medical and Dental University, ; Tokyo, Japan
                [9 ]GRID grid.411217.0, ISNI 0000 0004 0531 2775, Department of Clinical Oncology, , Kyoto University Hospital, ; Kyoto, Japan
                [10 ]GRID grid.63906.3a, ISNI 0000 0004 0377 2305, Children’s Cancer Center, , National Center for Child Health and Development, ; Tokyo, Japan
                [11 ]GRID grid.412167.7, ISNI 0000 0004 0378 6088, Division of Clinical Cancer Genomics, , Hokkaido University Hospital, ; Sapporo, Japan
                [12 ]GRID grid.411102.7, ISNI 0000 0004 0596 6533, Kobe University Hospital Cancer Center, ; Kobe, Japan
                [13 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Division of Genome Biology, , National Cancer Center Research Institute, ; Tokyo, Japan
                [14 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Division of Cellular Signaling, , National Cancer Center Research Institute, ; Tokyo, Japan
                [15 ]GRID grid.412757.2, ISNI 0000 0004 0641 778X, Department of Medical Oncology, , Tohoku University Hospital, ; Sendai, Japan
                [16 ]GRID grid.258622.9, ISNI 0000 0004 1936 9967, Department of Hematology and Rheumatology, , Kindai University Faculty of Medicine, ; Osakasayama, Japan
                [17 ]GRID grid.410813.f, ISNI 0000 0004 1764 6940, Department of Medical Oncology, , Toranomon Hospital, ; Tokyo, Japan
                [18 ]GRID grid.497282.2, Department of Gastroenterology and Gastrointestinal Oncology, , National Cancer Center Hospital East, ; Kashiwa, Japan
                [19 ]GRID grid.27476.30, ISNI 0000 0001 0943 978X, Department of Neurosurgery, , Nagoya University, ; Nagoya, Japan
                [20 ]GRID grid.258622.9, ISNI 0000 0004 1936 9967, Department of Genome Biology, , Kindai University Faculty of Medicine, ; Osakasayama, Japan
                [21 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, Department of Obstetrics and Gynecology, Faculty of Medicine, , The University of Tokyo, ; Tokyo, Japan
                [22 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Section of Information Technology Support, Center for Cancer Genomics and Advanced Therapeutics, , National Cancer Center, ; Tokyo, Japan
                [23 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Clinical Research Support Office, , National Cancer Center Hospital, ; Tokyo, Japan
                [24 ]GRID grid.26999.3d, ISNI 0000 0001 2151 536X, Department of Clinical Genomics, , The University of Tokyo, ; Tokyo, Japan
                [25 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Department of Laboratory Medicine, , National Cancer Center Hospital, ; Tokyo, Japan
                [26 ]GRID grid.497282.2, Department of Hepatobiliary and Pancreatic Oncology, , National Cancer Center Hospital East, ; Kashiwa, Japan
                [27 ]GRID grid.258622.9, ISNI 0000 0004 1936 9967, Medical Oncology, , Kindai University Faculty of Medicine, ; Osakasayama, Japan
                [28 ]GRID grid.69566.3a, ISNI 0000 0001 2248 6943, Department of Sociology, Graduate School of Arts and Letters, , Tohoku University, ; Sendai, Japan
                [29 ]GRID grid.261356.5, ISNI 0000 0001 1302 4472, Department of General Thoracic Surgery and Breast and Endocrine Surgery, , Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, ; Okayama, Japan
                [30 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Department of Hepatobiliary and Pancreatic Oncology, , National Cancer Center Hospital, ; Tokyo, Japan
                [31 ]GRID grid.136593.b, ISNI 0000 0004 0373 3971, Department of Cancer Genome Informatics, Graduate School of Medicine, , Osaka University, ; Osaka, Japan
                [32 ]GRID grid.272242.3, ISNI 0000 0001 2168 5385, Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, , National Cancer Center, ; 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577 Japan
                [33 ]GRID grid.452621.6, ISNI 0000 0004 1773 7973, Present Address: Konica Minolta Precision Medicine Japan, Inc., ; Tokyo, Japan
                Author information
                http://orcid.org/0000-0001-7507-2349
                Article
                1831
                10.1007/s10147-020-01831-6
                7819967
                33249514
                4fe1cefb-f2a9-40bc-a8a8-6cb6aaab57e2
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 October 2020
                : 30 October 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100003478, Ministry of Health, Labour and Welfare;
                Award ID: 19EA1001
                Award Recipient :
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                © Japan Society of Clinical Oncology 2021

                clinical practice guidance,cancer genomic profiling test,next-generation sequencing,solid cancer

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