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Lee JS, Cho EH, Kim B, Hong J, Kim YG, Kim Y, Jang JH, Lee ST, Kong SY, Lee W, Shin S, Song EY. Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays. Ann Lab Med 2024; 44:195-209. [PMID: 38221747 PMCID: PMC10813828 DOI: 10.3343/alm.2023.0389] [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: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co. Ltd., Seongnam, Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Li MM, Cottrell CE, Pullambhatla M, Roy S, Temple-Smolkin RL, Turner SA, Wang K, Zhou Y, Vnencak-Jones CL. Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology. J Mol Diagn 2023; 25:69-86. [PMID: 36503149 DOI: 10.1016/j.jmoldx.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance. In the implementation survey, 71% (157/220) of respondents have implemented the 2017 guidelines for variant classification and reporting either with or without modifications. Collectively, this study demonstrates that, although they may not yet be optimized, the 2017 guideline recommendations are being adopted for standardized somatic variant classification. The working group identified significant areas for future guideline improvement, including the need for a more granular and comprehensive classification system and education resources to meet the growing needs of both laboratory professionals and medical oncologists.
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Affiliation(s)
- Marilyn M Li
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Catherine E Cottrell
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Somak Roy
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Scott A Turner
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Kai Wang
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy L Vnencak-Jones
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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Fischer CG, Pallavajjala A, Jiang L, Anagnostou V, Tao J, Adams E, Eshleman JR, Gocke CD, Lin MT, Platz EA, Xian RR. Artificial intelligence-assisted serial analysis of clinical cancer genomics data identifies changing treatment recommendations and therapeutic targets. Clin Cancer Res 2022; 28:2361-2372. [PMID: 35312750 DOI: 10.1158/1078-0432.ccr-21-4061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Given the pace of predictive biomarker and targeted therapy development, it is unknown if repeat annotation of the same next-generation sequencing data can identify additional clinically actionable targets that could be therapeutically leveraged. In this study, we sought to determine the predictive yield of serial re-analysis of clinical tumor sequencing data. EXPERIMENTAL DESIGN Using artificial intelligence (AI)-assisted variant annotation, we retrospectively re-analyzed sequencing data from 2,219 cancer patients from a single academic medical center at 3-month intervals totaling 9 months in 2020. The yield of serial re-analysis was assessed by the proportion of patients with improved strength of therapeutic recommendations. RESULTS 1,775 patients (80%) had {greater than or equal to}1 potentially clinically actionable mutation at baseline, including 243 (11%) patients who had an alteration targeted by an FDA-approved drug for their cancer type. By month nine, the latter increased to 458 (21%) patients mainly due to a single pan-cancer agent directed against tumors with high tumor mutation burden. Within this timeframe, 67 new therapies became available and 45 were no longer available. Variant pathogenicity classifications also changed leading to changes in treatment recommendations for 124 patients (6%). CONCLUSIONS Serial re-annotation of tumor sequencing data improved the strength of treatment recommendations (based on level of evidence) in a mixed cancer cohort and showed substantial changes in available therapies and variant classifications. These results suggest a role for repeat analysis of tumor sequencing data in clinical practice, which can be streamlined with AI support.
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Affiliation(s)
| | | | - LiQun Jiang
- Johns Hopkins Medical Institutions, United States
| | - Valsamo Anagnostou
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jessica Tao
- Johns Hopkins Medical Institutions, United States
| | - Emily Adams
- Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | | | | | - Ming-Tseh Lin
- The Johns Hopkins School of Medicine, Baltimore, United States
| | - Elizabeth A Platz
- Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Rena R Xian
- Johns Hopkins Medical Institutions, Baltimore, MD, United States
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