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Leung ML. Counterpoint: Why the FDA Should Not Regulate Laboratory-Developed Tests. J Appl Lab Med 2024; 9:155-158. [PMID: 38167755 DOI: 10.1093/jalm/jfad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/18/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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2
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Nataren N, Yamada M, Prow T. Molecular Skin Cancer Diagnosis: Promise and Limitations. J Mol Diagn 2023; 25:17-35. [PMID: 36243291 DOI: 10.1016/j.jmoldx.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Skin cancer is a significant and increasing global health burden. Although the current diagnostic workflow is robust and able to provide clinically actionable results, it is subject to notable limitations. The training and expertise required for accurate diagnoses using conventional skin cancer diagnostics are significant, and patient access to this workflow can be limited by geographic location or unforeseen events, such as coronavirus disease 2019 (COVID-19). Molecular biomarkers have transformed diagnostics and treatment delivery in oncology. With rapid advancements in molecular biology techniques, understanding of the underlying molecular mechanism of cancer pathologies has deepened, yielding biomarkers that can be used to monitor the course of malignant diseases. Herein, commercially available, clinically validated, and emerging skin cancer molecular biomarkers are reviewed. The qualities of an ideal molecular biomarker are defined. The potential benefits and limitations of applying molecular biomarker testing over the course of skin cancer from susceptibility to treatment are explored, with a view to outlining a future model of molecular biomarker skin cancer diagnostics.
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Affiliation(s)
- Nathalie Nataren
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Miko Yamada
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Tarl Prow
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia; Skin Research Centre, York Biomedical Research Institute, Hull York Medical School, University of York, York, United Kingdom.
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3
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Liquid Chromatography-Tandem Mass Spectrometry in Newborn Screening Laboratories. Int J Neonatal Screen 2022; 8:ijns8040062. [PMID: 36547379 PMCID: PMC9781967 DOI: 10.3390/ijns8040062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Tandem mass spectrometry (MS/MS) is the most universal platform currently available for the analysis of enzymatic activities and biomarkers in dried blood spots (DBS) for applications in newborn screening (NBS). Among the MS/MS applications in NBS, the most common is flow-injection analysis (FIA-) MS/MS, where the sample is introduced as a bolus injection into the mass spectrometer without the prior fractionation of analytes. Liquid chromatography combined with MS/MS (LC-MS/MS) has been employed for second-tier tests to reduce the false-positive rate associated with several nonspecific screening markers, beginning two decades ago. More recently, LC-MS/MS has been applied to primary screening for new conditions for which FIA-MS/MS or other methods, including genomic screening, are not yet adequate. In addition to providing a list of the currently used LC-MS/MS-based assays for NBS, the authors share their experience regarding the maintenance requirements of LC-MS/MS vs. FIA-MS/MS systems. The consensus is that the maintenance of LC-MS/MS and FIA-MS/MS instrumentation is similar, and LC-MS/MS has the advantage of allowing for a larger number of diseases to be screened for in a multiplex, cost-effective fashion with a high throughput and an adequate turnaround time.
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4
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Morales RTT, Ko J. Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles. ACS NANO 2022; 16:11619-11645. [PMID: 35904433 PMCID: PMC10174080 DOI: 10.1021/acsnano.2c04337] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
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Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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The Significance of External Quality Assessment Schemes for Molecular Testing in Clinical Laboratories. Cancers (Basel) 2022; 14:cancers14153686. [PMID: 35954349 PMCID: PMC9367251 DOI: 10.3390/cancers14153686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Patients and clinicians often rely on the outcome of laboratory tests, but can we really trust these test results? Good quality management is key for laboratories to guarantee reliable test results. This review focusses on external quality assessment (EQA) schemes which are a tool for laboratories to examine and improve the quality of their testing routines. In this review, an overview of the role and importance of EQA schemes for clinical laboratories is given, and different types of EQA schemes and EQA providers available on the market are discussed, as well as recent developments in the EQA landscape. Abstract External quality assessment (EQA) schemes are a tool for clinical laboratories to evaluate and manage the quality of laboratory practice with the support of an independent party (i.e., an EQA provider). Depending on the context, there are different types of EQA schemes available, as well as various EQA providers, each with its own field of expertise. In this review, an overview of the general requirements for EQA schemes and EQA providers based on international guidelines is provided. The clinical and scientific value of these kinds of schemes for clinical laboratories, clinicians and patients are highlighted, in addition to the support EQA can provide to other types of laboratories, e.g., laboratories affiliated to biotech companies. Finally, recent developments and challenges in laboratory medicine and quality management, for example, the introduction of artificial intelligence in the laboratory and the shift to a more individual-approach instead of a laboratory-focused approach, are discussed. EQA schemes should represent current laboratory practice as much as possible, which poses the need for EQA providers to introduce latest laboratory innovations in their schemes and to apply up-to-date guidelines. By incorporating these state-of-the-art techniques, EQA aims to contribute to continuous learning.
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6
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Chakravarty D, Johnson A, Sklar J, Lindeman NI, Moore K, Ganesan S, Lovly CM, Perlmutter J, Gray SW, Hwang J, Lieu C, André F, Azad N, Borad M, Tafe L, Messersmith H, Robson M, Meric-Bernstam F. Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion. J Clin Oncol 2022; 40:1231-1258. [PMID: 35175857 DOI: 10.1200/jco.21.02767] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE An ASCO provisional clinical opinion offers timely clinical direction to ASCO's membership following publication or presentation of potentially practice-changing data from major studies. This provisional clinical opinion addresses the appropriate use of tumor genomic testing in patients with metastatic or advanced solid tumors. CLINICAL CONTEXT An increasing number of therapies are approved to treat cancers harboring specific genomic biomarkers. However, there is a lack of clarity as to when tumor genomic sequencing should be ordered, what type of assays should be performed, and how to interpret the results for treatment selection. PROVISIONAL CLINICAL OPINION Patients with metastatic or advanced cancer should undergo genomic sequencing in a certified laboratory if the presence of one or more specific genomic alterations has regulatory approval as biomarkers to guide the use of or exclusion from certain treatments for their disease. Multigene panel-based assays should be used if more than one biomarker-linked therapy is approved for the patient's disease. Site-agnostic approvals for any cancer with a high tumor mutation burden, mismatch repair deficiency, or neurotrophic tyrosine receptor kinase (NTRK) fusions provide a rationale for genomic testing for all solid tumors. Multigene testing may also assist in treatment selection by identifying additional targets when there are few or no genotype-based therapy approvals for the patient's disease. For treatment planning, the clinician should consider the functional impact of the targeted alteration and expected efficacy of genomic biomarker-linked options relative to other approved or investigational treatments.Additional information is available at www.asco.org/assays-and-predictive-markers-guidelines.
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Affiliation(s)
| | | | | | - Neal I Lindeman
- Brigham and Womens' Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | - Fabrice André
- PRISM, Precision Medicine Center, Institut Gustave Roussy, Villejuif, France
| | | | | | - Laura Tafe
- Dartmouth-Hitchcock Medical Center and The Geisel School of Medicine at Dartmouth, Darmouth, NH
| | | | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York City, NY
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7
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Pfeifer JD, Loberg R, Lofton-Day C, Zehnbauer BA. Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics. Am J Clin Pathol 2022; 157:628-638. [PMID: 34871357 DOI: 10.1093/ajcp/aqab164] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Diversity of laboratory-developed tests (LDTs) using next-generation sequencing (NGS) raises concerns about their accuracy for selection of targeted therapies. A working group developed a pilot study of traceable reference samples to measure NGS LDT performance among a cohort of clinical laboratories. METHODS Human cell lines were engineered via CRISPR/Cas9 and prepared as formalin-fixed, paraffin-embedded cell pellets ("wet" samples) to assess the entire NGS test cycle. In silico mutagenized NGS sequence files ("dry" samples) were used to assess the bioinformatics component of the NGS test cycle. Single and multinucleotide variants (n = 36) of KRAS and NRAS were tested at 5% or 15% variant allele fraction to determine eligibility for therapy with the EGFR inhibitor panitumumab in the setting of metastatic colorectal cancer. RESULTS Twenty-one (21/21) laboratories tested wet samples; 19 of 21 analyzed dry samples. Of the laboratories that tested both the wet and dry samples, 7 (37%) of 19 laboratories correctly reported all variants, 3 (16%) of 19 had fewer than five errors, and 9 (47%) of 19 had five or more errors. Most errors were false negatives. CONCLUSIONS Genetically engineered cell lines and mutagenized sequence files are complementary reference samples for evaluating NGS test performance among clinical laboratories using LDTs. Variable accuracy in detection of genetic variants among some LDTs may identify different patient populations for targeted therapy.
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Affiliation(s)
- John D Pfeifer
- Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Loberg
- Clinical Biomarkers and Diagnostics, Thousand Oaks, CA, USA
| | | | - Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
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8
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Bruehl FK, Kim AS, Li MM, Lindeman NI, Moncur JT, Souers RJ, Vasalos P, Voelkerding KV, Xian RR, Surrey LF. Tiered Somatic Variant Classification Adoption Has Increased Worldwide With Some Practice Differences Based on Location and Institutional Setting. Arch Pathol Lab Med 2022; 146:822-832. [PMID: 34979564 DOI: 10.5858/arpa.2021-0179-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (CAP) tier classification guideline provides a framework to standardize interpretation and reporting of somatic variants. OBJECTIVE.— To evaluate the adoption and performance of the 2017 guideline among laboratories performing somatic next-generation sequencing (NGS). DESIGN.— A survey was distributed to laboratories participating in NGS CAP proficiency testing for solid tumors (NGSST) and hematologic malignancies (NGSHM). RESULTS.— Worldwide, 64.4% (152 of 236) of NGSST and 66.4% (87 of 131) of NGSHM participants used tier classification systems, of which the 2017 guideline was used by 84.9% (129 of 152) of NGSST and 73.6% (64 of 87) of NGSHM participants. The 2017 guideline was modified by 24.4% (30 of 123) of NGSST and 21.7% (13 of 60) of NGSHM laboratories. Laboratories implementing the 2017 guideline were satisfied or very satisfied (74.2% [89 of 120] NGSST and 69.5% [41 of 59] NGSHM), and the impression of tier classification reproducibility was high (mean of 3.9 [NGSST] and 3.6 [NGSHM] on a 5-point scale). Of nonusers, 35.2% (38 of 108) of NGSST and 39.4% (26 of 66) of NGSHM laboratories were planning implementation. For future guideline revisions, respondents favored including variants to monitor disease (63.9% [78 of 122] NGSST, 80.0% [48 of 60] NGSHM) and germline variants (55.3% [63 of 114] NGSST, 75.0% [45 of 60] NGSHM). Additional subtiers were not favored by academic laboratories compared to nonacademic laboratories (P < .001 NGSST and P = .02 NGSHM). CONCLUSIONS.— The 2017 guideline has been implemented by more than 50.0% of CAP laboratories. While most laboratories using the 2017 guideline report satisfaction, thoughtful guideline modifications may further enhance the quality, reproducibility, and clinical utility of the 2017 guideline for tiered somatic variant classification.
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Affiliation(s)
- Frido K Bruehl
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Bruehl)
| | - Annette S Kim
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Marilyn M Li
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
| | - Neal I Lindeman
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Joel T Moncur
- The Joint Pathology Center, Office of the Director, Silver Spring, Maryland (Moncur), College of American Pathologists, Northfield, Illinois
| | - Rhona J Souers
- Biostatistics Department (Souers), College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | | | - Rena R Xian
- The Department of Pathology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland (Xian)
| | - Lea F Surrey
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
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9
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Hummel M, Hegewisch-Becker S, Neumann JHL, Vogel A. BRAF testing in metastatic colorectal carcinoma and novel, chemotherapy-free therapeutic options. DER PATHOLOGE 2021; 42:98-109. [PMID: 34259881 PMCID: PMC8571135 DOI: 10.1007/s00292-021-00946-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/25/2022]
Abstract
In the past 25 years, treatment of metastatic colorectal cancer (mCRC) has undergone profound changes. The approval of newer chemotherapeutics such as irinotecan and oxaliplatin was followed in 2005 by the first targeted therapies, for example, monoclonal antibodies directed against the epidermal growth factor receptor (EGFR), as cetuximab and panitumumab, or the angiogenesis inhibitors bevacizumab, ramucirumab, and aflibercept. With the rapidly progressing molecular characterization of mCRC in the last 10 years and the classification of the disease in four consensus subtypes, further changes are emerging, which will promote, among other things, the introduction of protein-kinase inhibitors developed for specific molecular aberrations as well as immune checkpoint inhibitors into the treatment algorithm.Thorough molecular pathologic testing is indispensable today for guideline-compliant treatment of mCRC patients. In addition to RAS testing as a precondition for the therapy decision with regard to cetuximab and panitumumab, BRAF testing is of considerable relevance to allow decision making with regard to the newly approved chemotherapy-free combination of the BRAF inhibitor encorafenib and cetuximab in cases where a BRAF-V600E mutation is detected. Additional diagnostic tests should also include genome instability (microsatellite instability). Overall, more and more molecular alterations need to be investigated simultaneously, so that the use of focused next-generation sequencing is increasingly recommended.This overview describes the prognostic relevance of BRAF testing in the context of molecular pathologic diagnostics of mCRC, presents new treatment options for BRAF-mutated mCRC patients, and explains which modern DNA analytical and immunohistochemical methods are available to detect BRAF mutations in mCRC patients.
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Affiliation(s)
- Michael Hummel
- Institut für Pathologie der Charité, Universitätsmedizin, Campus Charité Mitte, Virchowweg 16/17a, 10117, Berlin, Germany.
| | | | - Jens H L Neumann
- Pathologisches Institut der Medizinischen Fakultät, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Arndt Vogel
- Klinik für Gastroenterologie, Hepatologie und Endokrinologie, Medizinische Hochschule Hannover, Hannover, Germany
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10
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Hummel M, Hegewisch-Becker S, Neumann J, Vogel A. [BRAF-V600E testing in metastatic colorectal cancer and new, chemotherapy-free therapy options. German version]. DER PATHOLOGE 2021; 42:578-590. [PMID: 33956173 PMCID: PMC8536591 DOI: 10.1007/s00292-021-00942-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/24/2022]
Abstract
In the past 25 years, treatment of metastatic colorectal cancer (mCRC) has undergone profound changes. The approval of newer chemotherapeutics such as irinotecan and oxaliplatin was followed in 2005 by the first targeted therapies, for example, monoclonal antibodies directed against the epidermal growth factor receptor (EGFR), as cetuximab and panitumumab, or the angiogenesis inhibitors bevacizumab, ramucirumab, and aflibercept. With the rapidly progressing molecular characterization of mCRC in the last 10 years and the classification of the disease in four consensus subtypes, further changes are emerging, which will promote, among other things, the introduction of protein-kinase inhibitors developed for specific molecular aberrations as well as immune checkpoint inhibitors into the treatment algorithm.Thorough molecular pathologic testing is indispensable today for guideline-compliant treatment of mCRC patients. In addition to RAS testing as a precondition for the therapy decision with regard to cetuximab and panitumumab, BRAF testing is of considerable relevance to allow decision making with regard to the newly approved chemotherapy-free combination of the BRAF inhibitor encorafenib and cetuximab in cases where a BRAF-V600E mutation is detected. Additional diagnostic tests should also include genome instability (microsatellite instability). Overall, more and more molecular alterations need to be investigated simultaneously, so that the use of focused next-generation sequencing is increasingly recommended.This overview describes the prognostic relevance of BRAF testing in the context of molecular pathologic diagnostics of mCRC, presents new treatment options for BRAF-mutated mCRC patients, and explains which modern DNA analytical and immunohistochemical methods are available to detect BRAF mutations in mCRC patients.
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Affiliation(s)
- Michael Hummel
- Institut für Pathologie, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Virchowweg 16/17a, 10117, Berlin, Deutschland.
| | | | - Jens Neumann
- Pathologisches Institut, Medizinische Fakultät, Ludwig-Maximilians-Universität München, München, Deutschland
| | - Arndt Vogel
- Klinik für Gastroenterologie, Hepatologie und Endokrinologie, Medizinische Hochschule Hannover, Hannover, Deutschland
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11
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Salgado R, Gevaert T. Quantity of Immune Cells Predict Response to Immunotherapy in Cancer. EClinicalMedicine 2021; 41:101170. [PMID: 34746724 PMCID: PMC8554484 DOI: 10.1016/j.eclinm.2021.101170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp; Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
- Corresponding Author.
| | - Thomas Gevaert
- Organ Systems, KU Leuven, Leuven, Department of Pathology, AZ Klina, Brasschaat, Belgium
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12
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Marble HD, Bard AZ, Mizrachi MM, Lennerz JK. Temporary Regulatory Deviations and the Coronavirus Disease 2019 (COVID-19) PCR Labeling Update Study Indicate What Laboratory-Developed Test Regulation by the US Food and Drug Administration (FDA) Could Look Like. J Mol Diagn 2021; 23:1207-1217. [PMID: 34538703 PMCID: PMC8444018 DOI: 10.1016/j.jmoldx.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/20/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) response necessitated innovations and a series of regulatory deviations that also affected laboratory-developed tests (LDTs). To examine real-world consequences and specify regulatory paradigm shifts, legislative proposals were aligned on a common timeline with Emergency Use Authorization (EUA) of LDTs and the US Food and Drug Administration (FDA)-orchestrated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) labeling update study. The initial EUA adoption by LDT developers shows that the FDA can have oversight over LDTs. We used efficiency-corrected microcosting of our EUA PCR assay to estimate the national cost of the labeling update study to $0.3 to $1.4 million US dollars. Labeling update study performance data showed lower average detection limits in commercial in vitro diagnostic (IVD) assays versus LDTs (32,000 ± 75,000 versus 71,000 ± 147,000 nucleic acid amplification tests/mL; P = 0.04); however, comparison also shows that FDA review of IVD assays and LDTs did not prevent differences between initial and labeling update performance (IVD assay, P < 0.0001; LDT, P = 0.003). The regulatory shifts re-emphasized that both commercial tests and LDTs rely heavily on laboratory competence and procedures; however, lack of performance data on authorized tests, when clinically implemented, precludes assessment of the benefit related to regulatory review. Temporary regulatory deviations during the pandemic and regulatory science tools (ie, reference material) have generated valuable real-world evidence to inform pending legislation regarding LDT regulation.
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Affiliation(s)
- Hetal D Marble
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Adam Z Bard
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Mark M Mizrachi
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, New York; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts.
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13
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Lee Deak K, Jackson JB, Valkenburg KC, Keefer LA, Robinson Gerding KM, Angiuoli SV, Datto MB, McCall SJ. Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized Personal Genome Diagnostics, Inc., Elio Tissue Complete Kitted Solution. J Mol Diagn 2021; 23:1324-1333. [PMID: 34314880 PMCID: PMC8567158 DOI: 10.1016/j.jmoldx.2021.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/11/2021] [Accepted: 07/07/2021] [Indexed: 11/09/2022] Open
Abstract
Genomic tumor profiling by next-generation sequencing (NGS) allows for large-scale tumor testing to inform targeted cancer therapies and immunotherapies, and to identify patients for clinical trials. These tests are often underutilized in patients with late-stage solid tumors and are typically performed in centralized specialty laboratories, thereby limiting access to these complex tests. Personal Genome Diagnostics Inc., elio tissue complete NGS solution is a comprehensive DNA-to-report kitted assay and bioinformatics solution. Comparison of 147 unique specimens from >20 tumor types was performed using the elio tissue complete solution and Foundation Medicine's FoundationOne test, which is of similar size and gene content. The analytical performance of all genomic variant types was evaluated. In general, the overall mutational profile is highly concordant between the two assays, with agreement in sequence variants reported between panels demonstrating >95% positive percentage agreement for single-nucleotide variants and insertions/deletions in clinically actionable genes. Both copy number alterations and gene translocations showed 80% to 83% positive percentage agreement, whereas tumor mutation burden and microsatellite status showed a high level of concordance across a range of mutation loads and tumor types. The Personal Genome Diagnostics Inc., elio tissue complete assay is comparable to the FoundationOne test and will allow more laboratories to offer a diagnostic NGS assay in house, which will ultimately reduce time to result and increase the number of patients receiving molecular genomic profiling and personalized treatment.
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Affiliation(s)
- Kristen Lee Deak
- Department of Pathology, Duke University Medical Center, Durham, North Carolina.
| | | | | | | | | | | | - Michael B Datto
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Shannon J McCall
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
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14
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Zhang BM, Keegan A, Li P, Lindeman NI, Nagarajan R, Routbort MJ, Vasalos P, Kim AS, Merker JD. An Overview of Characteristics of Clinical Next-Generation Sequencing-Based Testing for Hematologic Malignancies. Arch Pathol Lab Med 2021; 145:1110-1116. [PMID: 33450747 DOI: 10.5858/arpa.2019-0661-cp] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— With the increasing integration of molecular alterations into the evaluation of hematologic malignancies (HM), somatic mutation profiling by next-generation sequencing (NGS) has become a common clinical testing strategy. Limited data are available about the characteristics of these assays. OBJECTIVE.— To describe assay characteristics, specimen requirements, and reporting practices for NGS-based HM testing using College of American Pathologists proficiency testing survey data. DESIGN.— The College of American Pathologists NGS Hematologic Malignancies Survey (NGSHM) results from 78 laboratories were used to determine laboratory practices in NGS-based HM testing. RESULTS.— The majority of laboratories performed tumor-only (88.5% [69 of 78]), targeted sequencing of cancer genes or mutation hotspots (98.7% [77 of 78]); greater than 90% performed testing on fresh bone marrow and peripheral blood. The majority of laboratories reported a 5% lower limit of detection for single-nucleotide variants (73.1% [57 of 78]) and small insertions and deletions (50.6% [39 of 77]). A majority of laboratories used benchtop sequencers and custom enrichment approaches. CONCLUSIONS.— This manuscript summarizes the characteristics of clinical NGS-based testing for the detection of somatic variants in HM. These data may be broadly useful to inform laboratory practice and quality management systems, regulation, and oversight of NGS testing, and precision medicine efforts using a data-driven approach.
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Affiliation(s)
- Bing M Zhang
- From the Department of Pathology, Stanford University School of Medicine, Stanford, California (Zhang)
| | - Alissa Keegan
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Peng Li
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, Utah (Li)
| | - Neal I Lindeman
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Rakesh Nagarajan
- PierianDx, St Louis, Missouri (Nagarajan).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Mark J Routbort
- the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Routbort).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, Illinois (Vasalos).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Annette S Kim
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Jason D Merker
- the Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill (Merker).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
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15
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Barnell EK, Newcomer KF, Skidmore ZL, Krysiak K, Anderson SR, Wartman LD, Oh ST, Welch JS, Stockerl-Goldstein KE, Vij R, Cashen AF, Pusic I, Westervelt P, Abboud CN, Ghobadi A, Uy GL, Schroeder MA, Dipersio JF, Politi MC, Spencer DH, Duncavage EJ, Ley TJ, Griffith M, Jacoby MA, Griffith OL. Impact of a 40-Gene Targeted Panel Test on Physician Decision Making for Patients With Acute Myeloid Leukemia. JCO Precis Oncol 2021; 5:PO.20.00182. [PMID: 34036230 PMCID: PMC8140802 DOI: 10.1200/po.20.00182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Physicians treating hematologic malignancies increasingly order targeted sequencing panels to interrogate recurrently mutated genes. The precise impact of these panels on clinical decision making is not well understood. METHODS Here, we report our institutional experience with a targeted 40-gene panel (MyeloSeq) that is used to generate a report for both genetic variants and variant allele frequencies for the treating physician (the limit of mutation detection is approximately one AML cell in 50). RESULTS In total, 346 sequencing reports were generated for 325 patients with suspected hematologic malignancies over an 8-month period (August 2018 to April 2019). To determine the influence of genomic data on clinical care for patients with acute myeloid leukemia (AML), we analyzed 122 consecutive reports from 109 patients diagnosed with AML and surveyed the treating physicians with a standardized questionnaire. The panel was ordered most commonly at diagnosis (61.5%), but was also used to assess response to therapy (22.9%) and to detect suspected relapse (15.6%). The panel was ordered at multiple timepoints during the disease course for 11% of patients. Physicians self-reported that 50 of 114 sequencing reports (44%) influenced clinical care decisions in 44 individual patients. Influences were often nuanced and extended beyond identifying actionable genetic variants with US Food and Drug Administration-approved drugs. CONCLUSION This study provides insights into how physicians are currently using multigene panels capable of detecting relatively rare AML cells. The most influential way to integrate these tools into clinical practice will be to perform prospective clinical trials that assess patient outcomes in response to genomically driven interventions.
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Affiliation(s)
- Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Kenneth F Newcomer
- Department of Surgery, Washington University School of Medicine, St Louis, MO
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Sydney R Anderson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Lukas D Wartman
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Stephen T Oh
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO.,Department of Medicine, Division of Hematology, Washington University School of Medicine, St Louis, MO
| | - John S Welch
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Keith E Stockerl-Goldstein
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Ravi Vij
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Amanda F Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Iskra Pusic
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Peter Westervelt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Camille N Abboud
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Armin Ghobadi
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Geoffrey L Uy
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - Mark A Schroeder
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - John F Dipersio
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Mary C Politi
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St Louis, MO
| | - David H Spencer
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Timothy J Ley
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.,Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO.,Department of Genetics, Washington University School of Medicine, St Louis, MO
| | - Meagan A Jacoby
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.,Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO.,Department of Genetics, Washington University School of Medicine, St Louis, MO
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16
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Salgado R, Bellizzi AM, Rimm D, Bartlett JMS, Nielsen T, Holger M, Laenkholm AV, Quinn C, Cserni G, Cunha IW, Alvarado-Cabrero I, Cree I. How current assay approval policies are leading to unintended imprecision medicine. Lancet Oncol 2020; 21:1399-1401. [PMID: 33098760 DOI: 10.1016/s1470-2045(20)30592-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/19/2022]
Affiliation(s)
- Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Department of Pathology, GZA-ZNA Hospitals, Wilrijk, Antwerp, Belgium.
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - David Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Torsten Nielsen
- Department of Pathology and Laboratory Medicine, Genetic Pathology Evaluation Centre, University of British Columbia, Vancouver, BC, Canada
| | - Moch Holger
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Cecily Quinn
- Department of Pathology, St Vincent's University Hospital, Dublin, Ireland
| | - Gábor Cserni
- Department of Pathology, Bács-Kiskun County Teaching Hospital, Kecskemét, Hungary; Department of Pathology, University of Szeged, Szeged, Hungary
| | - Isabela W Cunha
- Institute of Anatomical Pathology, Rede D'Or São Luiz Hospitals Network, São Paulo, Brazil; D'Or Institute for Research and Education, Rio de Janeiro and São Paulo, Brazil
| | - Isabel Alvarado-Cabrero
- Department of Pathology, Hospital de Oncología, CMN, SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Ian Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
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17
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Marble HD, Huang R, Dudgeon SN, Lowe A, Herrmann MD, Blakely S, Leavitt MO, Isaacs M, Hanna MG, Sharma A, Veetil J, Goldberg P, Schmid JH, Lasiter L, Gallas BD, Abels E, Lennerz JK. A Regulatory Science Initiative to Harmonize and Standardize Digital Pathology and Machine Learning Processes to Speed up Clinical Innovation to Patients. J Pathol Inform 2020; 11:22. [PMID: 33042601 PMCID: PMC7518200 DOI: 10.4103/jpi.jpi_27_20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/20/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
Unlocking the full potential of pathology data by gaining computational access to histological pixel data and metadata (digital pathology) is one of the key promises of computational pathology. Despite scientific progress and several regulatory approvals for primary diagnosis using whole-slide imaging, true clinical adoption at scale is slower than anticipated. In the U.S., advances in digital pathology are often siloed pursuits by individual stakeholders, and to our knowledge, there has not been a systematic approach to advance the field through a regulatory science initiative. The Alliance for Digital Pathology (the Alliance) is a recently established, volunteer, collaborative, regulatory science initiative to standardize digital pathology processes to speed up innovation to patients. The purpose is: (1) to account for the patient perspective by including patient advocacy; (2) to investigate and develop methods and tools for the evaluation of effectiveness, safety, and quality to specify risks and benefits in the precompetitive phase; (3) to help strategize the sequence of clinically meaningful deliverables; (4) to encourage and streamline the development of ground-truth data sets for machine learning model development and validation; and (5) to clarify regulatory pathways by investigating relevant regulatory science questions. The Alliance accepts participation from all stakeholders, and we solicit clinically relevant proposals that will benefit the field at large. The initiative will dissolve once a clinical, interoperable, modularized, integrated solution (from tissue acquisition to diagnostic algorithm) has been implemented. In times of rapidly evolving discoveries, scientific input from subject-matter experts is one essential element to inform regulatory guidance and decision-making. The Alliance aims to establish and promote synergistic regulatory science efforts that will leverage diverse inputs to move digital pathology forward and ultimately improve patient care.
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Affiliation(s)
- Hetal Desai Marble
- Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Richard Huang
- Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah Nixon Dudgeon
- Division of Imaging, Diagnostics, and Software Reliability, Center for Devices and Radiological Health, Food and Drug Administration, Office of Science and Engineering Laboratories, Silver Spring, MD, USA
| | | | - Markus D Herrmann
- Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Mike Isaacs
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew G Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashish Sharma
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jithesh Veetil
- Medical Device Innovation Consortium, Arlington, VA, USA
| | | | | | | | - Brandon D Gallas
- Division of Imaging, Diagnostics, and Software Reliability, Center for Devices and Radiological Health, Food and Drug Administration, Office of Science and Engineering Laboratories, Silver Spring, MD, USA
| | | | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
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18
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Konnick EQ. The regulatory landscape of precision oncology laboratory medicine in the United States - Perspective on the past 5 years and considerations for future regulation. Pract Lab Med 2020; 21:e00172. [PMID: 32509953 PMCID: PMC7261109 DOI: 10.1016/j.plabm.2020.e00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023] Open
Abstract
The regulatory landscape for precision oncology in the United States is complicated, with multiple governmental regulatory agencies with different scopes of jurisdiction. Several regulatory proposals have been introduced since the Food and Drug Administration released a draft guidance to regulate laboratory-developed tests in 2014. Key aspects of the most recent proposals and discussion of central arguments related to the regulation of precision oncology laboratory tests provides insight to stakeholders for future discussions related to regulation of laboratory tests.
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19
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Klein RD. Current Policy Challenges in Genomic Medicine. Clin Chem 2019; 66:61-67. [DOI: 10.1373/clinchem.2019.308775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/19/2019] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Molecular genetic testing has raised a variety of policy issues, ranging from privacy to reimbursement. Recently, payment policies have become of paramount importance as Medicare implemented the first significant change to test pricing since 1984 and announced a broad national coverage policy for the use of next-generation sequencing (NGS) in cancer patients that contains significant restrictions. Regulatory and oversight concerns have been important topics for discussion as the US Food and Drug Administration (FDA), Congress, and stakeholders have focused on new approaches to regulation of laboratory-developed tests (LDTs). Patents on gene sequences and relationships between genetic variants and clinical phenotypes have been points of contention since the field's inception. Two Supreme Court cases invalidated patents on gene sequences and biological relationships, ushering in the era of NGS and precision medicine. However, a recent legislative proposal threatens to reverse these gains and restore gene patents as barriers to progress in genetic and genomic testing and the implementation of genomic medicine.
CONTENT
This review discusses current issues in payment policy, laboratory oversight, and gene patenting and their potential impacts on genetic and genomic testing.
SUMMARY
Coverage and reimbursement policies present serious challenges to genetic and genomic testing. The potential for FDA regulation of LDTs looms as a significant threat to diagnostic innovation, patient access, and the viability of molecular genetic testing laboratories. Changes in patent law could cause gene patents to reemerge as barriers to the advancement of genomic medicine.
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Affiliation(s)
- Roger D Klein
- Center for Law, Science, and Innovation, Sandra Day O'Connor College of Law, Arizona State University, Tempe, AK
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20
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Abstract
OBJECTIVES To provide a clinical laboratory perspective on the Verifying Accurate Leading-edge IVCT Development Act (VALID) discussion draft. This potential legislative effort, if enacted, would overhaul the regulatory oversight of in vitro diagnostics (IVDs) in the United States and create a single system for regulation of conventional IVDs and laboratory-developed tests (LDTs). METHODS A concise literature-based review of LDT regulation is presented followed by a discussion of key concerns pertinent to clinical laboratories that should be considered in future IVD regulatory reform efforts. RESULTS Key issues identified include the importance of fostering innovation, preserving patient safety, protecting the practice of laboratory medicine, and minimizing undue regulatory burden. Clinical laboratories are not equivalent to manufacturing facilities and would therefore encounter challenges in implementing device-centric regulatory oversight models. CONCLUSIONS It is imperative that a clinical laboratory perspective on LDTs is understood and incorporated prior to advancement of future legislative proposals.
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Affiliation(s)
- Jonathan R Genzen
- Department of Pathology, University of Utah, Salt Lake City
- ARUP Laboratories, Salt Lake City, UT
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21
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Schreier J, Feeney R, Keeling P. Diagnostics Reform and Harmonization of Clinical Laboratory Testing. J Mol Diagn 2019; 21:737-745. [PMID: 31075512 DOI: 10.1016/j.jmoldx.2019.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022] Open
Abstract
Developments in diagnostics reform legislation in the United States are occurring at a rapid pace. The framework for future regulatory oversight of clinical laboratory testing is currently under intensive debate among stakeholders that represent patients, practitioners, laboratories, diagnostic manufacturers, and regulators. The importance of clinical laboratory test standardization is a key component of any plan for regulatory reform. A laboratory-developed test is performed in a specific laboratory setting, often led by clinical laboratory professionals who possess specific expertise for developing and running the test to fill a clinical need. A test commercially marketed as an in vitro diagnostic kit is designed to operate across a spectrum of laboratory settings in laboratories with a range of expertise. Both types of tests are stringently regulated, laboratory-developed tests by the Clinical Laboratory Improvement Amendments and in vitro diagnostic kits by the US Food and Drug Administration. Interlaboratory comparisons of laboratory-developed tests have been published, demonstrating highly reproducible results. Comparisons of laboratory-developed tests with in vitro diagnostic kits have also found high concordance. Several important clinical laboratory test standardization projects are currently under way. The US Food and Drug Administration has acknowledged the need for such standardization. In its most recent draft guidance, the agency requested input from the scientific community as to actions that can be taken to facilitate standardization.
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22
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Salgado R, Solit DB, Rimm DL, Bogaerts J, Canetta R, Lively T, Lyerly K, Span PN, Bateman-House A, Makady A, Bergmann L, Nagai S, Smith C, Robson M, Savage M, Voest E, Sweeney C, Lambin P, Thomas M, Harris L, Lacombe D, Massard C. Addressing the dichotomy between individual and societal approaches to personalised medicine in oncology. Eur J Cancer 2019; 114:128-136. [PMID: 31060925 DOI: 10.1016/j.ejca.2019.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022]
Abstract
Academic, industry, regulatory leaders and patient advocates in cancer clinical research met in November 2018 at the Innovation and Biomarkers in Cancer Drug Development meeting in Brussels to address the existing dichotomy between increasing calls for personalised oncology approaches based on individual molecular profiles and the need to make resource and regulatory decisions at the societal level in differing health-care delivery systems around the globe. Novel clinical trial designs, the utility and limitations of real-world evidence (RWE) and emerging technologies for profiling patient tumours and tumour-derived DNA in plasma were discussed. While randomised clinical trials remain the gold standard approach to defining clinical utility of local and systemic therapeutic interventions, the broader adoption of comprehensive tumour profiling and novel trial designs coupled with RWE may allow patient and physician autonomy to be appropriately balanced with broader assessments of safety and overall societal benefit.
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Affiliation(s)
- Roberto Salgado
- Department of Pathology GZA-ZNA, Antwerp, Belgium; Division of Research, Peter Mac Callum Cancer Center, Melbourne, Australia.
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David L Rimm
- Dept. of Pathology, Yale University School of Medicine, New Haven, CT, USA; Dept. of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | | | - Paul N Span
- Radiotherapy and OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Amr Makady
- The National Healthcare Institute (ZIN), Diemen, the Netherlands
| | - L Bergmann
- Medical Clinic II, University Hospital Frankfurt, Germany; Ambulantes Krebszentrum Frankfurt, Germany
| | - Sumimasa Nagai
- Translational Research Center, The University of Tokyo Hospital and PMDA, Tokyo, Japan
| | - Chris Smith
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emile Voest
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Philippe Lambin
- The D-Lab & The M-Lab, Department of Precision Medicine, GROW Research Institute for Oncology, Maastricht, The Netherlands
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23
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Moncur JT, Bartley AN, Bridge JA, Kamel-Reid S, Lazar AJ, Lindeman NI, Long TA, Merker JD, Rai AJ, Rimm DL, Rothberg PG, Vasalos P, Kim AS. Performance Comparison of Different Analytic Methods in Proficiency Testing for Mutations in the BRAF, EGFR, and KRAS Genes: A Study of the College of American Pathologists Molecular Oncology Committee. Arch Pathol Lab Med 2019; 143:1203-1211. [PMID: 30969158 DOI: 10.5858/arpa.2018-0396-cp] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The performance of laboratory testing has recently come under increased scrutiny as part of important and ongoing debates on regulation and reimbursement. To address this critical issue, this study compares the performance of assay methods, using either commercial kits or assays designed and implemented by single laboratories ("home brews"), including next-generation sequencing methods, on proficiency testing provided by the College of American Pathologists Molecular Oncology Committee. OBJECTIVE.— To compare the performance of different assay methods on College of American Pathologists proficiency testing for variant analysis of 3 common oncology analytes: BRAF, EGFR, and KRAS. DESIGN.— There were 6897 total responses across 35 different proficiency testing samples interrogating 13 different variants as well as wild-type sequences for BRAF, EGFR, and KRAS. Performance was analyzed by test method, kit manufacturer, variants tested, and preanalytic and postanalytic practices. RESULTS.— Of 26 reported commercial kits, 23 achieved greater than 95% accuracy. Laboratory-developed tests with no kit specified demonstrated 96.8% or greater accuracy across all 3 analytes (1123 [96.8%] acceptable of 1160 total responses for BRAF; 848 [97.5%] acceptable of 870 total responses for EGFR; 942 [97.0%] acceptable of 971 total responses for KRAS). Next-generation sequencing platforms (summed across all analytes and 2 platforms) demonstrated 99.4% accuracy for these analytes (165 [99.4%] acceptable of 166 total next-generation sequencing responses). Slight differences in performance were noted among select commercial assays, dependent upon the particular design and specificity of the assay. Wide differences were noted in the lower limits of neoplastic cellularity laboratories accepted for testing. CONCLUSIONS.— These data demonstrate the high degree of accuracy and comparable performance across all laboratories, regardless of methodology. However, care must be taken in understanding the diagnostic specificity and reported analytic sensitivity of individual methods.
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Affiliation(s)
- Joel T Moncur
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Angela N Bartley
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Julia A Bridge
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Suzanne Kamel-Reid
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alexander J Lazar
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Neal I Lindeman
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Thomas A Long
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Jason D Merker
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alex J Rai
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - David L Rimm
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Paul G Rothberg
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Patricia Vasalos
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Annette S Kim
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
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Merker JD, Devereaux K, Iafrate AJ, Kamel-Reid S, Kim AS, Moncur JT, Montgomery SB, Nagarajan R, Portier BP, Routbort MJ, Smail C, Surrey LF, Vasalos P, Lazar AJ, Lindeman NI. Proficiency Testing of Standardized Samples Shows Very High Interlaboratory Agreement for Clinical Next-Generation Sequencing-Based Oncology Assays. Arch Pathol Lab Med 2019; 143:463-471. [PMID: 30376374 PMCID: PMC6910717 DOI: 10.5858/arpa.2018-0336-cp] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing-based assays are being increasingly used in the clinical setting for the detection of somatic variants in solid tumors, but limited data are available regarding the interlaboratory performance of these assays. OBJECTIVE.— To examine proficiency testing data from the initial College of American Pathologists (CAP) Next-Generation Sequencing Solid Tumor survey to report on laboratory performance. DESIGN.— CAP proficiency testing results from 111 laboratories were analyzed for accuracy and associated assay performance characteristics. RESULTS.— The overall accuracy observed for all variants was 98.3%. Rare false-negative results could not be attributed to sequencing platform, selection method, or other assay characteristics. The median and average of the variant allele fractions reported by the laboratories were within 10% of those orthogonally determined by digital polymerase chain reaction for each variant. The median coverage reported at the variant sites ranged from 1922 to 3297. CONCLUSIONS.— Laboratories demonstrated an overall accuracy of greater than 98% with high specificity when examining 10 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 15% or greater. These initial data suggest excellent performance, but further ongoing studies are needed to evaluate the performance of lower variant allele fractions and additional variant types.
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Affiliation(s)
- Jason D. Merker
- Departments of Pathology & Laboratory Medicine and Genetics, Lineberger Comprehensive Cancer Center,
University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Kelly Devereaux
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Suzanne Kamel-Reid
- Departments of Pathology and Clinical Laboratory Genetics, The University Health Network and the University
of Toronto, Toronto, Ontario, Canada
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA, USA
| | - Joel T. Moncur
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Mark J. Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Craig Smail
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Lea F. Surrey
- Department of Pathology, Children’s Hospital of Philadelphia, University of Pennsylvania,
Philadelphia, PA
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, IL, USA
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas
MD Anderson Cancer Center, Houston, TX, USA
| | - Neal I. Lindeman
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA, USA
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25
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Surrey LF, Oakley FD, Merker JD, Long TA, Vasalos P, Moncur JT, Kim AS. Next-Generation Sequencing (NGS) Methods Show Superior or Equivalent Performance to Non-NGS Methods on BRAF, EGFR, and KRAS Proficiency Testing Samples. Arch Pathol Lab Med 2019; 143:980-984. [DOI: 10.5858/arpa.2018-0394-cp] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
There has been a rapid expansion of next-generation sequencing (NGS)–based assays for the detection of somatic variants in solid tumors. However, limited data are available regarding the comparative performance of NGS and non-NGS assays using standardized samples across a large number of laboratories.
Objective.—
To compare the performance of NGS and non-NGS assays using well-characterized proficiency testing samples provided by the College of American Pathologists (CAP) Molecular Oncology Committee. A secondary goal was to compare the use of preanalytic and postanalytic practices.
Design.—
A total of 17 343 responses were obtained from participants in the BRAF, EGFR, KRAS, and the Multigene Tumor Panel surveys across 84 different proficiency testing samples interrogating 16 variants and 3 wild-type sequences. Performance and preanalytic/postanalytic practices were analyzed by method.
Results.—
While both NGS and non-NGS achieved an acceptable response rate of greater than 95%, the overall performance of NGS methods was significantly better than that of non-NGS methods for the identification of variants in BRAF (overall 97.8% versus 95.6% acceptable responses, P = .001) and EGFR (overall 98.5% versus 97.3%, P = .01) and was similar for KRAS (overall 98.8% and 97.6%, P = .10). There were specific variant differences, but in all discrepant cases, NGS methods outperformed non-NGS methods. NGS laboratories also more consistently used preanalytic and postanalytic practices suggested by the CAP checklist requirements than non-NGS laboratories.
Conclusions.—
The overall analytic performance of both methods was excellent. For specific BRAF and EGFR variants, NGS outperformed non-NGS methods and NGS laboratories report superior adherence to suggested laboratory practices.
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Affiliation(s)
- Lea F. Surrey
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Fredrick D. Oakley
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Jason D. Merker
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Thomas A. Long
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Patricia Vasalos
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Joel T. Moncur
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
| | - Annette S. Kim
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Dr Surrey) Peoria Tazewell Pathology Group, Peoria, Illinois (Dr Oakley); the Department of Pathology, University of North Carolina, Chapel Hill (Dr Merker); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of Ame
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26
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Dagogo-Jack I, Azzolli CG, Fintelmann F, Mino-Kenudson M, Farago AF, Gainor JF, Jiang G, Piotrowska Z, Heist RS, Lennes IT, Temel JS, Mooradian MJ, Lin JJ, Digumarthy SR, Batten JM, Robinson H, Nose V, Rivera M, Nardi V, Dias-Santagata D, Le LP, Sequist LV, Pitman M, Shepard JAO, Shaw AT, Iafrate AJ, Lennerz JK. Clinical Utility of Rapid EGFR Genotyping in Advanced Lung Cancer. JCO Precis Oncol 2018; 2018:PO.17.00299. [PMID: 30370396 PMCID: PMC6200882 DOI: 10.1200/po.17.00299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Targeted therapy is the cornerstone of treatment of advanced EGFR-mutant non-small-cell lung cancer (NSCLC). Next-generation sequencing (NGS), the preferred method for genotyping, typically requires several weeks. Here, we assessed workflows designed to rapidly identify patients with actionable EGFR mutations and reduce time to initiation (TTI) of epidermal growth factor receptor (EGFR)-directed therapy. PATIENTS AND METHODS We performed rapid testing for EGFR L858R mutations and exon 19 deletions on paraffin-embedded or frozen section biopsy specimens from newly diagnosed patients with metastatic NSCLC by using an EGFR-specific assay (rapid test). To determine clinical utility, we assessed concordance with NGS results, turnaround time, and TTI of EGFR therapy, and we evaluated reimbursement data. RESULTS Between January 2015 and September 2017, we performed 243 rapid EGFR tests and identified EGFR mutations in 43 patients (18%). With NGS results as a reference, sensitivity and specificity of the rapid EGFR polymerase chain reaction assay were 98% and 100%, respectively. The median turnaround time for NGS was 14 days, compared with 7 days for rapid testing (P < .001). In the rapid group, 95% of patients received an EGFR inhibitor in the first-line setting. The median TTI of EGFR therapy was significantly shorter in the rapid cohort when compared with 121 historical cases (22 v 37 days; P = .01). Escalation of the initiative into an interdisciplinary ultra-rapid next-day frozen-section workflow for highly symptomatic patients (n = 8) resulted in a reduction in the median (± standard deviation) turnaround time to 1 ± 0.4 days and allowed several patients to initiate therapy within 1 week of biopsy. An extended 9-month clinical evaluation phase confirmed operational sustainability (turnaround times: ultra-rapid, 0.81 ± 0.4 days; rapid, 3 ± 1.5 days), and a 63% reimbursement rate indicated financial sustainability. CONCLUSION Rapid genotyping facilitates earlier initiation of EGFR-directed therapies without compromising NGS workflows.
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Affiliation(s)
| | | | | | | | | | | | - Ginger Jiang
- All authors: Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | | | | | | | | | - Vania Nose
- All authors: Massachusetts General Hospital, Boston, MA
| | - Miguel Rivera
- All authors: Massachusetts General Hospital, Boston, MA
| | | | | | - Long P. Le
- All authors: Massachusetts General Hospital, Boston, MA
| | | | - Martha Pitman
- All authors: Massachusetts General Hospital, Boston, MA
| | | | - Alice T. Shaw
- All authors: Massachusetts General Hospital, Boston, MA
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27
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Gong J, Li Y, Lin T, Feng X, Chu L. Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC Adv 2018; 8:27375-27381. [PMID: 35540013 PMCID: PMC9083282 DOI: 10.1039/c8ra05259j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/23/2018] [Indexed: 12/01/2022] Open
Abstract
With the continuous development and application of targeted drugs, it is particularly desirable to find a non-invasive diagnostic approach to screen patients for precision treatment. Specifically, detection of multiple cancer-related mutations is very important for targeted therapy and prediction of drug resistance. Although numerous advanced PCR methods have been developed to discriminate single nucleotide polymorphisms, their drawbacks significantly limit their application, such as low sensitivity and throughput, complicated operations, and expensive costs. In order to overcome these challenges, in this study, we developed a method combining multiplex and sensitive real-time PCR assay with rolling circle amplification. This allows specific and sensitive discrimination of the single nucleotide mutation and provides convenient multiplex detection by real-time PCR assay. The clinical potential of the MPRP assay was further demonstrated by comparing samples from 8 patients with a digital PCR assay. The coincident results between these two methods indicated that the MPRP assay can provide a specific, sensitive, and convenient method for multiplex detection of cancer-related mutations. The MPRP system for SNP discrimination was developed, which showed high specificity and sensitivity for multiplex detection of tumor-related mutations.![]()
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Affiliation(s)
| | - Yishuai Li
- Department of Thoracic Surgery
- Hebei Chest Hospital
- China
| | - Ting Lin
- Apexbio Biotech Co., LTD
- Beijing 100176
- China
| | | | - Li Chu
- Hebei Medical University
- China
- Department of Pharmacology
- Hebei University of Chinese Medicine
- China
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