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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: 81] [Impact Index Per Article: 40.5] [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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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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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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Nardi V, Tsuchiya KD, Kim AS, Bean LJH, Halley JG, Long TA, Szelinger S, Vasalos P, Thorson JA, Moyer AM, Moncur JT. Next-Generation Sequencing Somatic and Germline Assay Troubleshooting Guide Derived From Proficiency Testing Data. Arch Pathol Lab Med 2021; 146:451-461. [PMID: 34424952 DOI: 10.5858/arpa.2020-0842-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing-based assays are increasingly used in clinical molecular laboratories to detect somatic variants in solid tumors and hematologic malignancies and to detect constitutional variants. Proficiency testing data are potential sources of information about challenges in performing these assays. OBJECTIVE.— To examine the most common sources of unacceptable results from the College of American Pathologists Next-Generation Sequencing Bioinformatics, Hematological Malignancies, Solid Tumor, and Germline surveys, and provide recommendations on how to avoid these pitfalls and improve performance. DESIGN.— The College of American Pathologists next-generation sequencing somatic and germline proficiency testing survey results from 2016 to 2019 were analyzed to identify the most common causes of unacceptable results. RESULTS.— On somatic and germline proficiency testing surveys, 95.9% (18 815/19 623) and 97.8% (33 890/34 641) of all variants were correctly identified, respectively. The most common causes of unacceptable results related to sequencing were false-negative errors in genomic regions that were difficult to sequence because of high GC content. False-positive errors occurred in the context of homopolymers and pseudogenes. Recurrent errors in variant annotation were seen for dinucleotide and duplication variants and included unacceptable transcript selection and outdated variant nomenclature. A small percentage of preanalytic or postanalytic errors were attributed to specimen swaps and transcription errors. CONCLUSIONS.— Laboratories demonstrate overall excellent performance for detecting variants in both somatic and germline proficiency testing surveys. Proficiency testing survey results highlight infrequent, but recurrent, analytic and nonanalytic challenges in performing next- generation sequencing-based assays and point to remedies to help laboratories improve performance.
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Affiliation(s)
- Valentina Nardi
- From the Department of Pathology, Massachusetts General Hospital, Boston (Nardi)
| | - Karen D Tsuchiya
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington (Tsuchiya)
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Kim)
| | - Lora J H Bean
- Department of Pathology, PerkinElmer Genomics, Pittsburgh, Pennsylvania (Bean)
| | - Jaimie G Halley
- Proficiency Testing (Halley, Szelenger, Vasalos), Northfield, Illinois
| | | | | | - Patricia Vasalos
- Proficiency Testing (Halley, Szelenger, Vasalos), Northfield, Illinois
| | - John A Thorson
- College of American Pathologists, Northfield, Illinois; Department of Pathology, UC San Diego, Del Mar, California (Thorson)
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinc, Rochester, Minnesota (Moyer)
| | - Joel T Moncur
- the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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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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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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