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Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. Recommendations for Tumor Mutational Burden Assay Validation and Reporting: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. J Mol Diagn 2024; 26:653-668. [PMID: 38851389 DOI: 10.1016/j.jmoldx.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/05/2024] [Accepted: 05/07/2024] [Indexed: 06/10/2024] Open
Abstract
Tumor mutational burden (TMB) has been recognized as a predictive biomarker for immunotherapy response in several tumor types. Several laboratories offer TMB testing, but there is significant variation in how TMB is calculated, reported, and interpreted among laboratories. TMB standardization efforts are underway, but no published guidance for TMB validation and reporting is currently available. Recognizing the current challenges of clinical TMB testing, the Association for Molecular Pathology convened a multidisciplinary collaborative working group with representation from the American Society of Clinical Oncology, the College of American Pathologists, and the Society for the Immunotherapy of Cancer to review the laboratory practices surrounding TMB and develop recommendations for the analytical validation and reporting of TMB testing based on survey data, literature review, and expert consensus. These recommendations encompass pre-analytical, analytical, and postanalytical factors of TMB analysis, and they emphasize the relevance of comprehensive methodological descriptions to allow comparability between assays.
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Affiliation(s)
- Larissa V Furtado
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Carlo Bifulco
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Providence Portland Medical Center, Portland, Oregon
| | - Daniel Dolderer
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Jupiter Medical Center, Jupiter, Florida
| | - Susan J Hsiao
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Benjamin R Kipp
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Neal I Lindeman
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Weill Cornell Medicine, New York, New York
| | - Lauren L Ritterhouse
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Ahmet Zehir
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan A Nowak
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
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Zehir A, Nardi V, Konnick EQ, Lockwood CM, Long TA, Sidiropoulos N, Souers RJ, Vasalos P, Lindeman NI, Moncur JT. SPOT/Dx Pilot Reanalysis and College of American Pathologists Proficiency Testing for KRAS and NRAS Demonstrate Excellent Laboratory Performance. Arch Pathol Lab Med 2024; 148:139-148. [PMID: 37776255 DOI: 10.5858/arpa.2023-0322-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
CONTEXT.— The Sustainable Predictive Oncology Therapeutics and Diagnostics quality assurance pilot study (SPOT/Dx pilot) on molecular oncology next-generation sequencing (NGS) reportedly demonstrated performance limitations of NGS laboratory-developed tests, including discrepancies with a US Food and Drug Administration-approved companion diagnostic. The SPOT/Dx pilot methods differ from those used in proficiency testing (PT) programs. OBJECTIVE.— To reanalyze SPOT/Dx pilot data using PT program methods and compare to PT program data.Also see p. 136. DESIGN.— The College of American Pathologists (CAP) Molecular Oncology Committee reanalyzed SPOT/Dx pilot data applying PT program methods, adjusting for confounding conditions, and compared them to CAP NGS PT program performance (2019-2022). RESULTS.— Overall detection rates of KRAS and NRAS single-nucleotide variants (SNVs) and multinucleotide variants (MNVs) by SPOT/Dx pilot laboratories were 96.8% (716 of 740) and 81.1% (129 of 159), respectively. In CAP PT programs, the overall detection rates for the same SNVs and MNVs were 97.2% (2671 of 2748) and 91.8% (1853 of 2019), respectively. In 2022, the overall detection rate for 5 KRAS and NRAS MNVs in CAP PT programs was 97.3% (1161 of 1193). CONCLUSIONS.— CAP PT program data demonstrate that laboratories consistently have high detection rates for KRAS and NRAS variants. The SPOT/Dx pilot has multiple design and analytic differences with established PT programs. Reanalyzed pilot data that adjust for confounding conditions demonstrate that laboratories proficiently detect SNVs and less successfully detect rare to never-observed MNVs. The SPOT/Dx pilot results are not generalizable to all molecular oncology testing and should not be used to market products or change policy affecting all molecular oncology testing.
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Affiliation(s)
- Ahmet Zehir
- From the Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York (Zehir)
| | - Valentina Nardi
- the Department of Pathology, Massachusetts General Hospital, Mass General Brigham, Harvard Medical School, Boston (Nardi)
| | - Eric Q Konnick
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Christina M Lockwood
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Thomas A Long
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Nikoletta Sidiropoulos
- Pathology and Laboratory Medicine, University of Vermont Medical Center, Larner College of Medicine at the University of Vermont, Burlington (Sidiropoulos)
| | - Rhona J Souers
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos) Departments, College of American Pathologists, Northfield, Illinois
| | - Neal I Lindeman
- the Department of Pathology, Weill Cornell Medicine, New York, New York (Lindeman)
| | - Joel T Moncur
- the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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Harada S, Mackinnon AC. Navigating Next-Generation Sequencing Laboratory Developed Tests: A Critical Look at Proficiency Testing, US Food and Drug Administration Regulations, and Clinical Laboratory Performance. Arch Pathol Lab Med 2024; 148:136-138. [PMID: 37934951 DOI: 10.5858/arpa.2023-0477-ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2023] [Indexed: 11/09/2023]
Affiliation(s)
- Shuko Harada
- From the Department of Pathology, The University of Alabama, Birmingham
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Hagemann IS, Zehir A, Suarez CJ, Furtado LV, Halley J, Kane M, Mot N, Vasalos P, Moncur JT, Konnick EQ. In silico approaches to proficiency testing: Considerations for continued feasibility. J Mol Diagn 2023:S1525-1578(23)00079-X. [PMID: 37088136 DOI: 10.1016/j.jmoldx.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023] Open
Affiliation(s)
- Ian S Hagemann
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Stanford, California
| | - Larissa V Furtado
- Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jaimie Halley
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Megan Kane
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Nicole Mot
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Joel T Moncur
- Office of the Director, Joint Pathology Center, Silver Spring, MD
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.
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