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Hampel KJ, Gerrard DL, Francis D, Armstrong J, Cameron M, Ostafin A, Mahoney B, Malik M, Sidiropoulos N. When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform. J Appl Lab Med 2024; 9:716-727. [PMID: 38507614 DOI: 10.1093/jalm/jfae016] [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: 09/26/2023] [Accepted: 12/29/2023] [Indexed: 03/22/2024]
Abstract
BACKGROUND During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment. METHODS This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted. RESULTS Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months. CONCLUSIONS These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.
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Affiliation(s)
- Kenneth J Hampel
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Diana L Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Denise Francis
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Jordan Armstrong
- Technical Assistance Center for Biotek Products, Agilent Technologies Inc., Winooski, VT, United States
| | - Margaret Cameron
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Alexa Ostafin
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Briege Mahoney
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Miles Malik
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Nikoletta Sidiropoulos
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
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Lennerz JK, Salgado R, Kim GE, Sirintrapun SJ, Thierauf JC, Singh A, Indave I, Bard A, Weissinger SE, Heher YK, de Baca ME, Cree IA, Bennett S, Carobene A, Ozben T, Ritterhouse LL. Diagnostic quality model (DQM): an integrated framework for the assessment of diagnostic quality when using AI/ML. Clin Chem Lab Med 2023; 61:544-557. [PMID: 36696602 DOI: 10.1515/cclm-2022-1151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND Laboratory medicine has reached the era where promises of artificial intelligence and machine learning (AI/ML) seem palpable. Currently, the primary responsibility for risk-benefit assessment in clinical practice resides with the medical director. Unfortunately, there is no tool or concept that enables diagnostic quality assessment for the various potential AI/ML applications. Specifically, we noted that an operational definition of laboratory diagnostic quality - for the specific purpose of assessing AI/ML improvements - is currently missing. METHODS A session at the 3rd Strategic Conference of the European Federation of Laboratory Medicine in 2022 on "AI in the Laboratory of the Future" prompted an expert roundtable discussion. Here we present a conceptual diagnostic quality framework for the specific purpose of assessing AI/ML implementations. RESULTS The presented framework is termed diagnostic quality model (DQM) and distinguishes AI/ML improvements at the test, procedure, laboratory, or healthcare ecosystem level. The operational definition illustrates the nested relationship among these levels. The model can help to define relevant objectives for implementation and how levels come together to form coherent diagnostics. The affected levels are referred to as scope and we provide a rubric to quantify AI/ML improvements while complying with existing, mandated regulatory standards. We present 4 relevant clinical scenarios including multi-modal diagnostics and compare the model to existing quality management systems. CONCLUSIONS A diagnostic quality model is essential to navigate the complexities of clinical AI/ML implementations. The presented diagnostic quality framework can help to specify and communicate the key implications of AI/ML solutions in laboratory diagnostics.
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Affiliation(s)
- Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Grace E Kim
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Julia C Thierauf
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, German Cancer Research Center (DKFZ), Heidelberg University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, Heidelberg, Germany
| | - Ankit Singh
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | - Iciar Indave
- European Monitoring Centre for Drugs and Drug Addiction (EMCDDA), Lisbon, Portugal
| | - Adam Bard
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | | | - Yael K Heher
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | | | - Ian A Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Shannon Bennett
- Department of Laboratory Medicine and Pathology (DLMP), Mayo Clinic, Rochester, MN, USA
| | - Anna Carobene
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Tomris Ozben
- Medical Faculty, Dept. of Clinical Biochemistry, Akdeniz University, Antalya, Türkiye
- Medical Faculty, Clinical and Experimental Medicine, Ph.D. Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
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Vogeser M, Brüggemann M, Lennerz J, Stenzinger A, Gassner UM. Laboratory-Developed Tests in the New European Union 2017/746 Regulation: Opportunities and Risks. Clin Chem 2021; 68:40-42. [DOI: 10.1093/clinchem/hvab215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/21/2021] [Indexed: 01/20/2023]
Affiliation(s)
- Michael Vogeser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Germany
| | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig Holstein, Kiel, Germany
| | - Jochen Lennerz
- Center for Integrated Diagnostics, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | | | - Ulrich M Gassner
- Institute of Medical Device Law, Faculty of Law, University of Augsburg, Germany
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