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Dias-Santagata D, Heist RS, Bard AZ, da Silva AFL, Dagogo-Jack I, Nardi V, Ritterhouse LL, Spring LM, Jessop N, Farahani AA, Mino-Kenudson M, Allen J, Goyal L, Parikh A, Misdraji J, Shankar G, Jordan JT, Martinez-Lage M, Frosch M, Graubert T, Fathi AT, Hobbs GS, Hasserjian RP, Raje N, Abramson J, Schwartz JH, Sullivan RJ, Miller D, Hoang MP, Isakoff S, Ly A, Bouberhan S, Watkins J, Oliva E, Wirth L, Sadow PM, Faquin W, Cote GM, Hung YP, Gao X, Wu CL, Garg S, Rivera M, Le LP, John Iafrate A, Juric D, Hochberg EP, Clark J, Bardia A, Lennerz JK. Implementation and Clinical Adoption of Precision Oncology Workflows Across a Healthcare Network. Oncologist 2022; 27:930-939. [PMID: 35852437 PMCID: PMC9632318 DOI: 10.1093/oncolo/oyac134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Precision oncology relies on molecular diagnostics, and the value-proposition of modern healthcare networks promises a higher standard of care across partner sites. We present the results of a clinical pilot to standardize precision oncology workflows. METHODS Workflows are defined as the development, roll-out, and updating of disease-specific molecular order sets. We tracked the timeline, composition, and effort of consensus meetings to define the combination of molecular tests. To assess clinical impact, we examined order set adoption over a two-year period (before and after roll-out) across all gastrointestinal and hepatopancreatobiliary (GI) malignancies, and by provider location within the network. RESULTS Development of 12 disease center-specific order sets took ~9 months, and the average number of tests per indication changed from 2.9 to 2.8 (P = .74). After roll-out, we identified significant increases in requests for GI patients (17%; P < .001), compliance with testing recommendations (9%; P < .001), and the fraction of "abnormal" results (6%; P < .001). Of 1088 GI patients, only 3 received targeted agents based on findings derived from non-recommended orders (1 before and 2 after roll-out); indicating that our practice did not negatively affect patient treatments. Preliminary analysis showed 99% compliance by providers in network sites, confirming the adoption of the order sets across the network. CONCLUSION Our study details the effort of establishing precision oncology workflows, the adoption pattern, and the absence of harm from the reduction of non-recommended orders. Establishing a modifiable communication tool for molecular testing is an essential component to optimize patient care via precision oncology.
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Affiliation(s)
- Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Adam Z Bard
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura M Spring
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Nicholas Jessop
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander A Farahani
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jill Allen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Aparna Parikh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joseph Misdraji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Present affiliation: Department of Pathology, Yale University, New Haven, CT, USA
| | - Ganesh Shankar
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Justin T Jordan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew Frosch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Timothy Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Amir T Fathi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Gabriela S Hobbs
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Noopur Raje
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jeremy Abramson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joel H Schwartz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - David Miller
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven Isakoff
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Bouberhan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jaclyn Watkins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lori Wirth
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - William Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory M Cote
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Gao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Salil Garg
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Miguel Rivera
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ephraim P Hochberg
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Clark
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Thierauf JC, Farahani AA, Indave BI, Bard AZ, White VA, Smith CR, Marble H, Hyrcza MD, Chan JKC, Bishop J, Shi Q, Ely K, Agaimy A, Martinez-Lage M, Nose V, Rivera M, Nardi V, Dias-Santagata D, Garg S, Sadow P, Le LP, Faquin W, Ritterhouse LL, Cree IA, Iafrate AJ, Lennerz JK. Diagnostic Value of MAML2 Rearrangements in Mucoepidermoid Carcinoma. Int J Mol Sci 2022; 23:4322. [PMID: 35457138 PMCID: PMC9026998 DOI: 10.3390/ijms23084322] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023] Open
Abstract
Mucoepidermoid carcinoma (MEC) is often seen in salivary glands and can harbor MAML2 translocations (MAML2+). The translocation status has diagnostic utility as an objective confirmation of the MEC diagnosis, for example, when distinction from the more aggressive adenosquamous carcinoma (ASC) is not straightforward. To assess the diagnostic relevance of MAML2, we examined our 5-year experience in prospective testing of 8106 solid tumors using RNA-seq panel testing in combinations with a two-round Delphi-based scenario survey. The prevalence of MAML2+ across all tumors was 0.28% (n = 23/8106) and the majority of MAML2+ cases were found in head and neck tumors (78.3%), where the overall prevalence was 5.9% (n = 18/307). The sensitivity of MAML2 for MEC was 60% and most cases (80%) were submitted for diagnostic confirmation; in 24% of cases, the MAML2 results changed the working diagnosis. An independent survey of 15 experts showed relative importance indexes of 0.8 and 0.65 for "confirmatory MAML2 testing" in suspected MEC and ASC, respectively. Real-world evidence confirmed that the added value of MAML2 is a composite of an imperfect confirmation test for MEC and a highly specific exclusion tool for the diagnosis of ASC. Real-world evidence can help move a rare molecular-genetic biomarker from an emerging tool to the clinic.
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Affiliation(s)
- Julia C. Thierauf
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alex A. Farahani
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - B. Iciar Indave
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - Adam Z. Bard
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Valerie A. White
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - Cameron R. Smith
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Hetal Marble
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Martin D. Hyrcza
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB 2500, Canada;
| | - John K. C. Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China;
| | - Justin Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Qiuying Shi
- Department of Pathology, Emory University Hospital, Atlanta, GA 30322, USA;
| | - Kim Ely
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - Abbas Agaimy
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, 91054 Erlangen, Germany;
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Vania Nose
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Miguel Rivera
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Valentina Nardi
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Dora Dias-Santagata
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Salil Garg
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Peter Sadow
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Long P. Le
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - William Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Lauren L. Ritterhouse
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - A. John Iafrate
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Jochen K. Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
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3
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Siravegna G, O'Boyle CJ, Varmeh S, Queenan N, Michel A, Stein J, Thierauf J, Sadow PM, Faquin WC, Perry SK, Bard AZ, Wang W, Deschler DG, Emerick KS, Varvares MA, Park JC, Clark JR, Chan AW, Andreu Arasa VC, Sakai O, Lennerz J, Corcoran RB, Wirth LJ, Lin DT, Iafrate AJ, Richmon JD, Faden DL. Cell free HPV DNA provides an accurate and rapid diagnosis of HPV-associated head and neck cancer. Clin Cancer Res 2021; 28:719-727. [PMID: 34857594 DOI: 10.1158/1078-0432.ccr-21-3151] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE HPV-associated Head and Neck Squamous Cell Carcinoma(HPV+HNSCC) is the most common HPV-associated malignancy in the United States and continues to increase in incidence. Current diagnostic approaches for HPV+HNSCC rely on tissue biopsy followed by histomorphologic assessment and detection of HPV indirectly by p16 immunohistochemistry. Such approaches are invasive and have variable sensitivity. EXPERIMENTAL DESIGN We conducted a prospective observational study in 140 subjects (70 cases and 70 controls) to test the hypothesis that a non-invasive diagnostic approach for HPV+HNSCC would have improved diagnostic accuracy, lower cost, and shorter Diagnostic Interval compared to standard approaches. Blood was collected, processed for circulating tumor HPV DNA(ctHPVDNA) and analyzed with custom ddPCR assays for HPV genotypes 16,18, 33, 35 and 45. Diagnostic performance, cost and Diagnostic Interval were calculated for standard clinical work up and compared to a non-invasive approach using ctHPVDNA combined with cross-sectional imaging and physical exam findings. RESULTS Sensitivity and specificity of ctHPVDNA for detecting HPV+HNSCC was 98.4% and 98.6%. Sensitivity and specificity of a composite non-invasive diagnostic using ctHPVDNA and imaging/physical exam were 95.1% and 98.6%. Diagnostic accuracy of this non-invasive approach was significantly higher than standard of care (Youden index 0.937 vs 0.707, p=0.0006). Costs of non-invasive diagnostic were 36-38% less than standard clinical work up and the median Diagnostic Interval was 26 days less. CONCLUSIONS A non-invasive diagnostic approach for HPV+HNSCC demonstrated improved accuracy, reduced cost and a shorter time to diagnosis compared to standard clinical workup and could be a viable alternative in the future.
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Affiliation(s)
| | - Connor J O'Boyle
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear
| | | | - Natalia Queenan
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear
| | | | - Jarrod Stein
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Broad Institute
| | - Julia Thierauf
- Department of Otolaryngology, Head and Neck Surgery, 1985
| | | | | | - Simon K Perry
- Department of Pathology, Massachusetts General Hospital
| | - Adam Z Bard
- Department of Pathology, Massachusetts General Hospital
| | - Wei Wang
- 6. Departments of Medicine and Neurology, Brigham and Women's Hospital
| | - Daniel G Deschler
- Otology and Laryngology, Massachusetts Eye and Ear Infirmary and Harvard Medical School
| | - Kevin S Emerick
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Broad Institute
| | - Mark A Varvares
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary,, Harvard Medical School
| | - Jong C Park
- Hematology and Oncology, Massachusetts General Hospital
| | - John R Clark
- Hematology and Oncology, Massachusetts General Hospital/Harvard Medical School
| | - Annie W Chan
- Radiation Oncology, Massachusetts General Hospital
| | | | - Osamu Sakai
- Department or Radiology, Boston Medical Center
| | | | | | - Lori J Wirth
- Department of Medicine, Massachusetts General Hospital
| | | | | | - Jeremy D Richmon
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Broad Institute
| | - Daniel L Faden
- Otolaryngology-Head and Neck Suirgery, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Broad Institute
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Miller TE, Garcia Beltran WF, Bard AZ, Gogakos T, Anahtar MN, Astudillo MG, Yang D, Thierauf J, Fisch AS, Mahowald GK, Fitzpatrick MJ, Nardi V, Feldman J, Hauser BM, Caradonna TM, Marble HD, Ritterhouse LL, Turbett SE, Batten J, Georgantas NZ, Alter G, Schmidt AG, Harris JB, Gelfand JA, Poznansky MC, Bernstein BE, Louis DN, Dighe A, Charles RC, Ryan ET, Branda JA, Pierce VM, Murali MR, Iafrate AJ, Rosenberg ES, Lennerz JK. Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J 2020; 34:13877-13884. [PMID: 32856766 PMCID: PMC7461169 DOI: 10.1096/fj.202001700rr] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
The diagnosis of COVID-19 requires integration of clinical and laboratory data. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic assays play a central role in diagnosis and have fixed technical performance metrics. Interpretation becomes challenging because the clinical sensitivity changes as the virus clears and the immune response emerges. Our goal was to examine the clinical sensitivity of two most common SARS-CoV-2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. We conducted a single-center, retrospective study. To derive clinical sensitivity of PCR, we identified 209 PCR-positive SARS-CoV-2 patients with multiple PCR test results (624 total PCR tests) and calculated daily sensitivity from date of symptom onset or first positive test. Clinical sensitivity of PCR decreased with days post symptom onset with >90% clinical sensitivity during the first 5 days after symptom onset, 70%-71% from Days 9 to 11, and 30% at Day 21. To calculate daily clinical sensitivity by serology, we utilized 157 PCR-positive patients with a total of 197 specimens tested by enzyme-linked immunosorbent assay for IgM, IgG, and IgA anti-SARS-CoV-2 antibodies. In contrast to PCR, serological sensitivity increased with days post symptom onset with >50% of patients seropositive by at least one antibody isotype after Day 7, >80% after Day 12, and 100% by Day 21. Taken together, PCR and serology are complimentary modalities that require time-dependent interpretation. Superimposition of sensitivities over time indicate that serology can function as a reliable diagnostic aid indicating recent or prior infection.
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Affiliation(s)
- Tyler E. Miller
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Adam Z. Bard
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Tasos Gogakos
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Melis N. Anahtar
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Diane Yang
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Julia Thierauf
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Adam S. Fisch
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Grace K. Mahowald
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Megan J. Fitzpatrick
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Valentina Nardi
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | | | | | - Hetal D. Marble
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Lauren L. Ritterhouse
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Sara E. Turbett
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Julie Batten
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | | | - Jason B. Harris
- Division of Infectious DiseasesDepartment of PediatricsMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jeffrey A. Gelfand
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Mark C. Poznansky
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Bradley E. Bernstein
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - David N. Louis
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Anand Dighe
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Richelle C. Charles
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Edward T. Ryan
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - John A. Branda
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Virginia M. Pierce
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of PediatricsMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Mandakolathur R. Murali
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Allergy and ImmunologyDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - A. John Iafrate
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Eric S. Rosenberg
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jochen K. Lennerz
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
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