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Mac S, Shi S, Millson B, Tehrani A, Eberg M, Myageri V, Langley JM, Simpson S. Burden of illness associated with Respiratory Syncytial Virus (RSV)-related hospitalizations among adults in Ontario, Canada: A retrospective population-based study. Vaccine 2023; 41:5141-5149. [PMID: 37422377 DOI: 10.1016/j.vaccine.2023.06.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Globally, RSV is a common viral pathogen that causes 64 million acute respiratory infections annually. Our objective was to determine the incidence of hospitalization, healthcare resource use and associated costs of adults hospitalized with RSV in Ontario, Canada. METHODS To describe the epidemiology of adults hospitalized with RSV, we used a validated algorithm applied to a population-based healthcare utilization administrative dataset in Ontario, Canada. We created a retrospective cohort of incident hospitalized adults with RSV between September 2010 and August 2017 and followed each person for up to two years. To determine the burden of illness associated with hospitalization and post-discharge healthcare encounters each RSV-admitted patient was matched to two unexposed controls based on demographics and risk factors. Patient demographics were described and mean attributable 6-month and 2-year healthcare costs (2019 Canadian dollars) were estimated. RESULTS There were 7,091 adults with RSV-associated hospitalizations between 2010 and 2019 with a mean age of 74.6 years; 60.4 % were female. RSV-coded hospitalization rates increased from 1.4 to 14.6 per 100,000 adults between 2010-2011 and 2018-2019. The mean difference in healthcare costs between RSV-admitted patients and matched controls was $28,260 (95 % CI: $27,728 - $28,793) in the first 6 months and $43,721 over 2 years (95 % CI: $40,383 - $47,059) post-hospitalization. CONCLUSIONS RSV hospitalizations among adults increased in Ontario between 2010/11 to 2018/19 RSV seasons. RSV hospitalizations in adults were associated with increased attributable short-term and long-term healthcare costs compared to matched controls. Interventions that could prevent RSV in adults may reduce healthcare burden.
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Affiliation(s)
| | | | | | | | | | | | - Joanne M Langley
- Canadian Center for Vaccinology (Dalhousie University, IWK Health and Nova Scotia Health) Halifax, Nova Scotia, Canada
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Li MM, Cottrell CE, Pullambhatla M, Roy S, Temple-Smolkin RL, Turner SA, Wang K, Zhou Y, Vnencak-Jones CL. Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology. J Mol Diagn 2023; 25:69-86. [PMID: 36503149 DOI: 10.1016/j.jmoldx.2022.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance. In the implementation survey, 71% (157/220) of respondents have implemented the 2017 guidelines for variant classification and reporting either with or without modifications. Collectively, this study demonstrates that, although they may not yet be optimized, the 2017 guideline recommendations are being adopted for standardized somatic variant classification. The working group identified significant areas for future guideline improvement, including the need for a more granular and comprehensive classification system and education resources to meet the growing needs of both laboratory professionals and medical oncologists.
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Affiliation(s)
- Marilyn M Li
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Catherine E Cottrell
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Somak Roy
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Scott A Turner
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Kai Wang
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy L Vnencak-Jones
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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Grafodatskaya D, O'Rielly DD, Bedard K, Butcher DT, Howlett CJ, Lytwyn A, McCready E, Parboosingh J, Spriggs EL, Vaags AK, Stockley TL. Practice guidelines for BRCA1/2 tumour testing in ovarian cancer. J Med Genet 2022; 59:727-736. [PMID: 35393334 PMCID: PMC9340048 DOI: 10.1136/jmedgenet-2021-108238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/24/2022] [Indexed: 12/26/2022]
Abstract
The purpose of this document is to provide pre-analytical, analytical and post-analytical considerations and recommendations to Canadian clinical laboratories developing, validating and offering next-generation sequencing (NGS)-based BRCA1 and BRCA2 (BRCA1/2) tumour testing in ovarian cancers. This document was drafted by the members of the Canadian College of Medical Geneticists (CCMG) somatic BRCA Ad Hoc Working Group, and representatives from the Canadian Association of Pathologists. The document was circulated to the CCMG members for comment. Following incorporation of feedback, this document has been approved by the CCMG board of directors. The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada; however, they are not inclusive of all information laboratories should consider in the validation and use of NGS for BRCA1/2 tumour testing in ovarian cancers.
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Affiliation(s)
- Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Darren D O'Rielly
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Centre for Translational Genomes & Division of Genetics, Eastern Regional Health Authority, St. John's, Newfoundland, Canada
| | - Karine Bedard
- Département de Pathologie et Biologie cellulaire, Université de Montréal, Montreal, Québec, Canada.,Laboratoire de Diagnostic Moléculaire, Centre hospitalier de l'Université de Montréal, Montreal, Québec, Canada
| | - Darci T Butcher
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Wester University, London, Ontario, Canada
| | - Alice Lytwyn
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, Alberta Children's Hospital Research Institute for Child and Maternal Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Genetics and Genomics, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Elizabeth L Spriggs
- Genomics, Diagnostic Services, Shared Health Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrea K Vaags
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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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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From Information Overload to Actionable Insights: Digital Solutions for Interpreting Cancer Variants from Genomic Testing. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2040027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Given the increase in genomic testing in routine clinical use, there is a growing need for digital technology solutions to assist pathologists, oncologists, and researchers in translating variant calls into actionable knowledge to personalize patient management plans. In this article, we discuss the challenges facing molecular geneticists and medical oncologists in working with test results from next-generation sequencing for somatic oncology, and propose key considerations for implementing a decision support software to aid the interpretation of clinically important variants. In addition, we review results from an example decision support software, NAVIFY Mutation Profiler. NAVIFY Mutation Profiler is a cloud-based software that provides curation, annotation, interpretation, and reporting of somatic variants identified by next-generation sequencing. The software reports a tiered classification based on consensus recommendations from AMP, ASCO, CAP, and ACMG. Studies with NAVIFY Mutation Profiler demonstrated that the software provided timely updates and accurate curation, as well as interpretation of variant combinations, demonstrating that decision support tools can help advance implementation of precision oncology.
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Giles HH, Hegde MR, Lyon E, Stanley CM, Kerr ID, Garlapow ME, Eggington JM. The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy. Annu Rev Genomics Hum Genet 2021; 22:285-307. [PMID: 33900788 DOI: 10.1146/annurev-genom-121620-082709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value thatincorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts.
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Affiliation(s)
- Hunter H Giles
- Center for Genomic Interpretation, Sandy, Utah 84092, USA; , ,
| | - Madhuri R Hegde
- PerkinElmer Genomics, Waltham, Massachusetts 02450, USA; .,Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, Huntsville, Alabama 35806, USA;
| | - Christine M Stanley
- C2i Genomics, Cambridge, Massachusetts 02139, USA.,Variantyx, Framingham, Massachusetts 01701, USA;
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