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Morgan G, Casalino S, Chowdhary S, Frangione E, Fung CYJ, Lapadula E, Arnoldo S, Bearss E, Binnie A, Borgundvaag B, Briollais L, Dagher M, Devine L, Friedman SM, Khan Z, Mighton C, Nirmalanathan K, Richardson D, Stern S, Taher A, Wolday D, Lerner-Ellis J, Taher J. COVID-19 vaccine reactogenicity among participants enrolled in the GENCOV study. Vaccine 2024; 42:2733-2739. [PMID: 38521677 DOI: 10.1016/j.vaccine.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND GENCOV is a prospective, observational cohort study of COVID-19-positive adults. Here, we characterize and compare side effects between COVID-19 vaccines and determine whether reactogenicity is exacerbated by prior SARS-CoV-2 infection. METHODS Participants were recruited across Ontario, Canada. Participant-reported demographic and COVID-19 vaccination data were collected using a questionnaire. Multivariable logistic regression was performed to assess whether vaccine manufacturer, type, and previous SARS-CoV-2 infection are associated with reactogenicity. RESULTS Responses were obtained from n = 554 participants. Tiredness and localized side effects were the most common reactions across vaccine doses. For most participants, side effects occurred and subsided within 1-2 days. Recipients of Moderna mRNA and AstraZeneca vector vaccines reported reactions more frequently compared to recipients of a Pfizer-BioNTech mRNA vaccine. Previous SARS-CoV-2 infection was independently associated with developing side effects. CONCLUSIONS We provide evidence of relatively mild and short-lived reactions reported by participants who have received approved COVID-19 vaccines.
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Affiliation(s)
- Gregory Morgan
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Selina Casalino
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sunakshi Chowdhary
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Erika Frangione
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chun Yiu Jordan Fung
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Elisa Lapadula
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Saranya Arnoldo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Erin Bearss
- Mount Sinai Academic Family Health Team, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
| | - Alexandra Binnie
- Department of Critical Care, William Osler Health System, Etobicoke, ON M9V 1R8, Canada
| | - Bjug Borgundvaag
- Schwartz/Reisman Emergency Medicine Institute, Sinai Health System, Toronto, ON M5G 2A2, Canada
| | | | - Marc Dagher
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Women's College Hospital, Toronto, ON M5S 1B2, Canada
| | - Luke Devine
- Division of General Internal Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Steven M Friedman
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Emergency Medicine, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Zeeshan Khan
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada
| | - Chloe Mighton
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1A6, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
| | | | | | - Seth Stern
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada
| | - Ahmed Taher
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada; Division of Emergency Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Dawit Wolday
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jennifer Taher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Panchal S, Mahajan R, Aujla N, McKay P, Casalino S, Di Gioacchino V, Charames GS, Lefebvre M, Metcalfe KA, Akbari MR, McCuaig JM, Lerner-Ellis J. Recontact to return new or updated PALB2 genetic results in the clinical laboratory setting. J Med Genet 2024; 61:477-482. [PMID: 38124008 DOI: 10.1136/jmg-2023-109652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE The purpose of this study was to recontact individuals with clinically actionable test results identified through a retrospective research study and to provide a framework for laboratories to recontact patients. METHODS Genetic testing was conducted on 2977 individuals originally referred for BRCA1 and BRCA2 hereditary breast and ovarian cancer testing that had a negative genetic test result. A gene panel was used to identify pathogenic variants in known or newly discovered genes that could explain the underlying cause of disease; however, analysis was restricted to PALB2 for the purposes of this study. A patient recontact decision tree was developed to assist in the returning of updated genetic test results to clinics and patients. RESULTS Novel clinically actionable pathogenic variants were identified in the PALB2 gene in 18 participants (0.6%), the majority of whom were recontacted with their new or updated genetic test results. Eight individuals were unable to be recontacted; five individuals had already learnt about their new or updated findings from genetic testing outside the context of this study; three individuals prompted cascade testing in family members; two individuals were deceased. CONCLUSION Novel pathogenic variants in PALB2 were identified in 18 individuals through retrospective gene panel testing. Recontacting these individuals regarding these new or updated findings had a range of outcomes. The process of conveying genomic results within this framework can be effectively accomplished while upholding patient autonomy, potentially leading to advantageous outcomes for patients and their families.
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Affiliation(s)
- Seema Panchal
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Radhika Mahajan
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Navneet Aujla
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Paul McKay
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Selina Casalino
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - George S Charames
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Maude Lefebvre
- Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Kelly A Metcalfe
- Lawrence S Bloomberg Faculty of Nursing, University of Toronto, Toronto, Ontario, Canada
- Women's College Research Institute, Toronto, Ontario, Canada
| | | | - Jeanna Marie McCuaig
- University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
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3
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Mighton C, Noor A, Watkins N, Di Gioacchino V, Lerner-Ellis J, Wong A, Mukharryamova E, Anggala N, Chitayat D, Greenfeld E. Validation of low-pass genome sequencing for prenatal diagnosis. Prenat Diagn 2024; 44:443-453. [PMID: 38279846 DOI: 10.1002/pd.6525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/11/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024]
Abstract
OBJECTIVE Chromosomal microarray (CMA), while considered the gold standard for detecting copy number variants (CNVs) in prenatal diagnostics, has its limitations, including the necessity to replace aging microarray equipment, low throughput, a static design, and an inefficient multi-day workflow. This study evaluates the feasibility of low-pass genome sequencing (LP-GS) as a potential replacement for CMA in prenatal diagnostics. METHODS We comprehensively compared LP-GS at 10x and 5x average depths with CMA in a prenatal laboratory. We examined parameters, including concordance, sensitivity, specificity, workflow efficiency, and cost-effectiveness. RESULTS We found a high degree of agreement between LP-GS and CMA for detecting CNVs and absence of heterozygosity. Furthermore, compared to CMA, LP-GS increased workflow efficiency and proved to be cost-neutral at 10x and cost-effective at 5x. CONCLUSION Our study suggests that LP-GS is a promising alternative to CMA in prenatal diagnostics, offering advantages, including a more efficient workflow and scalability for larger testing volumes. Importantly, for clinical laboratories that have adopted next-generation sequencing in a separate capacity, LP-GS facilitates a unified NGS-centric approach, enabling workflow consolidation. By offering a single, streamlined platform for detecting a broad range of genetic variants, LP-GS may represent a critical step toward enhancing the diagnostic capabilities of prenatal laboratories.
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Affiliation(s)
- Chloe Mighton
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Institute of Health Policy Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Abdul Noor
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Wong
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elvira Mukharryamova
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nina Anggala
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elena Greenfeld
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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4
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Garg E, Arguello-Pascualli P, Vishnyakova O, Halevy AR, Yoo S, Brooks JD, Bull SB, Gagnon F, Greenwood CMT, Hung RJ, Lawless JF, Lerner-Ellis J, Dennis JK, Abraham RJS, Garant JM, Thiruvahindrapuram B, Jones SJM, Strug LJ, Paterson AD, Sun L, Elliott LT. Canadian COVID-19 host genetics cohort replicates known severity associations. PLoS Genet 2024; 20:e1011192. [PMID: 38517939 PMCID: PMC10990181 DOI: 10.1371/journal.pgen.1011192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 04/03/2024] [Accepted: 02/22/2024] [Indexed: 03/24/2024] Open
Abstract
The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X chromosome; conducted rare variant gene-based analysis and polygenic risk score testing. Population stratification was adjusted for using meta-analysis across ancestry groups. We replicated two loci identified by the HGI for COVID-19 severity: the LZTFL1/SLC6A20 locus on chromosome 3 and the FOXP4 locus on chromosome 6 (the latter with a variant significant at P < 5E-8). We found novel significant associations with MRAS and WDR89 in gene-based analyses, and constructed a polygenic risk score that explained 1.01% of the variance in severe COVID-19. This study provides independent evidence confirming the robustness of previously identified COVID-19 severity loci by the HGI and identifies novel genes for further investigation.
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Affiliation(s)
- Elika Garg
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paola Arguello-Pascualli
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Olga Vishnyakova
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Anat R. Halevy
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Samantha Yoo
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer D. Brooks
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Shelley B. Bull
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Celia M. T. Greenwood
- Gerald Bronfman Department of Oncology, Department of Epidemiology, Biostatistics and Occupational Health, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Rayjean J. Hung
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Jerald F. Lawless
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica K. Dennis
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rohan J. S. Abraham
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jean-Michel Garant
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Lisa J. Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Lei Sun
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Lloyd T. Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
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5
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Fung CYJ, Scott M, Lerner-Ellis J, Taher J. Applications of SARS-CoV-2 serological testing: impact of test performance, sample matrices, and patient characteristics. Crit Rev Clin Lab Sci 2024; 61:70-88. [PMID: 37800891 DOI: 10.1080/10408363.2023.2254390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023]
Abstract
Laboratory testing has been a key tool in managing the SARS-CoV-2 global pandemic. While rapid antigen and PCR testing has proven useful for diagnosing acute SARS-CoV-2 infections, additional testing methods are required to understand the long-term impact of SARS-CoV-2 infections on immune response. Serological testing, a well-documented laboratory practice, measures the presence of antibodies in a sample to uncover information about host immunity. Although proposed applications of serological testing for clinical use have previously been limited, current research into SARS-CoV-2 has shown growing utility for serological methods in these settings. To name a few, serological testing has been used to identify patients with past infections and long-term active disease and to monitor vaccine efficacy. Test utility and result interpretation, however, are often complicated by factors that include poor test sensitivity early in infection, lack of immune response in some individuals, overlying infection and vaccination responses, lack of standardization of antibody titers/levels between instruments, unknown titers that confer immune protection, and large between-individual biological variation following infection or vaccination. Thus, the three major components of this review will examine (1) factors that affect serological test utility: test performance, testing matrices, seroprevalence concerns and viral variants, (2) patient factors that affect serological response: timing of sampling, age, sex, body mass index, immunosuppression and vaccination, and (3) informative applications of serological testing: identifying past infection, immune surveillance to guide health practices, and examination of protective immunity. SARS-CoV-2 serological testing should be beneficial for clinical care if it is implemented appropriately. However, as with other laboratory developed tests, use of SARS-CoV-2 serology as a testing modality warrants careful consideration of testing limitations and evaluation of its clinical utility.
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Affiliation(s)
- Chun Yiu Jordan Fung
- Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Mackenzie Scott
- Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Taher
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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6
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Baltzan I, Knoppers BM, Nemetz ETA, Lerner-Ellis J, Bernier A, Devon K. The Deceased, Public Health, and Research: Proposing Legal Reforms. Biopreserv Biobank 2023. [PMID: 37943606 DOI: 10.1089/bio.2023.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
There is little guidance concerning biomedical research using tissues from deceased individuals. Unique ethical and legal challenges gained visibility during the coronavirus disease 2019 (COVID-19) pandemic, when important studies using genome sequencing required access to biological materials from deceased individuals. These studies proposed to determine whether specific genomic profiles were associated with important disease outcomes. Such research has previously required consent from next-of-kin or other surrogate decision makers. Ethics waivers for such consent vary within Canada. In Ontario, research ethics boards can grant waivers of consent if the Tri-Council Policy Statement-2 conditions are met. These include that the individual is not harmed, that the materials are essential to the research, and that privacy will be protected. Conversely, in Quebec, Civil Code article 22 imposes an obligation on researchers to seek consent from next-of-kin or another surrogate decision maker with no option for waivers. It became evident to researchers that these standards can sometimes impose an impracticable balance of risks and benefits, especially in public health emergencies. We seek to establish why and when consent requirements should be waived for public health and research involving the tissues of deceased individuals.
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Affiliation(s)
- Isabel Baltzan
- McGill University Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine and Health Sciences, Montreal, Canada
| | - Bartha Maria Knoppers
- McGill University Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine and Health Sciences, Montreal, Canada
| | | | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health and Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Alexander Bernier
- McGill University Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine and Health Sciences, Montreal, Canada
| | - Karen Devon
- Department of Surgery and Joint Centre for Bioethics, University of Toronto and Women's College Hospital and University Health Network, Toronto, Canada
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7
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Claus LR, Chen C, Stallworth J, Turner JL, Slaats GG, Hawks AL, Mabillard H, Senum SR, Srikanth S, Flanagan-Steet H, Louie RJ, Silver J, Lerner-Ellis J, Morel C, Mighton C, Sleutels F, van Slegtenhorst M, van Ham T, Brooks AS, Dorresteijn EM, Barakat TS, Dahan K, Demoulin N, Goffin EJ, Olinger E, Larsen M, Hertz JM, Lilien MR, Obeidová L, Seeman T, Stone HK, Kerecuk L, Gurgu M, Yousef Yengej FA, Ammerlaan CME, Rookmaaker MB, Hanna C, Rogers RC, Duran K, Peters E, Sayer JA, van Haaften G, Harris PC, Ling K, Mason JM, van Eerde AM, Steet R. Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease. Kidney Int 2023; 104:995-1007. [PMID: 37598857 PMCID: PMC10592035 DOI: 10.1016/j.kint.2023.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) resulting from pathogenic variants in PKD1 and PKD2 is the most common form of PKD, but other genetic causes tied to primary cilia function have been identified. Biallelic pathogenic variants in the serine/threonine kinase NEK8 cause a syndromic ciliopathy with extra-kidney manifestations. Here we identify NEK8 as a disease gene for ADPKD in 12 families. Clinical evaluation was combined with functional studies using fibroblasts and tubuloids from affected individuals. Nek8 knockout mouse kidney epithelial (IMCD3) cells transfected with wild type or variant NEK8 were further used to study ciliogenesis, ciliary trafficking, kinase function, and DNA damage responses. Twenty-one affected monoallelic individuals uniformly exhibited cystic kidney disease (mostly neonatal) without consistent extra-kidney manifestations. Recurrent de novo mutations of the NEK8 missense variant p.Arg45Trp, including mosaicism, were seen in ten families. Missense variants elsewhere within the kinase domain (p.Ile150Met and p.Lys157Gln) were also identified. Functional studies demonstrated normal localization of the NEK8 protein to the proximal cilium and no consistent cilia formation defects in patient-derived cells. NEK8-wild type protein and all variant forms of the protein expressed in Nek8 knockout IMCD3 cells were localized to cilia and supported ciliogenesis. However, Nek8 knockout IMCD3 cells expressing NEK8-p.Arg45Trp and NEK8-p.Lys157Gln showed significantly decreased polycystin-2 but normal ANKS6 localization in cilia. Moreover, p.Arg45Trp NEK8 exhibited reduced kinase activity in vitro. In patient derived tubuloids and IMCD3 cells expressing NEK8-p.Arg45Trp, DNA damage signaling was increased compared to healthy passage-matched controls. Thus, we propose a dominant-negative effect for specific heterozygous missense variants in the NEK8 kinase domain as a new cause of PKD.
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Affiliation(s)
- Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Gisela G Slaats
- Department of Nephrology and Hypertension, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra L Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Holly Mabillard
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sujata Srikanth
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Raymond J Louie
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Josh Silver
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Chantal Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eiske M Dorresteijn
- Department of Pediatric Nephrology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karin Dahan
- Institute Pathology and Genetic, Center of Human Genetics, Charleroi, Belgium
| | - Nathalie Demoulin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Jean Goffin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Olinger
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Martin Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Lena Obeidová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics, University Hospital Ostrava, Ostrava, Czech Republic; Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Larissa Kerecuk
- Birmingham Women's and Children's National Health Services (NHS) Foundation Trust, National Institute for Health Care and Research (NIHR) Clinical Research Network (CRN) West Midlands, Birmingham, UK
| | - Mihai Gurgu
- Fundeni Clinical Institute, Bucharest, Romania
| | - Fjodor A Yousef Yengej
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christian Hanna
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - R Curtis Rogers
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Karen Duran
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edith Peters
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John A Sayer
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK; National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Newcastle, UK
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Richard Steet
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA.
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8
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Wang Y, Ding Q, Prokopec S, Farncombe KM, Bruce J, Casalino S, McCuaig J, Szybowska M, van Engelen K, Lerner-Ellis J, Pugh TJ, Kim RH. Germline whole genome sequencing in adults with multiple primary tumors. Fam Cancer 2023; 22:513-520. [PMID: 37481477 DOI: 10.1007/s10689-023-00343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 07/24/2023]
Abstract
Multiple primary tumors (MPTs) are a harbinger of hereditary cancer syndromes. Affected individuals often fit genetic testing criteria for a number of hereditary cancer genes and undergo multigene panel testing. Other genomic testing options, such as whole exome (WES) and whole genome sequencing (WGS) are available, but the utility of these genomic approaches as a second-tier test for those with uninformative multigene panel testing has not been explored. Here, we report our germline sequencing results from WGS in 9 patients with MPTs who had non-informative multigene panel testing. Following germline WGS, sequence (agnostic or 735 selected genes) and copy number variant (CNV) analysis was performed according to the American College of Medical Genetics (ACMG) standards and guidelines for interpreting sequence variants and reporting CNVs. In this cohort, WGS, as a second-tier test, did not identify additional pathogenic or likely pathogenic variants in cancer predisposition genes. Although we identified a CHEK2 likely pathogenic variant and a MUTYH pathogenic variant, both were previously identified in the multigene panels and were not explanatory for the presented type of tumors. CNV analysis also failed to identify any pathogenic or likely pathogenic variants in cancer predisposition genes. In summary, after multigene panel testing, WGS did not reveal any additional pathogenic variants in patients with MPTs. Our study, based on a small cohort of patients with MPT, suggests that germline gene panel testing may be sufficient to investigate these cases. Future studies with larger sample sizes may further elucidate the additional utility of WGS in MPTs.
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Affiliation(s)
- Yiming Wang
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qiliang Ding
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephenie Prokopec
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeffrey Bruce
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Selina Casalino
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Jeanna McCuaig
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marta Szybowska
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kalene van Engelen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- London Health Science Centre, London, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
| | - Jordan Lerner-Ellis
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raymond H Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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9
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Morgan G, Casalino S, Chowdhary S, Frangione E, Fung CYJ, Haller S, Lapadula E, Scott M, Wolday D, Young J, Arnoldo S, Aujla N, Bearss E, Binnie A, Bombard Y, Borgundvaag B, Briollais L, Dagher M, Devine L, Faghfoury H, Friedman SM, Gingras AC, Goneau LW, Khan Z, Mazzulli T, McLeod SL, Nomigolzar R, Noor A, Pugh TJ, Richardson D, Satnam Singh HK, Simpson J, Stern S, Strug L, Taher A, Lerner-Ellis J, Taher J. Characterizing Risk Factors for Hospitalization and Clinical Characteristics in a Cohort of COVID-19 Patients Enrolled in the GENCOV Study. Viruses 2023; 15:1764. [PMID: 37632107 PMCID: PMC10457914 DOI: 10.3390/v15081764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
The GENCOV study aims to identify patient factors which affect COVID-19 severity and outcomes. Here, we aimed to evaluate patient characteristics, acute symptoms and their persistence, and associations with hospitalization. Participants were recruited at hospital sites across the Greater Toronto Area in Ontario, Canada. Patient-reported demographics, medical history, and COVID-19 symptoms and complications were collected through an intake survey. Regression analyses were performed to identify associations with outcomes including hospitalization and COVID-19 symptoms. In total, 966 responses were obtained from 1106 eligible participants (87% response rate) between November 2020 and May 2022. Increasing continuous age (aOR: 1.05 [95%CI: 1.01-1.08]) and BMI (aOR: 1.17 [95%CI: 1.10-1.24]), non-White/European ethnicity (aOR: 2.72 [95%CI: 1.22-6.05]), hypertension (aOR: 2.78 [95%CI: 1.22-6.34]), and infection by viral variants (aOR: 5.43 [95%CI: 1.45-20.34]) were identified as risk factors for hospitalization. Several symptoms including shortness of breath and fever were found to be more common among inpatients and tended to persist for longer durations following acute illness. Sex, age, ethnicity, BMI, vaccination status, viral strain, and underlying health conditions were associated with developing and having persistent symptoms. By improving our understanding of risk factors for severe COVID-19, our findings may guide COVID-19 patient management strategies by enabling more efficient clinical decision making.
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Affiliation(s)
- Gregory Morgan
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Selina Casalino
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sunakshi Chowdhary
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Erika Frangione
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chun Yiu Jordan Fung
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Simona Haller
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Elisa Lapadula
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Mackenzie Scott
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dawit Wolday
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Juliet Young
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Saranya Arnoldo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Navneet Aujla
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Erin Bearss
- Mount Sinai Academic Family Health Team, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
| | - Alexandra Binnie
- Department of Critical Care, William Osler Health System, Etobicoke, ON M9V 1R8, Canada
| | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1A6, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Bjug Borgundvaag
- Schwartz/Reisman Emergency Medicine Institute, Sinai Health System, Toronto, ON M5G 2A2, Canada
| | | | - Marc Dagher
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Women’s College Hospital, Toronto, ON M5S 1B2, Canada
| | - Luke Devine
- Division of General Internal Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hanna Faghfoury
- Fred A Litwin Family Centre in Genetic Medicine, University Health Network & Mount Sinai Hospital, Toronto, ON M5T 3H7, Canada
| | - Steven M. Friedman
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Emergency Medicine, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lee W. Goneau
- Dynacare Medical Laboratories, Brampton, ON L6T 5V1, Canada
| | - Zeeshan Khan
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Microbiology, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Shelley L. McLeod
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Schwartz/Reisman Emergency Medicine Institute, Sinai Health System, Toronto, ON M5G 2A2, Canada
| | | | - Abdul Noor
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Harpreet Kaur Satnam Singh
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jared Simpson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Seth Stern
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada
| | - Lisa Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Ahmed Taher
- Mackenzie Health, Richmond Hill, ON L4C 4Z3, Canada
- Division of Emergency Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jennifer Taher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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10
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Kodida R, Reble E, Clausen M, Shickh S, Mighton C, Sam J, Forster N, Panchal S, Aronson M, Semotiuk K, Graham T, Silberman Y, Randall Armel S, McCuaig JM, Cohn I, Morel CF, Elser C, Eisen A, Carroll JC, Glogowski E, Schrader KA, Di Gioacchino V, Lerner-Ellis J, Kim RH, Bombard Y. A model for the return and referral of all clinically significant secondary findings of genomic sequencing. J Med Genet 2023; 60:733-739. [PMID: 37217257 DOI: 10.1136/jmg-2022-109091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Secondary findings (SFs) identified through genomic sequencing (GS) can offer a wide range of health benefits to patients. Resource and capacity constraints pose a challenge to their clinical management; therefore, clinical workflows are needed to optimise the health benefits of SFs. In this paper, we describe a model we created for the return and referral of all clinically significant SFs, beyond medically actionable results, from GS. As part of a randomised controlled trial evaluating the outcomes and costs of disclosing all clinically significant SFs from GS, we consulted genetics and primary care experts to determine a feasible workflow to manage SFs. Consensus was sought to determine appropriate clinical recommendations for each category of SF and which clinician specialist would provide follow-up care. We developed a communication and referral plan for each category of SFs. This involved referrals to specialised clinics, such as an Adult Genetics clinic, for highly penetrant medically actionable findings. Common and non-urgent SFs, such as pharmacogenomics and carrier status results for non-family planning participants, were directed back to the family physician (FP). SF results and recommendations were communicated directly to participants to respect autonomy and to their FPs to support follow-up of SFs. We describe a model for the return and referral of all clinically significant SFs to facilitate the utility of GS and promote the health benefits of SFs. This may serve as a model for others returning GS results transitioning participants from research to clinical settings.
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Affiliation(s)
- Rita Kodida
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Salma Shickh
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Nicole Forster
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Seema Panchal
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Kara Semotiuk
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tracy Graham
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yael Silberman
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology & Toxicology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chantal F Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine Elser
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - June C Carroll
- Department of Family & Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Granovsky Gluskin Family Medicine Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Kasmintan A Schrader
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vanessa Di Gioacchino
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Raymond H Kim
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
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11
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Morgan G, Briollais L, Clausen M, Casalino S, Mighton C, Chowdhary S, Frangione E, Yiu Jordan Fung C, Arnoldo S, Bearss E, Binnie A, Borgundvaag B, Dagher M, Devine L, Friedman SM, Khan Z, McGeer A, McLeod SL, Richardson D, Stern S, Taher A, Wong I, Zarei N, Bombard Y, Lerner-Ellis J, Taher J. Public knowledge of SARS-CoV-2 serological and viral lineage laboratory testing and result interpretation: A GENCOV study cross-sectional survey. Clin Biochem 2023:110607. [PMID: 37406717 DOI: 10.1016/j.clinbiochem.2023.110607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/27/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
OBJECTIVES Concepts related to SARS-CoV-2 laboratory testing and result interpretation can be challenging to understand. A cross-sectional survey of COVID-19 positive adults residing in Ontario, Canada was conducted to explore how well people understand SARS-CoV-2 laboratory tests and their associated results. DESIGN AND METHODS Participants were recruited through fliers or by prospective recruitment of outpatients and hospitalized inpatients with COVID-19. Enrolled participants included consenting adults with a positive SARS-CoV-2 polymerase chain reaction test result. An 11-item questionnaire was developed by researchers, nurses, and physicians in the study team and was administered online between April 2021 to May 2022 upon enrolment into the study. RESULTS Responses were obtained from 940 of 1106 eligible participants (85% participation rate). Most respondents understood 1) that antibody results should not influence adherence to social distancing measures (n=602/888, 68%), 2) asymptomatic SARS-CoV-2 infection following test positivity (n=698/888, 79%), 3) serological test sensitivity in relation to post-infection timeline (n=540/891, 61%), and 4) limitations of experts' knowledge related to SARS-CoV-2 serology (n=693/887, 78%). Conversely, respondents demonstrated challenges understanding 1) conflicting molecular and serological test results and their relationship with immune protection (n=162/893, 18%) and 2) the impact of SARS-CoV-2 variants on vaccine effectiveness (n=235/891, 26%). Analysis of responses stratified by sociodemographic variables identified that respondents who were either: 1) female, 2) more educated, 3) aged 18-44, 4) from a high-income household, or 5) healthcare workers responded expectedly more often. CONCLUSIONS We have highlighted concepts related to SARS-CoV-2 laboratory tests and associated results which may be challenging to understand. The findings of this study enable us to identify 1) misconceptions related to various SARS-CoV-2 test results, 2) groups of individuals at risk, and 3) strategies to improve people's understanding of their test results.
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Affiliation(s)
- Gregory Morgan
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Marc Clausen
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Selina Casalino
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Chloe Mighton
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Sunakshi Chowdhary
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Erika Frangione
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Chun Yiu Jordan Fung
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Saranya Arnoldo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; William Osler Health System, Brampton, ON, Canada
| | - Erin Bearss
- Mount Sinai Academic Family Health Team, Mount Sinai Hospital, Toronto, ON, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Bjug Borgundvaag
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada; Department of Emergency Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Marc Dagher
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada; Women's College Hospital, Toronto, ON, Canada
| | - Luke Devine
- Division of General Internal Medicine, Mount Sinai Hospital, Toronto, ON, Canada; Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Steven M Friedman
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada; Emergency Medicine, University Health Network, Toronto, ON, Canada
| | | | - Allison McGeer
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Shelley L McLeod
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada; Schwartz/Reisman Emergency Medicine Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Seth Stern
- Mackenzie Health, Richmond Hill, ON, Canada
| | - Ahmed Taher
- Mackenzie Health, Richmond Hill, ON, Canada; Division of Emergency Medicine, University of Toronto, Toronto, ON, Canada
| | - Iris Wong
- Mackenzie Health, Richmond Hill, ON, Canada
| | | | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jennifer Taher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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12
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Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF, Paterson AD, Sun L, Zawati MH, Lerner-Ellis J, Abraham R, Birol I, Bourque G, Garant JM, Gosselin C, Li J, Whitney J, Thiruvahindrapuram B, Herbrick JA, Lorenti M, Reuter MS, Adeoye OO, Liu S, Allen U, Bernier FP, Biggs CM, Cheung AM, Cowan J, Herridge M, Maslove DM, Modi BP, Mooser V, Morris SK, Ostrowski M, Parekh RS, Pfeffer G, Suchowersky O, Taher J, Upton J, Warren RL, Yeung R, Aziz N, Turvey SE, Knoppers BM, Lathrop M, Jones S, Scherer SW, Strug LJ. HostSeq: a Canadian whole genome sequencing and clinical data resource. BMC Genom Data 2023; 24:26. [PMID: 37131148 PMCID: PMC10152008 DOI: 10.1186/s12863-023-01128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/22/2023] [Indexed: 05/04/2023] Open
Abstract
HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.
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Affiliation(s)
- S Yoo
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Ottawa, Ottawa, ON, Canada
| | - E Garg
- Simon Fraser University, Burnaby, BC, Canada
| | - L T Elliott
- Simon Fraser University, Burnaby, BC, Canada
| | - R J Hung
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - A R Halevy
- The Hospital for Sick Children, Toronto, ON, Canada
| | - J D Brooks
- University of Toronto, Toronto, ON, Canada
| | - S B Bull
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - F Gagnon
- University of Toronto, Toronto, ON, Canada
| | - Cmt Greenwood
- McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - J F Lawless
- University of Waterloo, Waterloo, ON, Canada
| | - A D Paterson
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L Sun
- University of Toronto, Toronto, ON, Canada
| | | | - J Lerner-Ellis
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - Rjs Abraham
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - I Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - G Bourque
- McGill University, Montreal, QC, Canada
| | - J-M Garant
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - C Gosselin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Whitney
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - J-A Herbrick
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M Lorenti
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M S Reuter
- The Hospital for Sick Children, Toronto, ON, Canada
| | - O O Adeoye
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S Liu
- The Hospital for Sick Children, Toronto, ON, Canada
| | - U Allen
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - F P Bernier
- University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital, Calgary, AB, Canada
| | - C M Biggs
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
- St. Paul's Hospital, Vancouver, BC, Canada
| | - A M Cheung
- University Health Network, Toronto, ON, Canada
| | - J Cowan
- University of Ottawa, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - M Herridge
- University Health Network, Toronto, ON, Canada
| | | | - B P Modi
- BC Children's Hospital, Vancouver, BC, Canada
| | - V Mooser
- McGill University, Montreal, QC, Canada
| | - S K Morris
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - M Ostrowski
- University of Toronto, Toronto, ON, Canada
- St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - R S Parekh
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- Women's College Hospital, Toronto, ON, Canada
| | - G Pfeffer
- University of Calgary, Calgary, AB, Canada
| | | | - J Taher
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - J Upton
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - R L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Rsm Yeung
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - N Aziz
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S E Turvey
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
| | | | - M Lathrop
- McGill University, Montreal, QC, Canada
| | - Sjm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - S W Scherer
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L J Strug
- The Hospital for Sick Children, Toronto, ON, Canada.
- University of Toronto, Toronto, ON, Canada.
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13
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Shickh S, Sebastian A, Clausen M, Mighton C, Elser C, Eisen A, Waldman L, Panchal S, Ward T, Carroll JC, Glogowski E, Schrader KA, Lerner-Ellis J, Kim RH, Thorpe KE, Bombard Y. Great expectations: patients' preferences for clinically significant results from genomic sequencing. Hum Genet 2023; 142:553-562. [PMID: 36943453 DOI: 10.1007/s00439-023-02543-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
We aimed to describe patient preferences for a broad range of secondary findings (SF) from genomic sequencing (GS) and factors driving preferences. We assessed preference data within a trial of the Genomics ADvISER, (SF decision aid) among adult cancer patients. Participants could choose from five categories of SF: (1) medically actionable; (2) polygenic risks; (3) rare diseases; (4) early-onset neurological diseases; and (5) carrier status. We analyzed preferences using descriptive statistics and drivers of preferences using multivariable logistic regression models. The 133 participants were predominantly European (74%) or East Asian or mixed ancestry (13%), female (90%), and aged > 50 years old (60%). The majority chose to receive SF. 97% (129/133) chose actionable findings with 36% (48/133) choosing all 5 categories. Despite the lack of medical actionability, participants were interested in receiving SF of polygenic risks (74%), carrier status (75%), rare diseases (59%), and early-onset neurologic diseases (53%). Older participants were more likely to be interested in receiving results for early-onset neurological diseases, while those exhibiting lower decisional conflict were more likely to select all categories. Our results highlight a disconnect between cancer patient preferences and professional guidelines on SF, such as ACMG's recommendations to only return medically actionable secondary findings. In addition to clinical evidence, future guidelines should incorporate patient preferences.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Agnes Sebastian
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Christine Elser
- University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Larissa Waldman
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Thomas Ward
- Zane Cohen Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - June C Carroll
- Ray D Wolfe Department of Family Medicine, Sinai Health, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Raymond H Kim
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network and Sinai Health, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kevin E Thorpe
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Applied Health Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
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14
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Shrestha M, Blay S, Liang S, Swanson D, Lerner-Ellis J, Dickson B, Wong A, Charames GS. Improving RNA fusion call confidence and reliability in molecular diagnostic testing. J Mol Diagn 2023; 25:320-330. [PMID: 36958423 DOI: 10.1016/j.jmoldx.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/17/2023] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Next-generation sequencing (NGS) is a superior method for detecting known and novel RNA fusions in formalin-fixed paraffin-embedded tissue over FISH and RT-PCR. However, confidence in fusion calling and true negatives may be compromised by poor RNA quality. Using a commercial panel of 507 genes and the recommended 3 million read threshold to accept results, two cases yielded false negatives while exceeding this recommendation during clinical validation. To develop a reliable quality control metric that better reflects internal sample quality and improve call confidence, gene expression across 361 patient tumor samples was evaluated to derive a set of 15 genes to serve as a proxy quality control (pQC). These 15 genes were assessed for their normalized expression using the sequencing data from each case and selected for robustness. A threshold of 11 pQC genes produced a 4.71% fail rate, selected for stringency as an acceptable level of repeat testing in the clinical setting, minimizing false negative calls. To increase the chance that low-quality samples pass pQC, a revision to the library preparation methodology was also tested, with 75% of previously failed samples passing pQC upon re-sequencing by increasing cDNA input. Taken together, an NGS analysis quality control tool is presented that serves as a surrogate for housekeeping genes and improves confidence in fusion calls.
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Affiliation(s)
- Mariusz Shrestha
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Sasha Blay
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Sydney Liang
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Brendan Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Andrew Wong
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - George S Charames
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
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15
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Thiryayi SA, Ettler H, Goebel EA, Prefontaine M, Paton TA, Wong A, Yee D, Agro E, Mayers J, Lerner-Ellis J, Turashvili G. BCOR Internal Tandem Duplication Associated Uterine Sarcoma: Expanding the Clinicopathologic Spectrum. Int J Gynecol Pathol 2022; 41:503-507. [PMID: 34456278 DOI: 10.1097/pgp.0000000000000822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The diagnosis of high-grade endometrial stromal sarcoma has become more refined following molecular characterization of these tumors. Recently BCOR internal tandem duplications (ITD) have been identified in a small number of high-grade endometrial stromal sarcoma. Here we present an additional case of this rare entity in a young woman in her late teens. She presented with menorrhagia and underwent resection of 2 uterine lesions. The tumor was a spindle cell neoplasm composed of long fascicles with low to moderate cellularity, mild to moderate cytologic atypia, and up to 2 mitotic figures per 10 high power fields. Necrosis was not identified. Immunohistochemical stains showed the tumor to be positive for cyclin D1 in >50% of tumor cells, focally positive for CD10, and negative for SMA, desmin, h-caldesmon, and ALK1. BCOR ITD was confirmed by polymerase chain reaction with subsequent Sanger sequencing. Clues to the diagnosis of BCOR ITD uterine sarcoma include young patient age, uniform nuclear features, and diffuse positivity for cyclin D1. These features should prompt further molecular interrogation for definitive diagnosis, which is important for prognostication.
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16
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Sam J, Reble E, Kodida R, Shaw A, Clausen M, Salazar MG, Shickh S, Mighton C, Carroll JC, Armel SR, Aronson M, Capo-Chichi JM, Cohn I, Eisen A, Elser C, Graham T, Ott K, Panchal S, Piccinin C, Schrader KA, Kim RH, Lerner-Ellis J, Bombard Y. A comprehensive genomic reporting structure for communicating all clinically significant primary and secondary findings. Hum Genet 2022; 141:1875-1885. [PMID: 35739291 DOI: 10.1007/s00439-022-02466-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/05/2022] [Indexed: 11/25/2022]
Abstract
Genomic sequencing (GS) can reveal secondary findings (SFs), findings unrelated to the reason for testing, that can be overwhelming to both patients and providers. An effective approach for communicating all clinically significant primary and secondary GS results is needed to effectively manage this large volume of results. The aim of this study was to develop a comprehensive approach to communicate all clinically significant primary and SF results. A genomic test report with accompanying patient and provider letters were developed in three phases: review of current clinical reporting practices, consulting with genetic and non-genetics experts, and iterative refinement through circulation to key stakeholders. The genomic test report and consultation letters present a myriad of clinically relevant GS results in distinct, tabulated sections, including primary (cancer) and secondary findings, with in-depth details of each finding generated from exome sequencing. They provide detailed variant and disease information, personal and familial risk assessments, clinical management details, and additional resources to help support providers and patients with implementing healthcare recommendations related to their GS results. The report and consultation letters represent a comprehensive approach to communicate all clinically significant SFs to patients and providers, facilitating clinical management of GS results.
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Affiliation(s)
- Jordan Sam
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Emma Reble
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Rita Kodida
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Angela Shaw
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Mariana Gutierrez Salazar
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
- University of Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
- University of Toronto, Toronto, ON, Canada
| | - June C Carroll
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Susan Randall Armel
- University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | | | - Iris Cohn
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Christine Elser
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Tracy Graham
- University of Toronto, Toronto, ON, Canada
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Karen Ott
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Seema Panchal
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | | | | | - Raymond H Kim
- University of Toronto, Toronto, ON, Canada
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- University of Toronto, Toronto, ON, Canada.
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
- University of Toronto, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
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17
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Shickh S, Mighton C, Clausen M, Adi-Wauran E, Hirjikaka D, Kodida R, Krishnapillai S, Reble E, Sam J, Shaw A, Lerner-Ellis J, Baxter NN, Laupacis A, Bombard Y. "Doctors shouldn't have to cheat the system": Clinicians' real-world experiences of the utility of genomic sequencing. Genet Med 2022; 24:1888-1898. [PMID: 35612591 DOI: 10.1016/j.gim.2022.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Emerging genetic tests such as genomic sequencing (GS) can generate a broad range of benefits, but funding criteria only prioritize diagnosis and clinical management. There is limited evidence on all types of benefits obtained from GS in practice. We aimed to explore real-world experiences of Canadian clinicians across specialties on the full range of benefits obtained from the results from GS. METHODS We conducted a qualitative study using semistructured interviews with Canadian clinicians. Transcripts were thematically analyzed using constant comparison. RESULTS In total, 25 clinicians participated, including 12 geneticists, 7 genetic counselors, 4 oncologists, 1 neurologist, and 1 family physician. Although diagnoses and management were the most valued benefits of GS, clinicians also prioritized nontraditional utility, such as access to community supports. However, clinicians felt "restricted" by funding bodies, which only approved funding when GS would inform diagnoses and management. Consequently, clinicians sought ways to "cheat the system" to access GS (eg, research testing) but acknowledged workarounds were burdensome, drove inequity, and undermined patient care. CONCLUSION Current governance structures undervalue real-world benefits of GS leading clinicians to adopt workarounds, which jeopardize patient care. These results support calls for the expansion of the definition of clinical utility and research to quantify the additional benefits.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Ella Adi-Wauran
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Daena Hirjikaka
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rita Kodida
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Suvetha Krishnapillai
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Angela Shaw
- Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nancy N Baxter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Andreas Laupacis
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada; Genomics Health Services and Policy Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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18
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Shickh S, Hirjikaka D, Clausen M, Kodida R, Mighton C, Reble E, Sam J, Panchal S, Aronson M, Graham T, Armel SR, Glogowski E, Elser C, Eisen A, Carroll JC, Shuman C, Seto E, Baxter NN, Scheer A, Shastri-Estrada S, Feldman G, Thorpe KE, Schrader KA, Lerner-Ellis J, Kim RH, Faghfoury H, Bombard Y. Genetics Adviser: a protocol for a mixed-methods randomised controlled trial evaluating a digital platform for genetics service delivery. BMJ Open 2022; 12:e060899. [PMID: 35487723 PMCID: PMC9058789 DOI: 10.1136/bmjopen-2022-060899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION The high demand for genetic tests and limited supply of genetics professionals has created a need for alternative service delivery models. Digital tools are increasingly being used to support multiple points in the genetic testing journey; however, none are transferable across multiple clinical specialties and settings nor do they encompass the entire trajectory of the journey. We aim to evaluate the effectiveness of the Genetics Adviser, an interactive, patient-facing, online digital health tool that delivers pre-test counselling, provides support during the waiting period for results, and returns results with post-test counselling, encompassing the entire patient genetic testing journey. METHODS AND ANALYSIS We will compare the Genetics Adviser paired with a brief genetic counselling session to genetic counselling alone in a randomised controlled trial. One hundred and forty patients who previously received uninformative genetic test results for their personal and family history of cancer will be recruited from familial cancer clinics in Toronto and offered all clinically significant results from genomic sequencing. Participants randomised into the intervention arm will use the Genetics Adviser to learn about genomic sequencing, receive pre-test counselling, support during the waiting period and results, supplemented with brief counselling from a genetic counsellor. Participants in the control arm will receive standard pre-test and post-test counselling for genomic sequencing from a genetic counsellor. Our primary outcome is decisional conflict following pre-test counselling from the Genetics Adviser+genetic counsellor or counsellor alone. Secondary outcomes include: knowledge, satisfaction with decision-making, anxiety, quality of life, psychological impact of results, empowerment, acceptability and economic impact for patients and the health system. A subset of patients will be interviewed to assess user experience. ETHICS AND DISSEMINATION This study has been approved by Clinical Trials Ontario Streamlined Research Ethics Review System (REB#20-035). Results will be shared through stakeholder workshops, national and international conferences and peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT04725565.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Daena Hirjikaka
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rita Kodida
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Seema Panchal
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tracy Graham
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Christine Elser
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - June C Carroll
- Ray D Wolfe Department of Family Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl Shuman
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Emily Seto
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Centre for Global eHealth Innovation, Techna Institute, University Health Network, Toronto, Ontario, Canada
| | - Nancy N Baxter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Adena Scheer
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | | | - Geoff Feldman
- Ontario Disability Coalition, Toronto, Ontario, Canada
| | - Kevin E Thorpe
- Applied Health Research Centre (AHRC), Li Ka Shing Knowledge Institute of St Michael's Hospital, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Kasmintan A Schrader
- BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Raymond H Kim
- The Hospital for Sick Children, Toronto, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Faghfoury
- Fred A Litwin and Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
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Hirjikaka D, Kodida R, Clausen M, Shickh S, Reble E, Mighton C, Sam J, Krishnapillai S, Adi-Wauran E, Feldman G, Glogowski E, Shastri-Estrada S, Scheer A, Seto E, Shuman C, Baxter NN, Eisen A, Elser C, Kim R, Lerner-Ellis J, Carroll J, Schrader K, Faghfoury H, Bombard Y. eP299: Genetics adviser: The development and usability testing of a new patient-centered digital health application to support clinical genomic testing. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Mighton C, Clausen M, Sebastian A, Muir S, Shickh S, Baxter NN, Scheer A, Glogowski E, Schrader K, Thorpe K, Kim T, Lerner-Ellis J, Kim R, Regier D, Bayoumi A, Bombard Y. eP502: How will returning variants of uncertain significance impact healthcare use? A cross-sectional survey. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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21
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Casalino S, Mighton C, Clausen M, Frangione E, Chowdhary S, Chung M, Jordan Fung CY, Morgan G, MacDonald G, Lapadula E, Faghfoury H, Arnoldo S, Bearss E, Binnie A, Borgundvaag B, Chertkow H, Devine L, Friedmen SM, Gingras AC, Khan Z, Mazzulli T, McGeer A, McLeod S, Pugh T, Richardson D, Simpson J, Stern S, Strug L, Taher A, Wong I, Zarei N, Kaushik D, Goneau L, Dagher M, Noor A, Greenfeld E, Bombard Y, Taher J, Lerner-Ellis J. eP294: Return of genome sequencing results in ostensibly healthy COVID-19 positive individuals: GENCOV Study Canada. Genet Med 2022. [PMCID: PMC8935071 DOI: 10.1016/j.gim.2022.01.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Frangione E, Chung M, Mighton C, Casalino S, Chowdhary S, Satnam Singh HK, Xu L, Di Iorio D, Jain A, Kidwai A, Wong Q, Aujla N, Li JM, Quraishi M, Morgan G, Clausen M, Jordan Fung CY, MacDonald G, Lapadula E, Arnoldo S, Bearss E, Binnie A, Borgundvaag B, Chertkow H, Devine L, Friedmen SM, Gingras AC, Khan Z, Mazzulli T, McGeer A, McLeod S, Pugh T, Richardson D, Simpson J, Stern S, Strug L, Taher A, Wong I, Zarei N, Kaushik D, Goneau L, Dagher M, Greenfeld E, Faghfoury H, Bombard Y, Noor A, Taher J, Lerner-Ellis J. eP325: Medically actionable DNA variation from the GENCOV COVID-19 Genome Sequencing Study. Genet Med 2022. [PMCID: PMC8935062 DOI: 10.1016/j.gim.2022.01.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Shickh S, Mighton C, Clausen M, Lerner-Ellis J, Baxter NN, Laupacis A, Bombard Y. eP513: “Doctors shouldn’t have to cheat the system”: Clinicians’ real-world experiences of the utility of genomic sequencing. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Kim SR, Tone A, Kim R, Cesari M, Clarke B, Hart T, Aronson M, Holter S, Lytwyn A, Maganti M, Oldfield L, Gallinger S, Bernardini MQ, Oza AM, Djordjevic B, Lerner-Ellis J, Van de Laar E, Vicus D, Pugh TJ, Pollett A, Ferguson SE, Eiriksson L. Brief family history questionnaire to screen for Lynch syndrome in women with newly diagnosed non-serous, non-mucinous ovarian cancers. Int J Gynecol Cancer 2022; 32:891-898. [PMID: 35012974 DOI: 10.1136/ijgc-2021-003082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES While ovarian cancer is the third most common Lynch syndrome-associated cancer in women, there is no established screening strategy to identify Lynch syndrome in this population. The objective of this study was to assess whether the 4-item brief Family History Questionnaire can be used as a screening tool to identify women with ovarian cancer at risk of Lynch syndrome. METHODS In this prospective cohort study, participants with newly diagnosed non-serous, non-mucinous ovarian cancer completed the brief Family History Questionnaire, extended Family History Questionnaire, and had tumors assessed with immunohistochemistry for mismatch repair proteins, MLH1 methylation, and microsatellite instability testing. All underwent universal germline testing for Lynch syndrome. Performance characteristics were compared between the brief Family History Questionnaire, extended Family History Questionnaire, immunohistochemistry±MLH1 methylation, and microsatellite instability testing. RESULTS Of 215 participants, 169 (79%) were evaluable with both the brief Family History Questionnaire and germline mutation status; 12 of these 169 were confirmed to have Lynch syndrome (7%). 10 of 12 patients (83%) with Lynch syndrome were correctly identified by the brief Family History Questionnaire, compared with 6 of 11 (55%) by the extended Family History Questionnaire, 11 of 13 (85%) by immunohistochemistry±MLH1 methylation, and 9 of 11 (82%) by microsatellite instability testing. The sensitivity, specificity, positive predictive values, and negative predictive values of the brief Family History Questionnaire were 83%, 65%, 15%, and 98%, respectively. A combined approach with immunohistochemistry and the brief Family History Questionnaire correctly identified all 12 patients with Lynch syndrome. The brief Family History Questionnaire was more sensitive than the extended Family History Questionnaire and took <10 min for each patient to complete. CONCLUSIONS The brief Family History Questionnaire alone or combined with immunohistochemistry may serve as an adequate screening strategy, especially in centers without access to universal tumor testing.
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Affiliation(s)
- Soyoun Rachel Kim
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada .,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada
| | - Raymond Kim
- Fred A Litwin Family Centre for Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada
| | - Matthew Cesari
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Blaise Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Tae Hart
- Department of Psychology, Ryerson University, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alice Lytwyn
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Manjula Maganti
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Division of General Surgery, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada
| | - Bojana Djordjevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada
| | - Danielle Vicus
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, University Health Network, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sarah Elizabeth Ferguson
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Sinai Health Systems, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Lua Eiriksson
- Department of Obstetrics and Gynecology, Juravinski Cancer Centre, McMaster University, Hamilton, Ontario, Canada
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25
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Okur V, Chen Z, Vossaert L, Peacock S, Rosenfeld J, Zhao L, Du H, Calamaro E, Gerard A, Zhao S, Kelsay J, Lahr A, Mighton C, Porter HM, Siemon A, Silver J, Svihovec S, Fong CT, Grant CL, Lerner-Ellis J, Manickam K, Madan-Khetarpal S, McCandless SE, Morel CF, Schaefer GB, Berry-Kravis EM, Gates R, Gomez-Ospina N, Qiu G, Zhang TJ, Wu Z, Meng L, Liu P, Scott DA, Lupski JR, Eng CM, Wu N, Yuan B. De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities. NPJ Genom Med 2021; 6:104. [PMID: 34876591 PMCID: PMC8651650 DOI: 10.1038/s41525-021-00268-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/28/2021] [Indexed: 11/26/2022] Open
Abstract
The histone H3 variant H3.3, encoded by two genes H3-3A and H3-3B, can replace canonical isoforms H3.1 and H3.2. H3.3 is important in chromatin compaction, early embryonic development, and lineage commitment. The role of H3.3 in somatic cancers has been studied extensively, but its association with a congenital disorder has emerged just recently. Here we report eleven de novo missense variants and one de novo stop-loss variant in H3-3A (n = 6) and H3-3B (n = 6) from Baylor Genetics exome cohort (n = 11) and Matchmaker Exchange (n = 1), of which detailed phenotyping was conducted for 10 individuals (H3-3A = 4 and H3-3B = 6) that showed major phenotypes including global developmental delay, short stature, failure to thrive, dysmorphic facial features, structural brain abnormalities, hypotonia, and visual impairment. Three variant constructs (p.R129H, p.M121I, and p.I52N) showed significant decrease in protein expression, while one variant (p.R41C) accumulated at greater levels than wild-type control. One H3.3 variant construct (p.R129H) was found to have stronger interaction with the chaperone death domain-associated protein 6.
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Affiliation(s)
- Volkan Okur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Zefu Chen
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Graduate School of Peking Union Medical College, 100005, Beijing, China
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lina Zhao
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Sen Zhao
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Jill Kelsay
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, 72701, USA
| | - Ashley Lahr
- Department of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, M5T 3M6, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, M5B 1A6, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
| | - Hillary M Porter
- Rare Disease Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Amy Siemon
- Nationwide Children's Hospital (NCH) and The Ohio State University College of Medicine Section of Genetic and Genomic Medicine, Columbus, OH, 43205, USA
| | - Josh Silver
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Shayna Svihovec
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, and Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Christina L Grant
- Rare Disease Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Jordan Lerner-Ellis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kandamurugu Manickam
- Nationwide Children's Hospital (NCH) and The Ohio State University College of Medicine Section of Genetic and Genomic Medicine, Columbus, OH, 43205, USA
| | - Suneeta Madan-Khetarpal
- Department of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Shawn E McCandless
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, and Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada
- Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, 72701, USA
| | - Elizabeth M Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Ryan Gates
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China.
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Baylor Genetics Laboratories, Houston, TX, 77021, USA.
- Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, UW, 98105, USA.
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26
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Taher J, Mighton C, Chowdhary S, Casalino S, Frangione E, Arnoldo S, Bearss E, Binnie A, Bombard Y, Borgundvaag B, Chertkow H, Clausen M, Devine L, Faghfoury H, Friedman SM, Gingras AC, Khan Z, Mazzulli T, McGeer A, McLeod SL, Pugh TJ, Richardson D, Simpson J, Stern S, Strug L, Taher A, Lerner-Ellis J. Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study. BMJ Open 2021; 11:e052842. [PMID: 34593505 PMCID: PMC8487020 DOI: 10.1136/bmjopen-2021-052842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION There is considerable variability in symptoms and severity of COVID-19 among patients infected by the SARS-CoV-2 virus. Linking host and virus genome sequence information to antibody response and biological information may identify patient or viral characteristics associated with poor and favourable outcomes. This study aims to (1) identify characteristics of the antibody response that result in maintained immune response and better outcomes, (2) determine the impact of genetic differences on infection severity and immune response, (3) determine the impact of viral lineage on antibody response and patient outcomes and (4) evaluate patient-reported outcomes of receiving host genome, antibody and viral lineage results. METHODS AND ANALYSIS A prospective, observational cohort study is being conducted among adult patients with COVID-19 in the Greater Toronto Area. Blood samples are collected at baseline (during infection) and 1, 6 and 12 months after diagnosis. Serial antibody titres, isotype, antigen target and viral neutralisation will be assessed. Clinical data will be collected from chart reviews and patient surveys. Host genomes and T-cell and B-cell receptors will be sequenced. Viral genomes will be sequenced to identify viral lineage. Regression models will be used to test associations between antibody response, physiological response, genetic markers and patient outcomes. Pathogenic genomic variants related to disease severity, or negative outcomes will be identified and genome wide association will be conducted. Immune repertoire diversity during infection will be correlated with severity of COVID-19 symptoms and human leucocyte antigen-type associated with SARS-CoV-2 infection. Participants can learn their genome sequencing, antibody and viral sequencing results; patient-reported outcomes of receiving this information will be assessed through surveys and qualitative interviews. ETHICS AND DISSEMINATION This study was approved by Clinical Trials Ontario Streamlined Ethics Review System (CTO Project ID: 3302) and the research ethics boards at participating hospitals. Study findings will be disseminated through peer-reviewed publications, conference presentations and end-users.
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Affiliation(s)
- Jennifer Taher
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Sunakshi Chowdhary
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Selina Casalino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Erika Frangione
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Saranya Arnoldo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- William Osler Health System, Brampton, Ontario, Canada
| | - Erin Bearss
- Mount Sinai Academic Family Health Team, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Bjug Borgundvaag
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Emergency Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Marc Clausen
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Luke Devine
- Division of General Internal Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Faghfoury
- Fred A Litwin and Family Centre in Genetic Medicine, University Health Network & Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Steven Marc Friedman
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Emergency Medicine, University Health Network, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Zeeshan Khan
- Mackenzie Health, Richmond Hill, Ontario, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Shelley L McLeod
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Schwartz/Reisman Emergency Medicine Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Jared Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Seth Stern
- Mackenzie Health, Richmond Hill, Ontario, Canada
| | - Lisa Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ahmed Taher
- Emergency Medicine, University Health Network, Toronto, Ontario, Canada
- Mackenzie Health, Richmond Hill, Ontario, Canada
- Division of Emergency Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
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Mighton C, Clausen M, Sebastian A, Muir SM, Shickh S, Baxter NN, Scheer A, Glogowski E, Schrader KA, Thorpe KE, Kim THM, Lerner-Ellis J, Kim RH, Regier DA, Bayoumi AM, Bombard Y. Patient and public preferences for being recontacted with updated genomic results: a mixed methods study. Hum Genet 2021; 140:1695-1708. [PMID: 34537903 DOI: 10.1007/s00439-021-02366-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/05/2021] [Indexed: 01/14/2023]
Abstract
Variants of uncertain significance (VUS) are frequently reclassified but recontacting patients with updated results poses significant resource challenges. We aimed to characterize public and patient preferences for being recontacted with updated results. A discrete choice experiment (DCE) was administered to representative samples of the Canadian public and cancer patients. DCE attributes were uncertainty, cost, recontact modality, choice of results, and actionability. DCE data were analyzed using a mixed logit model and by calculating willingness to pay (WTP) for types of recontact. Qualitative interviews exploring recontact preferences were analyzed thematically. DCE response rate was 60% (n = 1003, 50% cancer patient participants). 31 participants were interviewed (11 cancer patients). Interviews revealed that participants expected to be recontacted. Quantitatively, preferences for how to be recontacted varied based on certainty of results. For certain results, WTP was highest for being recontacted by a doctor with updates ($1075, 95% CI: $845, $1305) and for contacting a doctor to request updates ($1038, 95% CI: $820, $1256). For VUS results, WTP was highest for an online database ($1735, 95% CI: $1224, $2247) and for contacting a doctor ($1705, 95% CI: $1102, $2307). Qualitative data revealed that preferences for provider-mediated recontact were influenced by trust in healthcare providers. Preferences for a database were influenced by lack of trust in providers and desire for control. Patients and public participants support an online database (e.g. patient portal) to recontact for VUS, improving feasibility, and provider-mediated recontact for certain results, consistent with usual care.
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Affiliation(s)
- Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Marc Clausen
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Agnes Sebastian
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Sarah M Muir
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Nancy N Baxter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.,Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Adena Scheer
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Division of General Surgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kevin E Thorpe
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Theresa H M Kim
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Raymond H Kim
- University Health Network, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Dean A Regier
- BC Cancer, Vancouver, BC, Canada.,School of Population and Public Health (SPPH), University of British Columbia, Vancouver, BC, Canada
| | - Ahmed M Bayoumi
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Division of General Internal Medicine, Department of Medicine, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.
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Kim RS, Tone A, Kim R, Cesari M, Clarke B, Eiriksson LR, Tae H, Lytwyn A, Maganti M, Gallinger S, Bernardini M, Oza AM, Djordjevic B, Lerner-Ellis J, Van de Laar E, Vicus D, Pugh TJ, Pollett A, Ferguson SE. Performance characteristics of brief family history questionnaire to screen for Lynch syndrome in women with newly diagnosed ovarian cancers. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e22525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e22525 Background: Ovarian cancer (OC) is the third most common Lynch syndrome (LS)-associated cancer in women but there is no established screening strategy to identify LS in this population. An adequate family history may identify patients suspected of LS, prompting a referral to genetic assessment. We have previously validated the 4-item brief Family History Questionnaire (bFHQ) in endometrial cancers. The objective of this study was to assess whether bFHQ can be used as a screening tool to identify women with OC at risk of LS. Methods: Prospective cohort study recruited women with newly diagnosed non-serous/non-mucinous OC from three cancer centers in Ontario, Canada. Participants completed bHFQ, extended Family History Questionnaire (eFHQ; encompassing Amsterdam II criteria, Society of Gynecologic Oncology 20-25% criteria and Ontario Ministry of Health criteria), immunohistochemistry (IHC) for mismatch repair (MMR) proteins and universal germline testing for LS. The performance characteristics were compared between bFHQ, eFHQ, and IHC. Results: Of 215 participants, 169 (79%) were evaluable with both bFHQ and germline mutation status; 12 of these 169 were confirmed to have LS (7%). Nine of 12 patients (75%) with LS were correctly identified by bFHQ, compared to 6 of 11 (55%) by eFHQ and 11 of 13 (85%) by IHC. The sensitivity, specificity, positive predictive values and negative predictive values of bFHQ were 75%, 66%, 15% and 98%, compared to 55%, 92%, 35% and 96% for eFHQ and 85%, 90%, 39% and 99% for IHC respectively. IHC was the most sensitive and specific approach. The 4-item bFHQ was more sensitive than eFHQ and took less than 10 minutes for each patient to complete. Conclusions: Patient-administered bFHQ may serve as an adequate screening tool to triage women with OC for further genetic assessment for LS, especially in centers without access to universal tumor testing for IHC for MMR.[Table: see text]
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Affiliation(s)
- Rachel Soyoun Kim
- University of Toronto Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, ON, Canada
| | | | - Raymond Kim
- University Health Network/Mt Sinai Genetics, Toronto, ON, Canada
| | - Matthew Cesari
- University of Toronto-Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Blaise Clarke
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
| | | | - Hart Tae
- Department of Psychology, Ryerson University, Toronto, ON, Canada
| | - Alice Lytwyn
- Division of Anatomical Pathology, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | | | | | | | - Amit M. Oza
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Bojana Djordjevic
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | | | - Emily Van de Laar
- Princess Margaret Cancer Centre, Univeristy Health Network, Toronto, ON, Canada
| | - Danielle Vicus
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | | | | | - Sarah E. Ferguson
- Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
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29
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Kim SR, Tone A, Kim RH, Cesari M, Clarke BA, Eiriksson L, Hart TL, Aronson M, Holter S, Lytwyn A, Maganti M, Oldfield L, Gallinger S, Bernardini MQ, Oza AM, Djordjevic B, Lerner-Ellis J, Van de Laar E, Vicus D, Pugh TJ, Pollett A, Ferguson SE. Maximizing cancer prevention through genetic navigation for Lynch syndrome detection in women with newly diagnosed endometrial and nonserous/nonmucinous epithelial ovarian cancer. Cancer 2021; 127:3082-3091. [PMID: 33983630 PMCID: PMC8453540 DOI: 10.1002/cncr.33625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/14/2021] [Accepted: 04/09/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Despite recommendations for reflex immunohistochemistry (IHC) for mismatch repair (MMR) proteins to identify Lynch syndrome (LS), the uptake of genetic assessment by those who meet referral criteria is low. The authors implemented a comprehensive genetic navigation program to increase the uptake of genetic testing for LS in patients with endometrial cancer (EC) or nonserous/nonmucinous ovarian cancer (OC). METHODS Participants with newly diagnosed EC or OC were prospectively recruited from 3 cancer centers in Ontario, Canada. Family history questionnaires were used to assess LS-specific family history. Reflex IHC for MMR proteins was performed with the inclusion of clinical directives in pathology reports. A trained genetic navigator initiated a genetic referral on behalf of the treating physician and facilitated genetic referrals to the closest genetics center. RESULTS A total of 841 participants (642 with EC, 172 with OC, and 27 with synchronous EC/OC) consented to the study; 194 (23%) were MMR-deficient by IHC. Overall, 170 women (20%) were eligible for a genetic assessment for LS: 35 on the basis of their family history alone, 24 on the basis of their family history and IHC, 82 on the basis of IHC alone, and 29 on the basis of clinical discretion. After adjustments for participants who died (n = 6), 149 of 164 patients (91%) completed a genetic assessment, and 111 were offered and completed genetic testing. Thirty-four women (4.0% of the total cohort and 30.6% of those with genetic testing) were diagnosed with LS: 5 with mutL homolog 1 (MLH1), 9 with mutS homolog 2 (MSH2), 15 with mutS homolog 6 (MSH6), and 5 with PMS2. CONCLUSIONS The introduction of a navigated genetic program resulted in a high rate of genetic assessment (>90%) in patients with gynecologic cancer at risk for LS.
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Affiliation(s)
- Soyoun Rachel Kim
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
| | - Raymond H Kim
- Fred A. Litwin Family Centre for Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
| | - Matthew Cesari
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lua Eiriksson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Juravinski Cancer Centre, McMaster University, Hamilton, Ontario, Canada
| | - Tae L Hart
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Psychology, Ryerson University, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alice Lytwyn
- Division of Anatomical Pathology, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Manjula Maganti
- Department of Biostatistics, Princess Margaret Cancer Centre/University Health Network/University of Toronto, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Division of General Surgery, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
| | - Bojana Djordjevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada
| | - Danielle Vicus
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, University Health Network, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sarah E Ferguson
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre/University Health Network/Sinai Health Systems, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada.,Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
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Mighton C, Smith AC, Mayers J, Tomaszewski R, Taylor S, Hume S, Agatep R, Spriggs E, Feilotter HE, Semenuk L, Wong H, Lazo de la Vega L, Marshall CR, Axford MM, Silver T, Charames GS, Di Gioacchino V, Watkins N, Foulkes WD, Clavier M, Hamel N, Chong G, Lamont RE, Parboosingh J, Karsan A, Bosdet I, Young SS, Tucker T, Akbari MR, Speevak MD, Vaags AK, Lebo MS, Lerner-Ellis J. Data sharing to improve concordance in variant interpretation across laboratories: results from the Canadian Open Genetics Repository. J Med Genet 2021; 59:571-578. [PMID: 33875564 DOI: 10.1136/jmedgenet-2021-107738] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study aimed to identify and resolve discordant variant interpretations across clinical molecular genetic laboratories through the Canadian Open Genetics Repository (COGR), an online collaborative effort for variant sharing and interpretation. METHODS Laboratories uploaded variant data to the Franklin Genoox platform. Reports were issued to each laboratory, summarising variants where conflicting classifications with another laboratory were noted. Laboratories could then reassess variants to resolve discordances. Discordance was calculated using a five-tier model (pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), benign (B)), a three-tier model (LP/P are positive, VUS are inconclusive, LB/B are negative) and a two-tier model (LP/P are clinically actionable, VUS/LB/B are not). We compared the COGR classifications to automated classifications generated by Franklin. RESULTS Twelve laboratories submitted classifications for 44 510 unique variants. 2419 variants (5.4%) were classified by two or more laboratories. From baseline to after reassessment, the number of discordant variants decreased from 833 (34.4% of variants reported by two or more laboratories) to 723 (29.9%) based on the five-tier model, 403 (16.7%) to 279 (11.5%) based on the three-tier model and 77 (3.2%) to 37 (1.5%) based on the two-tier model. Compared with the COGR classification, the automated Franklin classifications had 94.5% sensitivity and 96.6% specificity for identifying actionable (P or LP) variants. CONCLUSIONS The COGR provides a standardised mechanism for laboratories to identify discordant variant interpretations and reduce discordance in genetic test result delivery. Such quality assurance programmes are important as genetic testing is implemented more widely in clinical care.
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Affiliation(s)
- Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Justin Mayers
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Sherryl Taylor
- Alberta Precision Laboratories, Edmonton, Alberta, Canada.,Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Stacey Hume
- Alberta Precision Laboratories, Edmonton, Alberta, Canada.,Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ron Agatep
- Shared Health, Winnipeg, Manitoba, Canada.,Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Elizabeth Spriggs
- Shared Health, Winnipeg, Manitoba, Canada.,Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Harriet E Feilotter
- Kingston Health Sciences Centre, Kingston, Ontario, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Laura Semenuk
- Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Henry Wong
- Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lorena Lazo de la Vega
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christian R Marshall
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Michelle M Axford
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Talia Silver
- Genome Diagnostics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - William D Foulkes
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Marcos Clavier
- Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - George Chong
- Lady David Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Ryan E Lamont
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sean S Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Mohammad Reza Akbari
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada .,Lunenfeld Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Shickh S, Rafferty SA, Clausen M, Kodida R, Mighton C, Panchal S, Lorentz J, Ward T, Watkins N, Elser C, Eisen A, Carroll JC, Glogowski E, Schrader KA, Lerner-Ellis J, Kim RH, Chitayat D, Shuman C, Bombard Y. The role of digital tools in the delivery of genomic medicine: enhancing patient-centered care. Genet Med 2021; 23:1086-1094. [PMID: 33654192 DOI: 10.1038/s41436-021-01112-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Alternative models of genetic counseling are needed to meet the rising demand for genomic sequencing. Digital tools have been proposed as a method to augment traditional counseling and reduce burden on professionals; however, their role in delivery of genetic counseling is not established. This study explored the role of the Genomics ADvISER, a digital decision aid, in delivery of genomic counseling. METHODS We performed secondary analysis of 52 pretest genetic counseling sessions that were conducted over the course of a randomized controlled trial evaluating the effectiveness of the Genomics ADvISER. As part of the trial, participants were randomized to receive standard counseling or use the tool and then speak with a counselor. A qualitative interpretive description approach using thematic analysis and constant comparison was used for analysis. RESULTS In the delivery of genomic counseling, the Genomics ADvISER contributed to enhancing counseling by (1) promoting informed dialogue, (2) facilitating preference-sensitive deliberation, and (3) deepening personalization of decisions, all of which represent fundamental principles of patient-centered care: providing clear high-quality information, respecting patients' values, preferences, and expressed needs, and providing emotional support. CONCLUSION This study demonstrates that our digital tool contributed to enhancing patient-centered care in the delivery of genomic counseling.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Sara A Rafferty
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marc Clausen
- St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Rita Kodida
- St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Seema Panchal
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | | | - Thomas Ward
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | | | - Christine Elser
- University Health Network, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - June C Carroll
- Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Raymond H Kim
- Hospital for Sick Children, Toronto, ON, Canada.,University Health Network, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - David Chitayat
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Cheryl Shuman
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.
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Oldfield LE, Li T, Tone A, Aronson M, Edwards M, Holter S, Quevedo R, Van de Laar E, Lerner-Ellis J, Pollett A, Clarke B, Tabori U, Gallinger S, Ferguson SE, Pugh TJ. An Integrative DNA Sequencing and Methylation Panel to Assess Mismatch Repair Deficiency. J Mol Diagn 2020; 23:242-252. [PMID: 33259954 DOI: 10.1016/j.jmoldx.2020.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/09/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022] Open
Abstract
Clinical testing for mismatch repair (MMR) deficiency often entails serial testing of tumor and constitutional DNA using multiple assays. To minimize cost and specimen requirements of MMR testing, we developed an integrated targeted sequencing protocol (termed MultiMMR) that tests for promoter methylation, mutations, copy number alterations, copy neutral loss of heterozygosity, and microsatellite instability from a single aliquot of DNA. Hybrid capture of DNA-sequencing libraries constructed with methylated adapters was performed on 142 samples (60 tumors and 82 constitutional samples) from 82 patients with MMR-associated colorectal, endometrial, and brain cancers as well as a synthetic DNA mix with 11 known mutations. The captured material was split to enable parallel bisulfite and conventional sequence analysis. The panel targeted microsatellite regions and 13 genes associated with MMR, hypermutation, and hereditary colorectal cancer. MultiMMR recapitulated clinical testing results in 23 of 24 cases, was able to explain MMR loss in an additional 29 of 48 patients with incomplete or inconclusive testing, and identified all 11 MMR variants within the synthetic DNA mix. Promoter methylation and microsatellite instability analysis found 95% and 97% concordance with clinical testing, respectively. We report the feasibility for amalgamation of the current stepwise and complex clinical testing workflow into an integrated test for hereditary and somatic causes of MMR deficiency.
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Affiliation(s)
- Leslie E Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rene Quevedo
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Blaise Clarke
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Uri Tabori
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sarah E Ferguson
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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Kim SR, Tone A, Kim R, Cesari M, Clarke B, Eiriksson L, Hart T, Aronson M, Holter S, Lytwyn A, Maganti M, Oldfield L, Gallinger S, Bernardini MQ, Oza AM, Djordjevic B, Lerner-Ellis J, Van de Laar E, Vicus D, Pugh TJ, Pollett A, Ferguson SE. Tumor site discordance in mismatch repair deficiency in synchronous endometrial and ovarian cancers. Int J Gynecol Cancer 2020; 30:1951-1958. [PMID: 33082239 DOI: 10.1136/ijgc-2020-001927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES For synchronous endometrial and ovarian cancers, most centers rely on mismatch repair testing of the endometrial cancer to identify Lynch syndrome, and neglect the ovarian tumor site completely. We examined the mismatch repair immunohistochemistry and microsatellite instability results from the endometrium and ovary to assess discordance between the tumor sites and between tests. METHODS 30 women with newly diagnosed synchronous endometrial and ovarian cancer were prospectively recruited from three cancer centers in Ontario, Canada. Both tumor sites were assessed for mismatch repair deficiency by immunohistochemistry and microsatellite instability test; discordance in results between tumor sites and discordance between test results at each site was examined. Cases with discordant results had tumors sequenced with a targeted panel in order to reconcile the findings. All women underwent mismatch repair gene germline testing. RESULTS Of 30 patients, 11 (37%) were mismatch repair deficient or microsatellite instable at either tumor site, with 5 (17%) testing positive for Lynch syndrome. Mismatch repair immunohistochemistry expression was discordant between endometrial and ovarian tumor sites in 2 of 27 patients (7%) while microsatellite instability results were discordant in 2 of 25 patients (8%). Relying on immunohistochemistry or microsatellite instability alone on the endometrial tumor would have missed one and three cases of Lynch syndrome, respectively. One patient with Lynch syndrome with a PMS2 pathogenic variant was not detected by either immunohistochemistry or microsatellite instability testing. The rate of discordance between immunohistochemistry and microsatellite instability test was 3.8% in the ovary and 12% in the endometrium. CONCLUSIONS There was discordance in immunohistochemistry and microsatellite instability results between tumor sites and between tests within each site. Endometrial tumor testing with mismatch repair immunohistochemistry performed well, but missed one case of Lynch syndrome. Given the high incidence of Lynch syndrome (17%), consideration may be given to germline testing in all patients with synchronous endometrial and ovarian cancers.
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Affiliation(s)
- Soyoun Rachel Kim
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada.,Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
| | - Alicia Tone
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Raymond Kim
- Fred A Litwin Family Centre for Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada.,Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Matthew Cesari
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Blaise Clarke
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lua Eiriksson
- Gynecologic Oncology, Juravinski Cancer Centre, Hamilton, Ontario, Canada
| | - Tae Hart
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada.,Psychology, Ryerson University, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alice Lytwyn
- Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Manjula Maganti
- Biostatistics, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- General Surgery, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada.,Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Bojana Djordjevic
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Danielle Vicus
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada.,Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - Aaron Pollett
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital Pathology and Laboratory Medicine, Toronto, Ontario, Canada
| | - Sarah Elizabeth Ferguson
- Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada .,Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
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Metcalfe KA, Eisen A, Poll A, Candib A, McCready D, Cil T, Wright F, Lerner-Ellis J, McCuaig J, Graham T, Sun P, Akbari M, Narod SA. Rapid Genetic Testing for BRCA1 and BRCA2 Mutations at the Time of Breast Cancer Diagnosis: An Observational Study. Ann Surg Oncol 2020; 28:2219-2226. [PMID: 32989658 DOI: 10.1245/s10434-020-09160-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND This study aimed to evaluate the impact of rapid genetic testing (RGT) for BRCA1 and BRCA2 at the time of breast cancer diagnosis on treatment choices. Bilateral mastectomy for the treatment of breast cancer in women with a BRCA1 or BRCA2 mutation offers a reduction in the risk of contralateral breast cancer. It is unclear whether offering RGT at the time of breast cancer diagnosis has an impact on women's surgical decision-making. METHODS Women with breast cancer diagnosed between June 2013 and May 2018 were recruited from four academic health sciences centers in Toronto, Canada. The participants completed a questionnaire before genetic testing, then one week and one year after disclosure of the genetic test result. Before surgery, RGT was performed. Diagnostic, pathologic, and treatment data were compared between those with and those without a BRCA mutation. RESULTS The study enrolled 1007 women who consented to RGT. The mean age of the participants was 46.3 years, and the median time to result disclosure was 10 days. A BRCA mutation was found in 6% of the women. The women with a BRCA mutation were significantly more likely to elect for bilateral mastectomy than the women without a BRCA mutation (p < 0.0001). Of the BRCA-positive patients, 95.7% reported that they used their genetic test result to make a surgical decision. CONCLUSIONS The women provided with RGT at the time of breast cancer diagnosis use the genetic information to make treatment decisions, and the majority of those identified with a BRCA mutation elect for a bilateral mastectomy.
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Affiliation(s)
- Kelly A Metcalfe
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, ON, Canada. .,Women's College Research Institute, Toronto, Canada.
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Aletta Poll
- Women's College Research Institute, Toronto, Canada
| | | | | | - Tulin Cil
- Princess Margaret Hospital, Toronto, Canada
| | | | | | | | - Tracy Graham
- Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Ping Sun
- Women's College Research Institute, Toronto, Canada
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Lerner-Ellis J, Mighton C, Lazaro C, Watkins N, Di Gioacchino V, Wong A, Chang MC, Charames GS. Correction to: Multigene panel testing for hereditary breast and ovarian cancer in the province of Ontario. J Cancer Res Clin Oncol 2020; 147:2487. [PMID: 32975687 DOI: 10.1007/s00432-020-03399-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada. .,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada. .,Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
| | - Chloe Mighton
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Conxi Lazaro
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Hereditary Cancer Program, ICO-IDIBELL, Barcelona, Spain.,Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada
| | - Nicholas Watkins
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Di Gioacchino
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Andrew Wong
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Martin C Chang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.,University of Vermont Cancer Center, Burlington, VT, USA
| | - George S Charames
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
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Shickh S, Gutierrez Salazar M, Zakoor KR, Lázaro C, Gu J, Goltz J, Kleinman D, Noor A, Khalouei S, Mighton C, Reble E, Kodida R, Bombard Y, DiTroia S, Baxter S, Watkins N, Care M, Adler A, Horsburgh S, Morar O, Murphy J, Nevay DL, Szybowska M, Aronson M, Panchal S, Godoy R, Holter S, Randall Armel S, Semotiuk K, Elser C, Kim RH, Chitayat D, So J, Faghfoury H, Silver J, Morel CF, Lerner-Ellis J. Exome and genome sequencing in adults with undiagnosed disease: a prospective cohort study. J Med Genet 2020; 58:275-283. [PMID: 32581083 DOI: 10.1136/jmedgenet-2020-106936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Exome and genome sequencing have been demonstrated to increase diagnostic yield in paediatric populations, improving treatment options and providing risk information for relatives. There are limited studies examining the clinical utility of these tests in adults, who currently have limited access to this technology. METHODS Patients from adult and cancer genetics clinics across Toronto, Ontario, Canada were recruited into a prospective cohort study evaluating the diagnostic utility of exome and genome sequencing in adults. Eligible patients were ≥18 years of age and suspected of having a hereditary disorder but had received previous uninformative genetic test results. In total, we examined the diagnostic utility of exome and genome sequencing in 47 probands and 34 of their relatives who consented to participate and underwent exome or genome sequencing. RESULTS Overall, 17% (8/47) of probands had a pathogenic or likely pathogenic variant identified in a gene associated with their primary indication for testing. The diagnostic yield for patients with a cancer history was similar to the yield for patients with a non-cancer history (4/18 (22%) vs 4/29 (14%)). An additional 24 probands (51%) had an inconclusive result. Secondary findings were identified in 10 patients (21%); three had medically actionable results. CONCLUSIONS This study lends evidence to the diagnostic utility of exome or genome sequencing in an undiagnosed adult population. The significant increase in diagnostic yield warrants the use of this technology. The identification and communication of secondary findings may provide added value when using this testing modality as a first-line test.
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Affiliation(s)
- Salma Shickh
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Mariana Gutierrez Salazar
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Kathleen-Rose Zakoor
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Conxi Lázaro
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet, Barcelona, Spain.,Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - Jessica Gu
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Genetics, Medcan Clinic, Toronto, Ontario, Canada
| | - Jamie Goltz
- University of Guelph, Guelph, Ontario, Canada
| | - Dakota Kleinman
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Abdul Noor
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Sam Khalouei
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Chloe Mighton
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rita Kodida
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Broad Institute, Cambridge, Massachusetts, USA
| | - Samantha Baxter
- Center for Mendelian Genomics, Broad Institute, Cambridge, Massachusetts, USA
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Arnon Adler
- Department of Cardiology, Peter Munk Cardiac Centre, Toronto General Hospital, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sheri Horsburgh
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Oana Morar
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Clinical Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Jillian Murphy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Dayna-Lynn Nevay
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Marta Szybowska
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Seema Panchal
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Ruth Godoy
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Lifelabs, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Familial Breast and Ovarian Cancer Clinic, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Christine Elser
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Raymond H Kim
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Joyce So
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Faghfoury
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Josh Silver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Chantal F Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
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Lerner-Ellis J, Sopik V, Wong A, Lázaro C, Narod SA, Charames GS. Retesting of women who are negative for a BRCA1 and BRCA2 mutation using a 20-gene panel. J Med Genet 2019; 57:380-384. [PMID: 31784482 DOI: 10.1136/jmedgenet-2019-106403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 10/04/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND The value of retesting women who previously tested negative for a pathogenic variant (mutation) in BRCA1 and BRCA2 using an expanded panel of breast and ovarian cancer genes is unclear. METHODS We studied 110 BRCA1/2-negative women who were retested using a panel of 20 breast and/or ovarian cancer susceptibility genes at the Advanced Molecular Diagnostics Laboratory (AMDL) at Mount Sinai Hospital in Toronto between March 2017 and March 2019. All patients had previously tested negative for BRCA pathogenic variants at the AMDL between January 2012 and March 2018 and were subsequently referred for retesting by their physician. RESULTS Overall, six pathogenic variants in genes other than BRCA1 and BRCA2 were found (prevalence 5.5%). There were two pathogenic variants found in RAD51C, and one found in each of BRIP1, PALB2, PMS2 and PTEN. The prevalence of pathogenic variants was 6.5% for women affected with cancer (6 of 93), including 4.9% for women with breast cancer (4 of 82) and 22.2% for women with ovarian cancer (2 of 9). None of the 17 unaffected women had a clinically significant or pathogenic variant. There were 44 women (40%) for whom the result of the panel test was inconclusive due to the detection of a variant of uncertain significance. CONCLUSIONS Our findings indicate that the retesting of BRCA1/2-negative individuals with an expanded panel of 20 breast and ovarian cancer genes can produce clinically relevant results, with a yield of 5.5% for pathogenic variants in genes other than BRCA1 and BRCA2.
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Affiliation(s)
- Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada .,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Victoria Sopik
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Conxi Lázaro
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
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Shickh S, Clausen M, Mighton C, Gutierrez Salazar M, Zakoor KR, Kodida R, Reble E, Elser C, Eisen A, Panchal S, Aronson M, Graham T, Armel SR, Morel CF, Fattouh R, Glogowski E, Schrader KA, Hamilton JG, Offit K, Robson M, Carroll JC, Isaranuwatchai W, Kim RH, Lerner-Ellis J, Thorpe KE, Laupacis A, Bombard Y. Health outcomes, utility and costs of returning incidental results from genomic sequencing in a Canadian cancer population: protocol for a mixed-methods randomised controlled trial. BMJ Open 2019; 9:e031092. [PMID: 31594892 PMCID: PMC6797333 DOI: 10.1136/bmjopen-2019-031092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Genomic sequencing has rapidly transitioned into clinical practice, improving diagnosis and treatment options for patients with hereditary disorders. However, large-scale implementation of genomic sequencing faces challenges, especially with regard to the return of incidental results, which refer to genetic variants uncovered during testing that are unrelated to the primary disease under investigation, but of potential clinical significance. High-quality evidence evaluating health outcomes and costs of receiving incidental results is critical for the adoption of genomic sequencing into clinical care and to understand the unintended consequences of adoption of genomic sequencing. We aim to evaluate the health outcomes and costs of receiving incidental results for patients undergoing genomic sequencing. METHODS AND ANALYSIS We will compare health outcomes and costs of receiving, versus not receiving, incidental results for adult patients with cancer undergoing genomic sequencing in a mixed-methods randomised controlled trial. Two hundred and sixty patients who have previously undergone first or second-tier genetic testing for cancer and received uninformative results will be recruited from familial cancer clinics in Toronto, Ontario. Participants in both arms will receive cancer-related results. Participants in the intervention arm have the option to receive incidental results. Our primary outcome is psychological distress at 2 weeks following return of results. Secondary outcomes include behavioural consequences, clinical and personal utility assessed over the 12 months after results are returned and health service use and costs at 12 months and 5 years. A subset of participants and providers will complete qualitative interviews about utility of incidental results. ETHICS AND DISSEMINATION This study has been approved by Clinical Trials Ontario Streamlined Research Ethics Review System that provides ethical review and oversight for multiple sites participating in the same clinical trial in Ontario.Results from the trial will be shared through stakeholder workshops, national and international conferences, and peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT03597165.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Mariana Gutierrez Salazar
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Kathleen-Rose Zakoor
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Rita Kodida
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Christine Elser
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Andrea Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Seema Panchal
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Tracy Graham
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Familial Breast Ovarian Cancer Clinic, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Chantal F Morel
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Fred A. Litwin Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Ramzi Fattouh
- Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - Kasmintan A Schrader
- Department of Molecular Oncology and Hereditary Cancer Program, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jada G Hamilton
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
- Breast Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - June C Carroll
- Ray D Wolfe Department of Family Medicine, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wanrudee Isaranuwatchai
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Centre for exceLlence in Economic Analysis Research (CLEAR), Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Raymond H Kim
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kevin E Thorpe
- Applied Health Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Andreas Laupacis
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Palliative Care, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
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Dossa F, Little T, Metcalfe K, Sutradhar R, Lerner-Ellis J, Meschino W, Eisen A, Baxter NN. What Comes Next? A Cohort Profile of Women Who Have Undergone BRCA1 and BRCA2 Testing in Ontario, Canada. J Am Coll Surg 2019. [DOI: 10.1016/j.jamcollsurg.2019.08.937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Metcalfe KA, Poll A, Eisen A, Lerner-Ellis J, Narod S. Outcomes associated with rapid genetic testing for BRCA1 and BRCA2 at time of breast cancer diagnosis. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1577 Background: Bilateral mastectomy improves survival for women with BRCA-associated breast cancer. Most women do not know their BRCA status at the time of BC diagnosis when making surgical decisions. Rapid genetic testing (RGT) allows a woman to have genetic test results prior to treatment decision making, but it is unclear if RGT has an impact on treatment choices. It is also unclear if there are psychosocial implications associated with genetic testing at the time of breast cancer diagnosis. The objective of the current study was to assess the impact of RGT at the time of BC diagnosis on surgical decision-making and psychosocial functioning. Methods: Eligible women were referred from participating surgeons at BC diagnosis. Women completed baseline questionnaires assessing treatment preferences, cancer related distress, anxiety, and depression. All participants received in-person pre-test genetic counselling and genetic test results were given within 10 days. Participants completed surveys at 1 week and 1 year post-genetic testing to assess treatments and psychosocial functioning. Results: 1010 women consented to participate and 60 (5.9%) were identified with a BRCA mutation. 15% of those identified with a BRCA mutation did not meet provincial eligibility criteria for genetic testing, and 20% were eligible prior to a breast cancer diagnosis but had not received testing. Mean levels of cancer-related distress, anxiety and depression declined significantly from baseline to 1 year for all women (all p < .05), and there were no differences at any time point between those with and without a BRCA mutation. Of those identified with a BRCA mutation, 67.3% reported that their surgery choice changed. 73.7% of BRCA carriers had a bilateral mastectomy, compared to 20.2% of BRCA negative (p < 0.001). Most women used genetic testing results for surgical decision making (96.1% of BRCA positive and 86.4% for negative). Conclusions: Rapid genetic testing for BRCA1 and BRCA2 at the time of BC diagnosis does not have a negative impact on psychosocial functioning. There are no differences in cancer-related distress, anxiety or depression between women who receive a positive result compare to a negative genetic test result. Furthermore, surgical choice changed for many women identified with a BRCA mutation, with the majority electing for bilateral mastectomy.
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Affiliation(s)
| | - Aletta Poll
- Women's College Hospital, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Odette Cancer Centre, Toronto, ON, Canada
| | | | - Steven Narod
- Women’s College Research Institute, Toronto, ON, Canada
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Mighton C, Carlsson L, Clausen M, Casalino S, Shickh S, McCuaig L, Joshi E, Panchal S, Graham T, Aronson M, Piccinin C, Winter-Paquette L, Semotiuk K, Lorentz J, Mancuso T, Ott K, Silberman Y, Elser C, Eisen A, Kim RH, Lerner-Ellis J, Carroll JC, Glogowski E, Schrader K, Bombard Y. Development of patient "profiles" to tailor counseling for incidental genomic sequencing results. Eur J Hum Genet 2019; 27:1008-1017. [PMID: 30846854 DOI: 10.1038/s41431-019-0352-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 01/17/2023] Open
Abstract
Guidelines recommend that providers engage patients in shared decision-making about receiving incidental results (IR) prior to genomic sequencing (GS), but this can be time-consuming, given the myriad of IR and variation in patients' preferences. We aimed to develop patient profiles to inform pre-test counseling for IR. We conducted semi-structured interviews with participants as a part of a randomized trial of the GenomicsADvISER.com, a decision aid for selecting IR. Interviews explored factors participants considered when deliberating over learning IR. Interviews were analyzed by thematic analysis and constant comparison. Participants were mostly female (28/31) and about half of them were over the age of 50 (16/31). We identified five patient profiles that reflect common contextual factors, attitudes, concerns, and perceived utility of IR. Information Enthusiasts self-identified as "planners" and valued learning most or all IR to enable planning and disease prevention because "knowledge is power". Concerned Individuals defined themselves as "anxious," and were reluctant to learn IR, anticipating negative psychological impacts from IR. Contemplators were discerning about the value and limitations of IR, weighing health benefits with the impacts of not being able to "un-know" information. Individuals of Advanced Life Stage did not consider IR relevant for themselves and primarily considered their implications for family members. Reassurance Seekers were reassured by previous negative genetic test results which shaped their expectations for receiving no IR: "hopefully [GS will] be negative, too. And then I can rest easy". These profiles could inform targeted counseling for IR by providing a framework to address common values, concerns. and misconceptions.
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Affiliation(s)
- Chloe Mighton
- University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | | | | | | | - Salma Shickh
- University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | - Laura McCuaig
- University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | - Esha Joshi
- University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | - Seema Panchal
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Tracy Graham
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Melyssa Aronson
- University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | - Laura Winter-Paquette
- University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Kara Semotiuk
- University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | - Talia Mancuso
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Karen Ott
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | | | | | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Raymond H Kim
- University Health Network, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - June C Carroll
- University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | | | - Yvonne Bombard
- University of Toronto, Toronto, ON, Canada. .,St. Michael's Hospital, Toronto, ON, Canada.
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Dossa F, Cusimano MC, Sutradhar R, Metcalfe K, Little T, Lerner-Ellis J, Eisen A, Meschino WS, Baxter NN. Real-world health services utilisation and outcomes after BRCA1 and BRCA2 testing in Ontario, Canada: the What Comes Next Cohort Study protocol. BMJ Open 2018; 8:e025317. [PMID: 30181190 PMCID: PMC6129086 DOI: 10.1136/bmjopen-2018-025317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Women who have pathogenic mutations in the BRCA1 and BRCA2 genes are at greatly increased risks for breast and ovarian cancers. Although risk-reduction strategies can be undertaken by these women, knowledge regarding the uptake of these strategies is limited. Additionally, the healthcare behaviours of women who receive inconclusive test results are not known. This study protocol describes the creation of a retrospective cohort of women who have undergone genetic testing for BRCA1 and BRCA2, linking genetic test results with administrative data to quantify the uptake of risk-reduction strategies and to assess long-term cancer and non-cancer outcomes after genetic testing. METHODS AND ANALYSIS Approximately two-thirds of BRCA1 and BRCA2 testing in Ontario, Canada is performed at North York General Hospital (NYGH) and Mount Sinai Hospital (MSH), Toronto. We will use registries at these sites to assemble a cohort of approximately 17 000 adult women who underwent BRCA1 and BRCA2 testing from January 2007 to April 2016. Trained chart abstractors will obtain detailed information for all women tested over this period, including demographics, personal and family cancer histories and genetic test results. We will link these data to provincial administrative databases, enabling assessment of healthcare utilisation and long-term outcomes after testing. Study outcomes will include the uptake of breast cancer screening and prophylactic breast and ovarian surgery, cancer incidence and mortality and incidence of non-cancer health outcomes, including cardiovascular, osteoporotic and neurodegenerative disease. ETHICS AND DISSEMINATION This study has been approved by the Research Ethics Boards at NYGH (no 16-0035), MSH (no 13-0124) and Sunnybrook Health Sciences Centre (no 275-2016). We plan to disseminate research findings through peer-reviewed publications and presentations at national and international meetings.
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Affiliation(s)
- Fahima Dossa
- Division of General Surgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Surgery, St Michael's Hospital, Toronto, Ontario, Canada
- Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Maria C Cusimano
- Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Rinku Sutradhar
- Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Institute for Clinical Evaluative Sciences, Toronto, Ontario, Canada
| | - Kelly Metcalfe
- Lawrence S Bloomberg Faculty of Nursing, University of Toronto, Toronto, Ontario, Canada
| | - Tari Little
- Department of Surgery, St Michael's Hospital, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Andrea Eisen
- Sunnybrook Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Wendy S Meschino
- Department of Molecular Genetics, North York General Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Nancy N Baxter
- Division of General Surgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Surgery, St Michael's Hospital, Toronto, Ontario, Canada
- Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Institute for Clinical Evaluative Sciences, Toronto, Ontario, Canada
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Bombard Y, Clausen M, Mighton C, Carlsson L, Casalino S, Glogowski E, Schrader K, Evans M, Scheer A, Baxter N, Hamilton JG, Lerner-Ellis J, Offit K, Robson M, Laupacis A. The Genomics ADvISER: development and usability testing of a decision aid for the selection of incidental sequencing results. Eur J Hum Genet 2018; 26:984-995. [PMID: 29703952 PMCID: PMC6018661 DOI: 10.1038/s41431-018-0144-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 02/08/2023] Open
Abstract
Guidelines recommend patients be informed of their incidental results (IR) when undergoing genomic sequencing (GS), yet there are limited tools to support patients' decisions about learning IR. The aim of this study is to develop and test the usability of a decision aid (DA) to guide patients' selection of IR, and to describe patients' preferences for learning IR following use of the DA. We developed and evaluated a DA using an iterative, mixed-methods process consisting of (1) prototype development, (2) feasibility testing, (3) cognitive interviews, (4) design and programming, and (5) usability testing. We created an interactive online DA called the Genomics ADvISER, a genomics decision AiD about Incidental SEquencing Results. The Genomics ADvISER begins with an educational whiteboard video, and then engages users in a values clarification exercise, knowledge quiz and final choice step, based on a 'binning' framework. Participants found the DA acceptable and intuitive to use. They were enthusiastic towards GS and IR; all selected multiple categories of IR. The Genomics ADvISER is a new patient-centered tool to support the clinical delivery of incidental GS results. The Genomics ADvISER fills critical care gaps, given the health care system's limited genomics expertise and capacity to convey the large volume of IR and their myriad of implications.
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Affiliation(s)
- Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada.
| | - Marc Clausen
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
| | | | - Selina Casalino
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - Michael Evans
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
| | - Adena Scheer
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Nancy Baxter
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Cancer Care Ontario, Toronto, ON, Canada
| | | | - Jordan Lerner-Ellis
- Mount Sinai Health System, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Laupacis
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, ON, Canada
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Shickh S, Clausen M, Mighton C, Casalino S, Joshi E, Glogowski E, Schrader KA, Scheer A, Elser C, Panchal S, Eisen A, Graham T, Aronson M, Semotiuk KM, Winter-Paquette L, Evans M, Lerner-Ellis J, Carroll JC, Hamilton JG, Offit K, Robson M, Thorpe KE, Laupacis A, Bombard Y. Evaluation of a decision aid for incidental genomic results, the Genomics ADvISER: protocol for a mixed methods randomised controlled trial. BMJ Open 2018; 8:e021876. [PMID: 29700101 PMCID: PMC5922516 DOI: 10.1136/bmjopen-2018-021876] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Genome sequencing, a novel genetic diagnostic technology that analyses the billions of base pairs of DNA, promises to optimise healthcare through personalised diagnosis and treatment. However, implementation of genome sequencing faces challenges including the lack of consensus on disclosure of incidental results, gene changes unrelated to the disease under investigation, but of potential clinical significance to the patient and their provider. Current recommendations encourage clinicians to return medically actionable incidental results and stress the importance of education and informed consent. Given the shortage of genetics professionals and genomics expertise among healthcare providers, decision aids (DAs) can help fill a critical gap in the clinical delivery of genome sequencing. We aim to assess the effectiveness of an interactive DA developed for selection of incidental results. METHODS AND ANALYSIS We will compare the DA in combination with a brief Q&A session with a genetic counsellor to genetic counselling alone in a mixed-methods randomised controlled trial. Patients who received negative standard cancer genetic results for their personal and family history of cancer and are thus eligible for sequencing will be recruited from cancer genetics clinics in Toronto. Our primary outcome is decisional conflict. Secondary outcomes are knowledge, satisfaction, preparation for decision-making, anxiety and length of session with the genetic counsellor. A subset of participants will complete a qualitative interview about preferences for incidental results. ETHICS AND DISSEMINATION This study has been approved by research ethics boards of St. Michael's Hospital, Mount Sinai Hospital and Sunnybrook Health Sciences Centre. This research poses no significant risk to participants. This study evaluates the effectiveness of a novel patient-centred tool to support clinical delivery of incidental results. Results will be shared through national and international conferences, and at a stakeholder workshop to develop a consensus statement to optimise implementation of the DA in practice. TRIAL REGISTRATION NUMBER NCT03244202; Pre-results.
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Affiliation(s)
- Salma Shickh
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Marc Clausen
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Chloe Mighton
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Selina Casalino
- St. Michael’s Hospital, Toronto, Ontario, Canada
- Faculty of Science, McMaster University, Hamilton, Ontario, Canada
| | - Esha Joshi
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | | | - Kasmintan A Schrader
- Hereditary Cancer Program, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Adena Scheer
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | | | - Seema Panchal
- Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Tracy Graham
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Kara M Semotiuk
- Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | | | - Michael Evans
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - June C Carroll
- University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Jada G Hamilton
- Memorial Sloan Kettering Cancer Center, New York, Ontario, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, Ontario, USA
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, Ontario, USA
| | - Kevin E Thorpe
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Applied Health Research Centre, Li Ka Shing Institute, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Andreas Laupacis
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Yvonne Bombard
- University of Toronto, Toronto, Ontario, Canada
- St. Michael’s Hospital, Toronto, Ontario, Canada
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Parra-Herran C, Lerner-Ellis J, Xu B, Khalouei S, Bassiouny D, Cesari M, Ismiil N, Nofech-Mozes S. Molecular-based classification algorithm for endometrial carcinoma categorizes ovarian endometrioid carcinoma into prognostically significant groups. Mod Pathol 2017; 30:1748-1759. [PMID: 28776572 DOI: 10.1038/modpathol.2017.81] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/06/2017] [Accepted: 05/07/2017] [Indexed: 02/07/2023]
Abstract
The Cancer Genome Atlas classification divides endometrial carcinoma in biologically distinct groups, and testing for p53, mismatch repair proteins (MMR), and polymerase ɛ (POLE) exonuclease domain mutations has been shown to predict the molecular subgroup and clinical outcome. While abnormalities in these markers have been described in ovarian endometrioid carcinoma, their role in predicting its molecular profile and prognosis is still not fully explored. Patients with ovarian endometrioid carcinomas treated surgically in a 14-year period were selected. Only tumors with confirmation of endometrioid histology and negative WT1 and Napsin-A were included. POLE mutational analysis and immunohistochemistry for p53, MLH1, MSH2, MSH6, and PMS2 was performed in formalin-fixed, paraffin-embedded tissue. Following the molecular classifier proposed for endometrial carcinoma (Br J Cancer2015;113:299-310), cases were classified as POLE mutated, MMR abnormal, p53 abnormal, and p53 wild type. Clinicopathologic information was recorded, including patient outcome. In all, 72 cases were included, distributed as follows: 7 (10%) POLE mutated; 6 (8%) MMR abnormal; 17 (24%) p53 abnormal; and 42 (58%) p53 wild type. The molecular classification correlated with disease-free survival in multivariate analysis (P=0.003), independently of tumor grade and stage. Correlation with overall survival approached statistical significance (P=0.051). POLE-mutated and MMR-abnormal tumors had excellent survival, whereas p53-abnormal tumors had significantly higher rates of recurrence and death. Ovarian endometroid carcinoma can be classified in clinically meaningful subgroups by testing for molecular surrogates, akin to endometrial cancer. MMR and POLE alterations seem to identify a subset of ovarian endometrioid carcinomas with excellent outcome; conversely, abnormal p53 carries a worse prognosis. In the era of personalized medicine, the use of these markers in the routine evaluation of ovarian endometrioid tumors should be considered.
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Affiliation(s)
- Carlos Parra-Herran
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Bin Xu
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sam Khalouei
- Department of Pathology and Laboratory Medicine, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Dina Bassiouny
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Pathology, Mansoura University, Mansoura, Egypt
| | - Matthew Cesari
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Nadia Ismiil
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sharon Nofech-Mozes
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Parra-Herran C, Lerner-Ellis J, Xu B, Bassiouny D, Cesari M, Ismiil N, Nofech-Mozes S. Molecular-based classification algorithm for endometrial carcinoma to categorize ovarian endometrioid carcinoma into prognostically significant groups. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e17081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e17081 Background: The Cancer Genome Atlas classification divides endometrial carcinoma in biologically distinct groups, and testing for p53, mismatch repair proteins (MMR) and polymerase ɛ (POLE) exonuclease domain mutations has been shown to predict the molecular subgroup and clinical outcome. While abnormalities in these markers have been described in ovarian endometrioid carcinoma (OEC), their role in predicting its molecular profile and prognosis is still not fully explored. Methods: OECs resected in a 14 year period were retrieved. Only tumors with confirmed endometrioid histology and negative WT1 were included. POLE mutational analysis and immunohistochemistry for p53, MLH1, MSH2, MSH6 and PMS2 was performed in formalin-fixed, paraffin-embedded tissue. Following the molecular classifier proposed for endometrial carcinoma ( B J Cancer 2015;113:299-310), cases were classified as: POLE mutated, MMR abnormal, p53 abnormal and p53 wild type. Clinicopathologic information was recorded including patient outcome. Results: 73 tumors were successfully reviewed and tested. Of these, 8 (11%) were POLE mutated, 6 (8%) were MMR abnormal and 17 (23%) were p53 abnormal; the remaining 42 cases (58%) were p53 wild type (no POLE, p53 or MMR abnormalities). Mean follow-up period was 69 months (median 62, range 1-179). The molecular classification was an independent predictor for disease free and overall survival on multivariate analysis (p = 0.005 and 0.045 respectively, Cox proportional hazard model). POLE mutated and MMR abnormal groups had 100% 5 year DFS and OS. p53 wild type cases had intermediate survival rates (86% DFS and OS). Conversely, the p53 abnormal group had worse outcomes with 42% DFS and 76% OS at 5 years. Conclusions: OEC can be classified into prognostically distinct subgroups by testing for molecular surrogates, akin to endometrial cancer. MMR and POLE alterations seem to identify a subset of ovarian endometrioid carcinomas with excellent outcome; conversely, abnormal p53 expression carries a worse prognosis. In the era of personalized medicine, the use of these markers in the routine evaluation of ovarian endometrioid tumors should be considered.
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Affiliation(s)
- Carlos Parra-Herran
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | | | - Bin Xu
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Dina Bassiouny
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Matthew Cesari
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Nadia Ismiil
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Sharon Nofech-Mozes
- University of Toronto - Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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Abstract
1527 Background: In Canada, genetic testing for BRCA1 and BRCA2 is available free of charge to women who meet eligibility criteria, based on personal and family history of cancer. Less than 10% of women are identified with a BRCA mutation, despite features of hereditary cancer. PALB2 has been identified as a moderate penetrance gene in various populations. In the current study, we examined the frequency of PALB2 mutations in women with breast or ovarian cancer who met criteria for genetic testing for BRCA1 and BRCA2and tested negative. Methods: DNA samples from women with breast or ovarian cancer, who met criteria for provincial BRCA1 and BRCA2 genetic testing and tested negative between the years of 2007 and 2014 were included in this study. All 13 coding exons of PALB2 plus 20 base pairs from the exon boundaries were amplified using Wafergen SmartChip technology. The amplified DNA were paired-end sequenced at 2x250 cycles using an Illumina MiSeq sequencer. Results: 2,225 women with breast cancer and 429 women with ovarian cancer were tested for PALB2 mutations. No PALB2 mutations were found in women with ovarian cancer. Seventeen deleterious PALB2 mutations were detected in women with breast cancer (0.8%). The frequency of PALB2 mutations was significantly higher in women with bilateral breast cancer (2.4%) compared to women with unilateral breast cancer (0.6%) (p = 0.01). There was no significant difference in age at diagnosis between those with and without a PALB2mutation (50.9 years vs 53.8 years; p = 0.34). Conclusions: Genetic testing for PALB2 should be considered for high-risk women with breast cancer, especially those who present with bilateral breast cancer. However, PALB2 does not appear to contribute to ovarian cancer which has implications for counselling women who are identified with a PALB2 mutation.
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Affiliation(s)
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Steven Narod
- Women’s College Research Institute, Toronto, ON, Canada
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Lerner-Ellis J, Donenberg T, Ahmed H, George S, Wharfe G, Chin S, Lowe D, Royer R, Zhang S, Narod S, Hurley J, Akbari MR. A high frequency of PALB2 mutations in Jamaican patients with breast cancer. Breast Cancer Res Treat 2017; 162:591-596. [PMID: 28194609 DOI: 10.1007/s10549-017-4148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 01/09/2023]
Abstract
PURPOSE Jamaica is an island nation with one of the highest breast cancer incidence rates in the Caribbean (40/100,000 per year). The contribution of cancer susceptibility gene mutations to the burden of breast cancer in Jamaica has not yet been explored. We sought to determine the prevalence of germline mutations in BRCA1, BRCA2, and PALB2 in 179 unselected Jamaican women with breast cancer. METHODS We sequenced the entire coding regions of BRCA1, BRCA2, and PALB2 for all the study subjects. RESULTS Overall, 8 of 179 patients (4.5%) had a mutation in one of the three genes: one in BRCA1, two in BRCA2, and five in PALB2. CONCLUSIONS These data suggest that in addition to BRCA1 and BRCA2, PALB2 should be included in genetic testing for breast cancer patients in Jamaica.
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Affiliation(s)
- Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Talia Donenberg
- Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | - Humayun Ahmed
- Women's College Research Institute, Women's College Hospital, 76 Grenville St.Room 6421, Toronto, ON, M5S 1B2, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Sophia George
- Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | | | - Sheray Chin
- University of the West Indies, Mona, Jamaica
| | - Dwight Lowe
- University of the West Indies, Mona, Jamaica
| | - Robert Royer
- Women's College Research Institute, Women's College Hospital, 76 Grenville St.Room 6421, Toronto, ON, M5S 1B2, Canada
| | - Shiyu Zhang
- Women's College Research Institute, Women's College Hospital, 76 Grenville St.Room 6421, Toronto, ON, M5S 1B2, Canada
| | - Steven Narod
- Women's College Research Institute, Women's College Hospital, 76 Grenville St.Room 6421, Toronto, ON, M5S 1B2, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Judith Hurley
- Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, 76 Grenville St.Room 6421, Toronto, ON, M5S 1B2, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
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Connor AA, Lerner-Ellis J, Akbari MR, Cybulski C, Lubinski J, Badouel C, McNeill H, Dowty JG, Clendenning M, Buchanan DD. Abstract A23: Rare variants in the FAT1 gene may predispose to familial colorectal cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.crc16-a23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Population- and family-based studies suggest germline predisposition in up to 35% of colorectal cancer (CRC) cases. Known genetic factors, including three highly penetrant Mendelian cancer syndromes and approximately 45 low penetrant alleles, account for less than 15% of all CRC and only a small proportion of early onset CRC. Identifying the genes responsible for the “missing” CRC predisposition will inform prevention and management.
Methods: Our discovery cohort were selected to enrich for likely heritable susceptibility and consisted of 127 CRC cases from 86 pedigrees selected from Canadian and Australian CRC Family Registries (CCFRs) that met the Familial Colorectal Cancer Type X definition (satisfy Amsterdam I Criteria and lack other features of known cancer syndromes). Germline DNA from multiple CRC–affected individuals per pedigree underwent whole exome sequencing. The two replication cohorts were composed of pedigrees with multiple generations affected by CRC, one an Australian cohort of 166 families from which multiple affected and unaffected members were genotyped for rare (<0.01 MAF) germline likely deleterious variants in FAT1, the other a Polish cohort of 496 probands that underwent targeted next generation sequencing of FAT1. Alignment and variant calling followed the Genome Analysis Tool Kit “best practices”, and ANNOVAR was used for functional effect, allele frequency and intolerance score annotations. Variant filtering and statistical analysis were done in R (version 3.0). A hemizygous transgenic mouse model of our top genetic candidate was developed and exposed to intra-peritoneal azoxymethane (AOM) to induce colonic dysplasia. Necropsies were performed at 6 months of age, and the colons underwent gross and histologic inspection. This work was supported by grant UM1 CA167551 from the National Cancer Institute (NCI) to the Colon Cancer Family Registry.
Outcomes: Using filter-based approaches in our discovery cohort, we identified rare, non-silent variants in FAT1 that co-segregated with CRC in Ontario (Canadian), Newfoundland (Canadian) and Australian pedigrees, including one stopgain variant that was found in all 4 affected of one Ontario pedigree and in 2 of 6 unaffected. Somatic loss of heterozygosity of FAT1 was seen in available FFPE tumors from 3 Ontario and 4 Australian pedigrees by either Sanger sequencing or microarray. Modified segregation analysis of genotyped multi-case families from the Australian CCFR demonstrated an overall increased risk for CRC in FAT1 carriers (HR 1.44, 95%CI 1.05-1.97), with greater hazard ratios (>2.5) for individual FAT1 variants identified in sufficient numbers of families. Deep sequencing in 496 Polish probands identified 4 additional rare truncating FAT1 variants. Using the ExAC database as controls, variant-level association analyses of the Polish cohort cases revealed two strongly predisposing FAT1 rare missense variants, namely c.T9440G (OR 7.53, 95%CI 4.1-12.8, Fisher's exact test, q < 0.05 by false discovery rates) and c.G3067A (OR 10.8, 95%CI 3.3-26.8, q < 0.05). Gene-level association testing was also significant for increased CRC risk when considering all rare, non-silent FAT1 variants (OR 2.2, 95%CI 1.8-2.6, q < 0.05). 30 FAT1 hemizygous and 28 wild type mice on a CD1 background, balanced for sex and weight, did not show differences in number or greatest size of aberrant crypts, adenoma or adenocarcinoma.
Conclusions: We have shown that rare germline variants in FAT1 may predispose to CRC. Discovery of such causal genes and associated pathways will improve our understanding of early onset CRC for both familial and sporadic cases. Stratifying CRC risk by familial susceptibility genes should foster tailored, cost-effective primary and secondary prevention strategies.
Citation Format: Ashton A. Connor, Jordan Lerner-Ellis, Mohammad R. Akbari, Cezary Cybulski, J Lubinski, Caroline Badouel, Helen McNeill, James G. Dowty, Mark Clendenning, Daniel D. Buchanan. Rare variants in the FAT1 gene may predispose to familial colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A23.
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Affiliation(s)
| | | | | | - Cezary Cybulski
- 2Pomeranian Medical University, Szczecin, West Pomeranian, Poland,
| | - J Lubinski
- 2Pomeranian Medical University, Szczecin, West Pomeranian, Poland,
| | | | | | - James G. Dowty
- 3University of Melbourne, Melbourne, Victoria, Australia
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Metcalfe KA, Narod S, Eisen A, Lerner-Ellis J. Treatment decision making and psychosocial outcomes associated with rapid genetic testing for BRCA1 and BRCA2 in women newly diagnosed with breast cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.1586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Steven Narod
- Women's College Research Institute, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Odette Cancer Centre, Toronto, ON, Canada
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