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Regier DA, Loewen R, Chan B, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, van Karnebeek C, Race S, Elliott AM, Dragojlovic N, Lynd LD, Weymann D. Real-world diagnostic outcomes and cost-effectiveness of genome-wide sequencing for developmental and seizure disorders: Evidence from Canada. Genet Med 2024; 26:101069. [PMID: 38205742 DOI: 10.1016/j.gim.2024.101069] [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: 07/21/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
PURPOSE To determine real-world diagnostic rates, cost trajectories, and cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children with developmental and/or seizure disorders in British Columbia, Canada. METHODS Based on medical records review, we estimated real-world costs and outcomes for 491 patients who underwent standard of care (SOC) diagnostic testing at British Columbia Children's Hospital. Results informed a state-transition Markov model examining cost-effectiveness of 3 competing diagnostic strategies: (1) SOC with last-tier access to ES, (2) streamlined ES access, and (3) first-tier GS. RESULTS Through SOC, 49.4% (95% CI: 40.6, 58.2) of patients were diagnosed at an average cost of C$11,683 per patient (95% CI: 9200, 14,166). Compared with SOC, earlier ES or GS access yielded similar or improved diagnostic rates and shorter times to genetic diagnosis, with 94% of simulations demonstrating cost savings for streamlined ES and 60% for first-tier GS. Net benefit from the perspective of the health care system was C$2956 (95% CI: -608, 6519) for streamlined ES compared with SOC. CONCLUSION Using real-world data, we found earlier access to ES may yield more rapid genetic diagnosis of childhood developmental and seizure disorders and cost savings compared with current practice in a Canadian health care system.
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Affiliation(s)
- Dean A Regier
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Brandon Chan
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children's Hospital Research Institute, Vancouver, Canada; Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Simone Race
- Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada; Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, Canada
| | - Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada.
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2
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Pizzo E, Gianino MM, Damiani G. Cost-Effectiveness of Whole-Genome vs Whole-Exome Sequencing Among Children With Suspected Genetic Disorders. JAMA Netw Open 2024; 7:e2353514. [PMID: 38277144 PMCID: PMC10818217 DOI: 10.1001/jamanetworkopen.2023.53514] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Importance The diagnosis of rare diseases and other genetic conditions can be daunting due to vague or poorly defined clinical features that are not recognized even by experienced clinicians. Next-generation sequencing technologies, such as whole-genome sequencing (WGS) and whole-exome sequencing (WES), have greatly enhanced the diagnosis of genetic diseases by expanding the ability to sequence a large part of the genome, rendering a cost-effectiveness comparison between them necessary. Objective To assess the cost-effectiveness of WGS compared with WES and conventional testing in children with suspected genetic disorders. Design, Setting, and Participants In this economic evaluation, a bayesian Markov model was implemented from January 1 to June 30, 2023. The model was developed using data from a cohort of 870 pediatric patients with suspected genetic disorders who were enrolled and underwent testing in the Ospedale Pediatrico Bambino Gesù, Rome, Italy, from January 1, 2015, to December 31, 2022. The robustness of the model was assessed through probabilistic sensitivity analysis and value of information analysis. Main Outcomes and Measures Overall costs, number of definitive diagnoses, and incremental cost-effectiveness ratios per diagnosis were measured. The cost-effectiveness analyses involved 4 comparisons: first-tier WGS with standard of care; first-tier WGS with first-tier WES; first-tier WGS with second-tier WES; and first-tier WGS with second-tier WGS. Results The ages of the 870 participants ranged from 0 to 18 years (539 [62%] girls). The results of the analysis suggested that adopting WGS as a first-tier strategy would be cost-effective compared with all other explored options. For all threshold levels above €29 800 (US $32 408) per diagnosis that were tested up to €50 000 (US $54 375) per diagnosis, first-line WGS vs second-line WES strategy (ie, 54.6%) had the highest probability of being cost-effective, followed by first-line vs second-line WGS (ie, 54.3%), first-line WGS vs the standard of care alternative (ie, 53.2%), and first-line WGS vs first-line WES (ie, 51.1%). Based on sensitivity analyses, these estimates remained robust to assumptions and parameter uncertainty. Conclusions and Relevance The findings of this economic evaluation encourage the development of policy changes at various levels (ie, macro, meso, and micro) of international health systems to ensure an efficient adoption of WGS in clinical practice and its equitable access.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Elena Pizzo
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Maria Michela Gianino
- Department of Public Health Sciences and Paediatrics, Università di Torino, Turin, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
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3
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Botos L, Szatmári E, Nagy GR. Prenatal and postnatal genetic testing toward personalized care: The non-invasive perinatal testing. Mol Cell Probes 2023; 72:101942. [PMID: 37951513 DOI: 10.1016/j.mcp.2023.101942] [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: 10/10/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
This article investigates how non-invasive prenatal testing and the incorporation of genomic sequencing into newborn screening postnatally are transforming perinatal care. They improve the accuracy of prenatal and neonatal screening, allowing for early interventions and personalized therapies. Non-invasive prenatal testing before birth and saliva-sample-based newborn genomic sequencing after birth can be collectively referred to as non-invasive perinatal testing. Non-invasive prenatal testing is particularly useful for aneuploidy, whereas performance markers worsen as DNA abnormalities shrink in size. Screening for clinically actionable diseases in childhood would be crucial to personalized medical therapy, as the postnatal period remains appropriate for screening for the great majority of monogenic disorders. While genomic data can help diagnose uncommon diseases, challenges like ethics and equity necessitate joint approaches for appropriate integration in this revolutionary journey toward personalized care.
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Affiliation(s)
- Lilla Botos
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Erzsébet Szatmári
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Gyula Richárd Nagy
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary; Intelligenetic Healthcare Services Ltd., Budapest, Hungary.
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Dulsamphan T, Juntama P, Suwanpanich C, Isaranuwatchai W, Silzle M, Poonmaksatit S, Boonsimma P, Shotelersuk V, Visudtibhan A, Lusawat A, Kamolvisit W, Kapol N, Lochid-amnuay S, Sribundit N, Samprasit N, Morton A, Teerawattananon Y. Can knowledgeable experts assess costs and outcomes as if they were ignorant? An experiment within precision medicine evaluation. Int J Technol Assess Health Care 2023; 40:e4. [PMID: 37973547 PMCID: PMC10859837 DOI: 10.1017/s0266462323002714] [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: 03/02/2023] [Revised: 08/08/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVES The purpose of this study is to evaluate the validity of the standard approach in expert judgment for evaluating precision medicines, in which experts are required to estimate outcomes as if they did not have access to diagnostic information, whereas in fact, they do. METHODS Fourteen clinicians participated in an expert judgment task to estimate the cost and medical outcomes of the use of exome sequencing in pediatric patients with intractable epilepsy in Thailand. Experts were randomly assigned to either an "unblind" or "blind" group; the former was provided with the exome sequencing results for each patient case prior to the judgment task, whereas the latter was not provided with the exome sequencing results. Both groups were asked to estimate the outcomes for the counterfactual scenario, in which patients had not been tested by exome sequencing. RESULTS Our study did not show significant results, possibly due to the small sample size of both participants and case studies. CONCLUSIONS A comparison of the unblind and blind approach did not show conclusive evidence that there is a difference in outcomes. However, until further evidence suggests otherwise, we recommend the blind approach as preferable when using expert judgment to evaluate precision medicines because this approach is more representative of the counterfactual scenario than the unblind approach.
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Affiliation(s)
- Thamonwan Dulsamphan
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Parntip Juntama
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Chotika Suwanpanich
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Wanrudee Isaranuwatchai
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Madison Silzle
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Sathida Poonmaksatit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ponghatai Boonsimma
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Anannit Visudtibhan
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Wuttichart Kamolvisit
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Nattiya Kapol
- Department of Health Consumer Protection and Pharmacy Administration, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Surasit Lochid-amnuay
- Department of Health Consumer Protection and Pharmacy Administration, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Namfon Sribundit
- Department of Health Consumer Protection and Pharmacy Administration, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | | | - Alec Morton
- Department of Management Science, Strathclyde Business School, University of Strathclyde, Glasgow, UK
| | - Yot Teerawattananon
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
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5
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Damiani G. Bayesian cost-effectiveness analysis of Whole genome sequencing versus Whole exome sequencing in a pediatric population with suspected genetic disorders. Eur J Health Econ 2023:10.1007/s10198-023-01644-0. [PMID: 37975990 DOI: 10.1007/s10198-023-01644-0] [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] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Genetic diseases are medical conditions caused by sequence or structural changes in an individual's genome. Whole exome sequencing (WES) and whole genome sequencing (WGS) are increasingly used for diagnosing suspected genetic conditions in children to reduce the diagnostic delay and accelerating the implementation of appropriate treatments. While more information is becoming available on clinical efficacy and economic sustainability of WES, the broad implementation of WGS is still hindered by higher complexity and economic issues. The aim of this study is to estimate the cost-effectiveness of WGS versus WES and standard testing for pediatric patients with suspected genetic disorders. A Bayesian decision tree model was set up. Model parameters were retrieved both from hospital administrative datasets and scientific literature. The analysis considered a lifetime time frame and adopted the perspective of the Italian National Health Service (NHS). Bayesian inference was performed using the Markov Chain Monte Carlo simulation method. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI). The present analysis showed that implementing first-line WGS would be a cost-effective strategy, against the majority of the other tested alternatives at a threshold of €30,000-50,000, for diagnosing outpatient pediatric patients with suspected genetic disorders. According to the sensitivity analyses, the findings were robust to most assumption and parameter uncertainty. Lessons learnt from this modeling study reinforces the adoption of first-line WGS, as a cost-effective strategy, depending on actual difficulties for the NHS to properly allocate limited resources.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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6
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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7
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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8
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Lantos JD, Brunelli L, Hayeems RZ. Understanding the Clinical Utility of Genome Sequencing in Critically Ill Newborns. J Pediatr 2023; 258:113438. [PMID: 37088180 DOI: 10.1016/j.jpeds.2023.113438] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023]
Abstract
Diagnostic genome sequencing (GS) in newborns may have many benefits. More accurate diagnosis could spur the development of innovative genomic therapies. A precise diagnosis could help doctors and parents anticipate clinical problems and inform a family's future reproductive choices. However, the integration of GS into neonatal care remains associated with a variety of ethical controversies, including concerns about informed consent, about interpreting uncertain results, about resource allocation and whether access to genomic services could exacerbate health disparities, and about the effect of genome diagnostics on people with disabilities. There also remains significant uncertainty about which babies should be tested and when and how the potential benefits of GS ought to be measured. Probably related to these challenges, some payors have been reluctant to cover the cost of GS for critically ill newborns. Much of the reluctance appears to turn on questions about the clinical benefit associated with GS and whether and for whom GS will be cost-effective. These situations point to the urgent need for careful assessments of the clinical utility of GS in critically ill infants. In this paper, we critically examine the ways in which the clinical utility of GS has been evaluated in this patient population. We focus on "change of management" (COM), a widely used measure of clinical utility for diagnostic GS. We suggest that this measure is often ambiguous because not all COMs can be attributed to genomic results and because not all COMs lead to patient benefit. Finally, we suggest ways that measurement of clinical utility could be improved.
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Affiliation(s)
| | - Luca Brunelli
- University of Utah/Primary Children's Hospital, Salt Lake City, UT
| | - Robin Z Hayeems
- The Hospital for Sick Children/University of Toronto, Toronto, ON, Canada
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9
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Nurchis MC, Raspolini GM, Heidar Alizadeh A, Altamura G, Radio FC, Tartaglia M, Dallapiccola B, Damiani G. Organizational Aspects of the Implementation and Use of Whole Genome Sequencing and Whole Exome Sequencing in the Pediatric Population in Italy: Results of a Survey. J Pers Med 2023; 13:899. [PMID: 37373888 DOI: 10.3390/jpm13060899] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study explores the organizational aspects of whole genome sequencing (WGS) implementation for pediatric patients with suspected genetic disorders in Italy, comparing it with whole exome sequencing (WES). Health professionals' opinions were collected through an internet-based survey and analyzed using a qualitative summative content analysis methodology. Among the 16 respondents, most were clinical geneticists performing only WES, while 5 also used WGS. The key differences identified include higher needs for analyzing genome rearrangements following WES, greater data storage and security requirements for WGS, and WGS only being performed in specific research studies. No difference was detected in centralization and decentralization issues. The main cost factors included genetic consultations, library preparation and sequencing, bioinformatic analysis, interpretation and confirmation, data storage, and complementary diagnostic investigations. Both WES and WGS decreased the need for additional diagnostic analyses when not used as last-resort tests. Organizational aspects were similar for WGS and WES, but economic evidence gaps may exist for WGS in clinical settings. As sequencing costs decline, WGS will likely replace WES and traditional genetic testing. Tailored genomic policies and cost-effectiveness analyses are needed for WGS implementation in health systems. WGS shows promise for enhancing genetics knowledge and expediting diagnoses for pediatric patients with genetic disorders.
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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10
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Metivier E, Prasad M, Prasad C. Neonatal hyperinsulinism-broadening the differential diagnosis. Paediatr Child Health 2023; 28:67-68. [PMID: 37151925 PMCID: PMC10156923 DOI: 10.1093/pch/pxac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/04/2022] [Indexed: 12/23/2022] Open
Affiliation(s)
- Emma Metivier
- Western University Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Madhavi Prasad
- Western University Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Chitra Prasad
- Western University Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
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11
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Wiener EK, Buchanan J, Krause A, Lombard Z. Retrospective file review shows limited genetic services fails most patients - an argument for the implementation of exome sequencing as a first-tier test in resource-constraint settings. Orphanet J Rare Dis 2023; 18:81. [PMID: 37046271 PMCID: PMC10091645 DOI: 10.1186/s13023-023-02642-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/09/2022] [Accepted: 02/12/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Exome sequencing is recommended as a first-line investigation for patients with a developmental delay or intellectual disability. This approach has not been implemented in most resource-constraint settings, including Africa, due to the high cost of implementation. Instead, patients have limited access to services and testing options. Here, we evaluate the effectiveness of a limited genetic testing strategy and contrast the findings to a conceivable outcome if exome sequencing were available instead. RESULTS A retrospective audit of 934 patient files presenting to a medical genetics clinic in South Africa showed that 83% of patients presented with developmental delay as a clinical feature. Patients could be divided into three groups, representing distinct diagnostic pathways. Patient Group A (18%; mean test cost $131) were confirmed with aneuploidies, following a simple, inexpensive test. Patient Group B (25%; mean test cost $140) presented with clinically recognizable conditions but only 39% received a genetic diagnostic confirmation due to limited testing options. Patient Group C - the largest group (57%; mean test cost $337) - presented with heterogenous conditions and DD, and 92% remained undiagnosed after limited available testing was performed. CONCLUSIONS Patients with DD are the largest group of patients seen in medical genetics clinics in South Africa. When clinical features are not distinct, limited testing options drastically restricts diagnostic yield. A cost- and time analysis shows most patients would benefit from first-line exome sequencing, reducing their individual diagnostic odysseys.
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Affiliation(s)
- Emma K Wiener
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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12
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Rezapour A, Souresrafil A, Barzegar M, Sheikhy-Chaman M, Tatarpour P. Economic evaluation of next-generation sequencing techniques in diagnosis of genetic disorders: A systematic review. Clin Genet 2023; 103:513-528. [PMID: 36808726 DOI: 10.1111/cge.14313] [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: 09/28/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023]
Abstract
In recent years, massively parallel sequencing or next generation sequencing (NGS) has considerably changed both the research and diagnostic fields, and rapid developments have led to the combination of NGS techniques in clinical practice, ease of analysis, and detection of genetic mutations. This article aimed at reviewing the economic evaluation studies of the NGS techniques in the diagnosis of genetic diseases. In this systematic review, scientific databases (PubMed, EMBASE, Web of Science, Cochrane, Scopus, and CEA registry) were searched from 2005 to 2022 to identify the related literature on the economic evaluation of NGS techniques in the diagnosis of genetic diseases. Full-text reviews and data extraction were all performed by two independent researchers. The quality of all the articles included in this study was evaluated using the Checklist of Quality of Health Economic Studies (QHES). Out of 20 521 screened abstracts, 36 studies met the inclusion criteria. The mean score of the QHES checklist for the studies was 0.78 (high quality). Seventeen studies were conducted based on modeling. Cost-effectiveness analysis, cost-utility analysis, and cost-minimization analysis were done in 26 studies, 13 studies, and 1 study, respectively. Based on the available evidence and findings, exome sequencing, which is one of the NGS techniques, could have the potential to be used as a cost-effective genomic test to diagnose children with suspected genetic diseases. The results of the present study support the cost-effectiveness of exome sequencing in diagnosing suspected genetic disorders. However, the use of exome sequencing as a first- or second-line diagnostic test is still controversial. Most studies have been conducted in high-income countries, and research on the cost-effectiveness of NGS methods is recommended in low- and middle-income countries.
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Affiliation(s)
- Aziz Rezapour
- Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Aghdas Souresrafil
- Department of Health Services and Health Promotion, School of Health, Occupational Environment Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Barzegar
- Department of English Language, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Sheikhy-Chaman
- Department of Health Economics, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Parvin Tatarpour
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
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14
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Ediae GU, Lemire G, Chisholm C, Hartley T, Eaton A, Osmond M, Rojas SK, Huang L, Gillespie M, Sawyer SL, Boycott KM. The implementation of an enhanced clinical model to improve the diagnostic yield of exome sequencing for patients with a rare genetic disease: A Canadian experience. Am J Med Genet A 2023; 191:338-347. [PMID: 36331261 DOI: 10.1002/ajmg.a.63022] [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: 09/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
The introduction of clinical exome sequencing (ES) has provided a unique opportunity to decrease the diagnostic odyssey for patients living with a rare genetic disease (RGD). ES has been shown to provide a diagnosis in 29%-57% of patients with a suspected RGD, with as many as 70% remaining undiagnosed. There is a need to advance the clinical model of care by more formally integrating approaches that were previously considered research into an enhanced diagnostic workflow. We developed an Exome Clinic, which set out to evaluate a workflow for improving the diagnostic yield of ES for patients with an undiagnosed RGD. Here, we report the outcomes of 47 families who underwent clinical ES in the first year of the clinic. The diagnostic yield from clinical ES was 40% (19/47). Families who remained undiagnosed after ES had the opportunity for follow-up studies that included phenotyping and candidate variant segregation in relatives, genomic matchmaking, and ES reanalysis. This enhanced diagnostic workflow increased the diagnostic yield to 55% (26/47), predominantly through the resolution of variants and genes of uncertain significance. We advocate that this approach be integrated into mainstream clinical practice and highlight the importance of a coordinated translational approach for patients with RGD.
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Affiliation(s)
- Grace Uwaila Ediae
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Alison Eaton
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Lijia Huang
- Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Meredith Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
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15
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Félix TM, Fischinger Moura de Souza C, Oliveira JB, Rico-Restrepo M, Zanoteli E, Zatz M, Giugliani R. Challenges and recommendations to increasing the use of exome sequencing and whole genome sequencing for diagnosing rare diseases in Brazil: an expert perspective. Int J Equity Health 2023; 22:11. [PMID: 36639662 PMCID: PMC9837951 DOI: 10.1186/s12939-022-01809-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
Early diagnosis of genetic rare diseases is an unmet need in Brazil, where an estimated 10-13 million people live with these conditions. Increased use of chromosome microarray assays, exome sequencing, and whole genome sequencing as first-tier testing techniques in suitable indications can shorten the diagnostic odyssey, eliminate unnecessary tests, procedures, and treatments, and lower healthcare expenditures. A selected panel of Brazilian experts in fields related to rare diseases was provided with a series of relevant questions to address before a multi-day conference. Within this conference, each narrative was discussed and edited through numerous rounds of discussion until agreement was achieved. The widespread adoption of exome sequencing and whole genome sequencing in Brazil is limited by various factors: cost and lack of funding, reimbursement, awareness and education, specialist shortages, and policy issues. To reduce the burden of rare diseases and increase early diagnosis, the Brazilian healthcare authorities/government must address the barriers to equitable access to early diagnostic methods for these conditions. Recommendations are provided, including broadening approved testing indications, increasing awareness and education efforts, increasing specialist training opportunities, and ensuring sufficient funding for genetic testing.
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Affiliation(s)
- Têmis Maria Félix
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - Carolina Fischinger Moura de Souza
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - João Bosco Oliveira
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Edmar Zanoteli
- grid.11899.380000 0004 1937 0722Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Mayana Zatz
- grid.11899.380000 0004 1937 0722Human Genome and Stem-cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Roberto Giugliani
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil ,House of Rares, Porto Alegre, Rio Grande do Sul Brazil
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16
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Hayeems RZ, Bernier F, Boycott KM, Hartley T, Michaels-Igbokwe C, Marshall DA. Positioning whole exome sequencing in the diagnostic pathway for rare disease to optimise utility: a protocol for an observational cohort study and an economic evaluation. BMJ Open 2022; 12:e061468. [PMID: 36216418 PMCID: PMC9557316 DOI: 10.1136/bmjopen-2022-061468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Despite the superior diagnostic performance of exome and genome sequencing compared with conventional genetic tests, evidence gaps related to clinical utility and cost effectiveness have limited their availability in routine clinical practice in many jurisdictions. To inform adoption and reimbursement policy, this protocol provides a chain of evidence approach to determining the diagnostic utility, clinical utility and cost-effectiveness of whole exome sequencing (WES) from seven medical genetic centres in two Canadian provinces. METHODS AND ANALYSIS Using a multicentre observational cohort design, we will extract data specific to the pre-WES diagnostic pathway and 1-year post-WES medical management from electronic medical records for 650 patients with rare disease of suspected genetic aetiology who receive WES. The date from the clinical record will be linked to provincial administrative health database to capture healthcare resource use and estimate costs. Our analysis will: (1) define and describe diagnostic testing pathways that occur prior to WES among patients with rare disease, (2) determine the diagnostic utility of WES, characterised as the proportion of patients for whom causative DNA variants are identified, (3) determine the clinical utility of WES, characterised as a change in medical management triggered by WES results, (4) determine the pattern and cost of health service utilisation prior and 1 year following WES among patients who receive a diagnosis, do not receive a diagnosis, or receive an uncertain diagnosis and (5) estimate the cost-effectiveness of WES compared with conventional diagnostic testing pathways, measured by the incremental cost per additional patient diagnosed by WES using simulation modelling. ETHICS AND DISSEMINATION This protocol was approved by Clinical Trials Ontario (CTO-1577) and research ethics boards at the University of Calgary (REB18-0744 and REB20-1449) and University of Alberta (Pro0009156). Findings will be disseminated through academic publications and policy reports.
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Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Francois Bernier
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Paediatrics, Facuty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Christine Michaels-Igbokwe
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Deborah A Marshall
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
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17
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Nurchis MC, Riccardi MT, Damiani G. Health technology assessment of whole genome sequencing in the diagnosis of genetic disorders: a scoping review of the literature. Int J Technol Assess Health Care 2022; 38:e71. [PMID: 36016516 DOI: 10.1017/S0266462322000496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE The aim of this scoping review is to map the available evidence about the use of health technology assessment (HTA) in the assessment of whole genome sequencing (WGS). METHODS A scoping review methodology was adopted. The population, concept, and context framework was used to build up the research question and to establish the eligibility criteria. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews was adopted to implement a comprehensive search strategy. Evidence was retrieved from scientific databases and HTA organizations Web sites. Reports were classified as full HTA, mini-HTA, rapid reviews or other. RESULTS The search strategy identified seven reports. Five HTA organizations from five countries elaborated the reports: one full HTA, four rapid reviews, and two classified as others. The reports were mainly focused on the evaluation of the clinical utility and cost-effectiveness of genome-wide sequencing as well as informing policy questions by providing analyses of organizational and ethical considerations. CONCLUSIONS Few HTA organizations are drafting reports for WGS. It is essential to stimulate a critical reflection during the elaboration of HTA reports for WGS to steer choices of decision makers in the establishment of priorities for research and policy and reimbursement rates.
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18
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Wojcik MH, Del Rosario MC, Agrawal PB. Perspectives of United States neonatologists on genetic testing practices. Genet Med 2022; 24:1372-1377. [PMID: 35304021 DOI: 10.1016/j.gim.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/05/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Genetic disorders often present in the neonatal intensive care unit (NICU), and detecting or confirming these diagnoses has been shown to impact care. However, the availability and use of genetic testing, particularly exome or genome sequencing, among NICUs varies widely. We therefore sought to investigate practice patterns related to genetic testing in NICUs around the country to identify and quantify potential discrepancies. METHODS We designed a survey that was distributed to neonatologists via email. The survey contained questions related to test availability and desirability, the process of test ordering in NICU, and general comfort with ordering and interpreting genetic testing. Demographic data related to the survey participants and characteristics of their NICU were also obtained. RESULTS In total, 162 neonatologists completed the survey, representing 40 states and 112 distinct NICUs. Although nearly all (93.2%) neonatologists attributed a high level of importance to identifying a genetic diagnosis for their patients, genetic consultations were only available at 78% of NICUs and exome or genome sequencing was not available on a regular basis (69% of NICUs). CONCLUSION Although, among US neonatologists surveyed, most feel that genetic tests are indicated for their patients, these are not always clinically available. Further research into implementation barriers is warranted.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA.
| | - Maya C Del Rosario
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA.
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19
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Rodriguez Llorian E, Dragojlovic N, Campbell TM, Friedman JM, Osiovich H, Elliott AM, Lynd LD. The effect of rapid exome sequencing on downstream health care utilization for infants with suspected genetic disorders in an intensive care unit. Genet Med 2022; 24:1675-1683. [PMID: 35622065 DOI: 10.1016/j.gim.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/06/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/12/2023] Open
Abstract
PURPOSE This study aimed to compare downstream utilization of medical services among critically ill infants admitted to intensive care units who received rapid exome sequencing (ES) and those who followed alternative diagnostic testing pathways. METHODS Using propensity score-weighted regression models including sex, age at admission, and severity indicators, we compared a group of 47 infants who underwent rapid ES with a group of 211 infants who did not receive rapid ES. Utilization and cost indicators were compared between cohorts using negative binomial models for utilization and two-part models for costs. RESULTS After controlling for patients' sociodemographic and clinical characteristics, we found no statistically significant difference in outpatient visits, hospitalizations, intensive care unit or total length of stay, or length of stay-associated costs between the cohorts at 12- or 26-month follow-up. Similarly, there was no evidence of higher utilization or costs by the ES group when infants who died were removed from the analysis. CONCLUSION When examining utilization during and beyond the diagnostic trajectory, there is no evidence that ES changes frequency of outpatient visits or use of in-hospital resources in critically ill infants with suspected genetic disorders.
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Affiliation(s)
- Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teresa M Campbell
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- Division of Neonatology, Department of Paediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia, Canada.
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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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21
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Borle K, Kopac N, Dragojlovic N, Rodriguez Llorian E, Friedman JM, Elliott AM, Lynd LD. Where is genetic medicine headed? Exploring the perspectives of Canadian genetic professionals on future trends using the Delphi method. Eur J Hum Genet 2022; 30:496-504. [PMID: 35031678 PMCID: PMC9090755 DOI: 10.1038/s41431-021-01017-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Driven by technological and scientific advances, the landscape of genetic medicine is rapidly changing, which complicates strategic planning and decision-making in this area. To address this uncertainty, we sought to understand genetic professionals' opinions about the future of clinical genetic and genomic services in Canada. We used the Delphi method to survey Canadian genetic professionals about their perspectives on whether scenarios about changes in service delivery and the use of genomic testing would be broadly implemented in their jurisdiction by 2030. We conducted two survey rounds; the response rates were 32% (27/84) and 67% (18/27), respectively. The most likely scenario was the universal use of noninvasive prenatal screening. The least likely scenarios involved population-based genome-wide sequencing for unaffected individuals. Overall, the scenarios perceived as most likely were those that have existing evidence about their benefit and potential medical necessity, whereas scenarios were seen as unlikely if they involved emerging technologies. Participants expected that the need for genetic healthcare services would increase by 2030 owing to changes in clinical guidelines and increased use of genome-wide sequencing. This study highlights the uncertainty in the future of genetic and genomic service provision and contributes evidence that could be used to inform strategic planning in clinical genetics.
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Affiliation(s)
- Kennedy Borle
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nicola Kopac
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada.,BC Women's Hospital Research Institute, Vancouver, BC, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada. .,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, BC, Canada.
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22
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Hayeems RZ, Marshall CR, Gillespie MK, Szuto A, Chisholm C, Stavropoulos DJ, Venkataramanan V, Tsiplova K, Sawyer S, Price EM, Lau L, Khan R, Lee W, Huang L, Jarinova O, Ungar WJ, Mendoza-Londono R, Somerville MJ, Boycott KM. Comparing genome sequencing technologies to improve rare disease diagnostics: a protocol for the evaluation of a pilot project, Genome-wide Sequencing Ontario. CMAJ Open 2022; 10:E460-E465. [PMID: 35609929 PMCID: PMC9259466 DOI: 10.9778/cmajo.20210272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Genome-wide sequencing has emerged as a promising strategy for the timely diagnosis of rare diseases, but it is not yet available as a clinical test performed in Canadian diagnostic laboratories. We describe the protocol for evaluating a 2-year pilot project, Genome-wide Sequencing Ontario, to offer high-quality clinical genome-wide sequencing in Ontario, Canada. METHODS The Genome-wide Sequencing Ontario protocol was codesigned by the Ontario Ministry of Health, the Hospital for Sick Children in Toronto and the Children's Hospital of Eastern Ontario in Ottawa. Enrolment of a prospective cohort of patients began on Apr. 1, 2021. Eligible cases with blood samples available for the index case and both parents (i.e., trios) are randomized to receive exome sequencing or genome sequencing. We will collect patient-level data and ascertain costs associated with the laboratory workflow for exome sequencing and genome sequencing. We will compare point estimates for the diagnostic utility and timeliness of exome sequencing and genome sequencing, and we will determine an incremental cost-effectiveness ratio (expressed as the incremental cost of genome sequencing versus exome sequencing per additional patient with a causal variant detected). INTERPRETATION Findings from this work will provide robust evidence for the diagnostic utility, cost-effectiveness and timeliness of exome sequencing and genome sequencing, and will be disseminated via academic publications and policy briefs. Findings will inform provincial and cross-provincial policy related to the long-term organization, delivery and reimbursement of clinical-grade genome diagnostics for rare disease.
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Affiliation(s)
- Robin Z Hayeems
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont.
| | - Christian R Marshall
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Meredith K Gillespie
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Anna Szuto
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Caitlin Chisholm
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Dimitri J Stavropoulos
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Viji Venkataramanan
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Kate Tsiplova
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Sarah Sawyer
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - E Magda Price
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Lynette Lau
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Reem Khan
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Whiwon Lee
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Lijia Huang
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Olga Jarinova
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Wendy J Ungar
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Roberto Mendoza-Londono
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Martin J Somerville
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
| | - Kym M Boycott
- Program in Child Health Evaluative Sciences (Hayeems, Venkataramanan, Tsiplova, Lee, Ungar), Hospital for Sick Children Research Institute; Department of Paediatric Laboratory Medicine (Marshall, Stavropoulos, Lau, Somerville), Hospital for Sick Children, Toronto, Ont.; Department of Laboratory Medicine and Pathobiology, (Marshall, Stavropoulos, Somerville), University of Toronto, Toronto, Ont.; Children's Hospital of Eastern Ontario Research Institute (Gillespie, Price, Boycott), University of Ottawa, Ottawa, Ont.; Division of Clinical and Metabolic Genetics (Szuto, Khan, Lee, Mendoza-Londono), Hospital for Sick Children, Toronto, Ont.; Department of Genetics (Chisholm, Sawyer, Huang, Jarinova, Boycott), Children's Hospital of Eastern Ontario, Ottawa, Ont
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Zhang C, Owen LA, Lillvis JH, Zhang SX, Kim IK, DeAngelis MM. AMD Genomics: Non-Coding RNAs as Biomarkers and Therapeutic Targets. J Clin Med 2022; 11:jcm11061484. [PMID: 35329812 PMCID: PMC8954267 DOI: 10.3390/jcm11061484] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/03/2022] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 12/04/2022] Open
Abstract
Age-related macular degeneration (AMD) is a progressive neurodegenerative disease that is the world’s leading cause of blindness in the aging population. Although the clinical stages and forms of AMD have been elucidated, more specific prognostic tools are required to determine when patients with early and intermediate AMD will progress into the advanced stages of AMD. Another challenge in the field has been the appropriate development of therapies for intermediate AMD and advanced atrophic AMD. After numerous negative clinical trials, an anti-C5 agent and anti-C3 agent have recently shown promising results in phase 3 clinical trials, in terms of slowing the growth of geographic atrophy, an advanced form of AMD. Interestingly, both drugs appear to be associated with an increased incidence of wet AMD, another advanced form of the disease, and will require frequent intravitreal injections. Certainly, there remains a need for other therapeutic agents with the potential to prevent progression to advanced stages of the disease. Investigation of the role and clinical utility of non-coding RNAs (ncRNAs) is a major advancement in biology that has only been minimally applied to AMD. In the following review, we discuss the clinical relevance of ncRNAs in AMD as both biomarkers and therapeutic targets.
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Affiliation(s)
- Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
| | - Leah A. Owen
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Sarah X. Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Correspondence: (I.K.K.); (M.M.D.)
| | - Margaret M. DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Correspondence: (I.K.K.); (M.M.D.)
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Nurchis MC, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Tartaglia M, Cicchetti A, Dallapiccola B, Damiani G. Incremental net benefit of Whole Genome Sequencing for newborns and children with suspected genetic disorders: systematic review and meta-analysis of cost-effectiveness evidence. Health Policy 2022; 126:337-345. [DOI: 10.1016/j.healthpol.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
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Hayeems RZ, Michaels-Igbokwe C, Venkataramanan V, Hartley T, Acker M, Gillespie M, Ungar WJ, Mendoza-Londona R, Bernier FP, Boycott KM, Marshall DA. The complexity of diagnosing rare disease: An organizing framework for outcomes research and health economics based on real-world evidence. Genet Med 2021:S1098-3600(21)05383-1. [PMID: 34906497 DOI: 10.1016/j.gim.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/05/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE To facilitate robust economic analyses of clinical exome and genome sequencing, this study was taken up with the objective of establishing a framework for organizing diagnostic testing trajectories for patients with rare disease. METHODS We collected diagnostic investigations-related data before exome sequencing from the medical records of 228 cases. Medical geneticist experts participated in a consensus building process to develop the SOLVE Framework for organizing the complex range of observed tests. Experts categorized tests as indicator or nonindicator tests on the basis of their specificity for diagnosing rare diseases. Face validity was assessed using case vignettes. RESULTS Most cases had symptom onset at birth (42.5%) or during childhood (43.4%) and had intellectual disability (73.3%). On average, the time spent seeking a diagnosis before sequencing was 1989 days (SD = 2137) and included 16 tests (SD = 14). Agreement across experts on test categories ranged from 83% to 96%. The SOLVE Framework comprised observed tests, including 186 indicator and 39 nonindicator tests across cytogenetic/molecular, biochemical, imaging, electrical, and pathology test categories. CONCLUSION Real-world diagnostic testing data can be ascertained and organized to reflect the complexity of the journey of the patients with rare diseases. SOLVE Framework will improve the accuracy and certainty associated with value-based assessments of genomic sequencing.
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Schroeder BE, Gonzaludo N, Everson K, Than KS, Sullivan J, Taft RJ, Belmont JW. The diagnostic trajectory of infants and children with clinical features of genetic disease. NPJ Genom Med 2021; 6:98. [PMID: 34811359 PMCID: PMC8609026 DOI: 10.1038/s41525-021-00260-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/08/2020] [Accepted: 10/21/2021] [Indexed: 11/09/2022] Open
Abstract
We characterized US pediatric patients with clinical indicators of genetic diseases, focusing on the burden of disease, utilization of genetic testing, and cost of care. Curated lists of diagnosis, procedure, and billing codes were used to identify patients with clinical indicators of genetic disease in healthcare claims from Optum's de-identified Clinformatics® Database (13,076,038 unique patients). Distinct cohorts were defined to represent permissive and conservative estimates of the number of patients. Clinical phenotypes suggestive of genetic diseases were observed in up to 9.4% of pediatric patients and up to 44.7% of critically-ill infants. Compared with controls, patients with indicators of genetic diseases had higher utilization of services (e.g., mean NICU length of stay of 31.6d in a cohort defined by multiple congenital anomalies or neurological presentations compared with 10.1d for patients in the control population (P < 0.001)) and higher overall costs. Very few patients received any genetic testing (4.2-8.4% depending on cohort criteria). These results highlight the substantial proportion of the population with clinical features associated with genetic disorders and underutilization of genetic testing in these populations.
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Affiliation(s)
| | - Nina Gonzaludo
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA USA
| | | | | | | | - Ryan J. Taft
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA USA
| | - John W. Belmont
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA USA
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Lantos JD. Sources of Unease About the Use of Genome Sequencing for Diagnosing Rare Diseases in Children. J Pediatr 2021; 237:13-5. [PMID: 34166672 DOI: 10.1016/j.jpeds.2021.06.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
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Li C, Vandersluis S, Holubowich C, Ungar WJ, Goh ES, Boycott KM, Sikich N, Dhalla I, Ng V. Correspondence on "cost or price of sequencing? implications for economic evaluations in genomic medicine" by Grosse and Gudgeon. Genet Med 2021; 24:251-252. [PMID: 34906460 DOI: 10.1016/j.gim.2021.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Chunmei Li
- Ontario Health (Quality), Toronto, Ontario, Canada.
| | | | | | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Elaine S Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute (CHEO), University of Ottawa, Ottawa, Ontario, Canada
| | - Nancy Sikich
- Ontario Health (Quality), Toronto, Ontario, Canada
| | - Irfan Dhalla
- Ontario Health (Quality), Toronto, Ontario, Canada; Unity Health Toronto, Toronto, Ontario, Canada
| | - Vivian Ng
- Ontario Health (Quality), Toronto, Ontario, Canada
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Han JY, Park J. A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review. Genes (Basel) 2021; 12:1388. [PMID: 34573370 PMCID: PMC8472681 DOI: 10.3390/genes12091388] [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] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
The terminal 14q32 duplication has been reported often in association with other cytogenetic abnormalities, and individuals with this specific duplication showed varying degrees of developmental delay/intellectual disability (DD/ID) and growth retardation (GR), and distinct facial dysmorphisms. Herein, based on the limited cases of terminal duplication of 14q32 known to date, we present new affected siblings presenting with DD/ID, GR, and facial dysmorphism, as well as cerebral infarction caused by recurrent de novo der(14)t(14;14)(p11.2;q32.1) leading to terminal duplication of 14q32. We used coverage analysis generated via duo exome sequencing, performed chromosomal microarray (CMA) as a confirmatory test, and compared our findings with those reported previously. Coverage analysis generated via duo exome sequencing revealed a 17.2 Mb heterozygous duplication at chromosome 14q32.11-q32.33 with a Z ratio ranging between 0.5 and 1 in the proband and her elder brother. As a complementary method, CMA established a terminal duplication described as the arr[hg19]14q32.11q32.33(90,043,558_107,258,824)x3 in the proband and her elder brother; however, the parents and other siblings showed normal karyotyping and no abnormal gain or loss of CMA results. Five candidate genes, BCL11B, CCNK, YY1, DYNC1H1, and PACS2, were associated with the clinical phenotypes in our cases. Although the parents had normal chromosomes, two affected cases carrying terminal duplication of 14q32 can be explained by gonadal mosaicism. Further studies are needed to establish the association between cerebrovascular events and terminal duplication of chromosome 14q32, including investigation into the cytogenetics of patients with precise clinical descriptions.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Korea
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Grosse SD, Gudgeon JM. Cost or price of sequencing? Implications for economic evaluations in genomic medicine. Genet Med 2021; 23:1833-5. [PMID: 34113006 DOI: 10.1038/s41436-021-01223-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
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Wu Y, Balasubramaniam S, Rius R, Thorburn DR, Christodoulou J, Goranitis I. Genomic sequencing for the diagnosis of childhood mitochondrial disorders: a health economic evaluation. Eur J Hum Genet 2021; 30:577-586. [PMID: 34099885 PMCID: PMC9090793 DOI: 10.1038/s41431-021-00916-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022] Open
Abstract
The diagnostic and clinical benefits of genomic sequencing are being increasingly demonstrated across multiple rare genetic conditions. Despite the expanding clinical literature, there is a significant paucity of health economics evidence to inform the prioritization and implementation of genomic sequencing. This study aims to evaluate whether genomic sequencing for pediatric-onset mitochondrial disorders (MDs) is cost-effective and cost-beneficial relative to conventional care from an Australian healthcare system perspective. Two independent and complementary health economic modeling approaches were used. Approach 1 used a decision tree to model the costs and outcomes associated with genomic sequencing and conventional care. Approach 2 used a discrete-event simulation to incorporate heterogeneity in the condition and clinical practice. Deterministic and probabilistic sensitivity analyses were performed. Genomic sequencing was less costly and more effective compared with conventional care, saving AU$1997 (Approach 1) to AU$8823 (Approach 2) per child tested, while leading to an additional 11 (Approach 1) to 14 (Approach 2) definitive diagnoses per 100 children tested. The mean monetary value of the incremental benefits of genomic sequencing was estimated at AU$5890 (95% CI: AU$5730-$6046). Implementation of genomic sequencing for MDs in Australia could translate to an annual cost-saving of up to AU$0.7 million. Genomic sequencing is cost-saving relative to traditional investigative approaches, while enabling more diagnoses to be made in a timely manner, offering substantial personal benefits to children and their families. Our findings support the prioritization of genomic sequencing for children with MDs.
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Affiliation(s)
- You Wu
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - David R Thorburn
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, Australia
| | - John Christodoulou
- Australian Genomics Health Alliance, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia. .,Australian Genomics Health Alliance, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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Cernat A, Hayeems RZ, Prosser LA, Ungar WJ. Incorporating Cascade Effects of Genetic Testing in Economic Evaluation: A Scoping Review of Methodological Challenges. Children (Basel) 2021; 8:children8050346. [PMID: 33925765 PMCID: PMC8145875 DOI: 10.3390/children8050346] [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] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022]
Abstract
Cascade genetic testing is indicated for family members of individuals testing positive on a genetic test, and is particularly relevant for child health because of their vulnerability and the long-term health and economic implications. Cascade testing has patient- and health system-level implications; however cascade costs and health effects are not routinely considered in economic evaluation. The methodological challenges associated with incorporating cascade effects in economic evaluation require examination. The purpose of this scoping review was to identify published economic evaluations that considered cascade genetic testing. Citation databases were searched for English-language economic evaluations reporting on cascade genetic testing. Nineteen publications were included. In four, genetic testing was used to identify new index patients—cascade effects were also considered; thirteen assessed cascade genetic testing strategies for the identification of at-risk relatives; and two calculated the costs of cascade genetic testing as a secondary objective. Methodological challenges associated with incorporating cascade effects in economic evaluation are related to study design, costing, measurement and valuation of health outcomes, and modeling. As health economic studies may currently be underestimating both the cost and health benefits attributable to genetic technologies through omission of cascade effects, development of methods to address these difficulties is required.
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Affiliation(s)
- Alexandra Cernat
- Child Health Evaluative Sciences, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (A.C.); (R.Z.H.)
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 1P8, Canada
| | - Robin Z. Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (A.C.); (R.Z.H.)
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 1P8, Canada
| | - Lisa A. Prosser
- Susan B. Meister Child Health Evaluation and Research Center, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
- Department of Health Management and Policy, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Wendy J. Ungar
- Child Health Evaluative Sciences, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (A.C.); (R.Z.H.)
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 1P8, Canada
- Correspondence:
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