1
|
The Genetics of Intellectual Disability. Brain Sci 2023; 13:brainsci13020231. [PMID: 36831774 PMCID: PMC9953898 DOI: 10.3390/brainsci13020231] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of ~2-3% in the general population, having a large societal impact. The underlying cause of ID is largely of genetic origin; however, identifying this genetic cause has in the past often led to long diagnostic Odysseys. Over the past decades, improvements in genetic diagnostic technologies and strategies have led to these causes being more and more detectable: from cytogenetic analysis in 1959, we moved in the first decade of the 21st century from genomic microarrays with a diagnostic yield of ~20% to next-generation sequencing platforms with a yield of up to 60%. In this review, we discuss these various developments, as well as their associated challenges and implications for the field of ID, which highlight the revolutionizing shift in clinical practice from a phenotype-first into genotype-first approach.
Collapse
|
2
|
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] [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.
Collapse
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
| |
Collapse
|
3
|
Rooney K, Sadikovic B. DNA Methylation Episignatures in Neurodevelopmental Disorders Associated with Large Structural Copy Number Variants: Clinical Implications. Int J Mol Sci 2022; 23:ijms23147862. [PMID: 35887210 PMCID: PMC9324454 DOI: 10.3390/ijms23147862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Large structural chromosomal deletions and duplications, referred to as copy number variants (CNVs), play a role in the pathogenesis of neurodevelopmental disorders (NDDs) through effects on gene dosage. This review focuses on our current understanding of genomic disorders that arise from large structural chromosome rearrangements in patients with NDDs, as well as difficulties in overlap of clinical presentation and molecular diagnosis. We discuss the implications of epigenetics, specifically DNA methylation (DNAm), in NDDs and genomic disorders, and consider the implications and clinical impact of copy number and genomic DNAm testing in patients with suspected genetic NDDs. We summarize evidence of global methylation episignatures in CNV-associated disorders that can be used in the diagnostic pathway and may provide insights into the molecular pathogenesis of genomic disorders. Finally, we discuss the potential for combining CNV and DNAm assessment into a single diagnostic assay.
Collapse
Affiliation(s)
- Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Correspondence: ; Tel.: +1-519-685-8500 (ext. 53074)
| |
Collapse
|
4
|
Aaltio J, Hyttinen V, Kortelainen M, Frederix GWJ, Lönnqvist T, Suomalainen A, Isohanni P. Cost-effectiveness of whole-exome sequencing in progressive neurological disorders of children. Eur J Paediatr Neurol 2022; 36:30-36. [PMID: 34852981 DOI: 10.1016/j.ejpn.2021.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 09/22/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022]
Abstract
OBJECTIVES To clarify the diagnostic utility and the cost-effectiveness of whole-exome sequencing (WES) as a routine early-diagnostic tool in children with progressive neurological disorders. METHODS Patients with infantile-onset severe neurological diseases or childhood-onset progressive neurological disorders were prospectively recruited to this WES study, in the pediatric neurology clinic at Helsinki University Hospital during 2016-2018. A total of 48 patients underwent a singleton WES. A control group of 49 children underwent traditional diagnostic examinations and were retrospectively collected from the hospital records. Their use of health care services, related to the diagnostic process, was gathered. Incremental cost-effectiveness ratio (ICER) per additional diagnosis was calculated from the health care provider perspective. Bootstrapping methods were used to estimate the uncertainty of cost-effectiveness outcomes. RESULTS WES provided a better diagnostic yield (38%) than diagnostic pathway that did not prioritize WES in early diagnosis (25%). WES outperformed other diagnostic paths especially when made early, within one year of first admission (44%). Cost-effectiveness in our results are conservative, affected by WES costs during 2016-18. CONCLUSIONS WES is an efficient and cost-effective diagnostic tool that should be prioritized in early diagnostic path of children with progressive neurological disorders. The progressively decreasing price of the test improves cost-effectiveness further.
Collapse
Affiliation(s)
- Juho Aaltio
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland.
| | - Virva Hyttinen
- VATT Institute for Economic Research, Helsinki, Finland; Department of Health and Social Management, University of Eastern Finland, Kuopio, Finland
| | - Mika Kortelainen
- VATT Institute for Economic Research, Helsinki, Finland; Department of Economics, Turku School of Economics, Turku, Finland
| | - Gerardus W J Frederix
- Department of Genetics, University Medical Center, Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, the Netherlands
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland; HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland; Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
5
|
The complexity of diagnosing rare disease: An organizing framework for outcomes research and health economics based on real-world evidence. Genet Med 2021; 24:694-702. [PMID: 34906497 DOI: 10.1016/j.gim.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [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.
Collapse
|
6
|
Cost-effectiveness of genome sequencing for diagnosing patients with undiagnosed rare genetic diseases. Genet Med 2021; 24:109-118. [PMID: 34906478 DOI: 10.1016/j.gim.2021.08.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/26/2020] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
PURPOSE To estimate the cost-effectiveness of genome sequencing (GS) for diagnosing critically ill infants and noncritically ill pediatric patients (children) with suspected rare genetic diseases from a United States health sector perspective. METHODS A decision-analytic model was developed to simulate the diagnostic trajectory of patients. Parameter estimates were derived from a targeted literature review and meta-analysis. The model simulated clinical and economic outcomes associated with 3 diagnostic pathways: (1) standard diagnostic care, (2) GS, and (3) standard diagnostic care followed by GS. RESULTS For children, costs of GS ($7284) were similar to that of standard care ($7355) and lower than that of standard care followed by GS pathways ($12,030). In critically ill infants, when cost estimates were based on the length of stay in the neonatal intensive care unit, the lowest cost pathway was GS ($209,472). When only diagnostic test costs were included, the cost per diagnosis was $17,940 for standard, $17,019 for GS, and $20,255 for standard care followed by GS. CONCLUSION The results of this economic model suggest that GS may be cost neutral or possibly cost saving as a first line diagnostic tool for children and critically ill infants.
Collapse
|
7
|
Olde Keizer RACM, Henneman L, Ploos van Amstel JK, Vissers LELM, Frederix GWJ. Economic evaluations of exome and genome sequencing in pediatric genetics: considerations towards a consensus strategy. J Med Econ 2021; 24:60-70. [PMID: 34915793 DOI: 10.1080/13696998.2021.2009725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Next Generation Sequencing (NGS) is increasingly used for the diagnosis of rare genetic disorders. The aim of this study is to review the different approaches for economic evaluations of Next Generation Sequencing (NGS) in pediatric care used to date, to identify all costs, effects, and time horizons taken into account. METHODS A systematic literature review was conducted to identify published economic evaluations of NGS applications in pediatric diagnostics, i.e. exome sequencing (ES) and/or genome sequencing (GS). Information regarding methodological approach, costs, effects, and time horizon was abstracted from these publications. RESULTS Twenty-eight economic evaluations of ES/GS within pediatrics were identified. Costs included were mainly restricted to direct in-hospital healthcare costs and varied widely in inclusion of sort of costs and time-horizon. Nineteen studies included diagnostic yield and eight studies included cost-effectiveness as outcome measures. Studies varied greatly in terms of included sort of costs data, effects, and time horizon. CONCLUSION Large differences in inclusion of cost and effect parameters were identified between studies. Validity of outcomes can therefore be questioned, which hinders valid comparison and widespread generalization of conclusions. In addition to current health economic guidance, specific guidance for evaluations in pediatric care is therefore necessary to improve the validity of outcomes and furthermore facilitate comparable decision-making for implementing novel NGS-based diagnostic modalities in pediatric genetics and beyond.
Collapse
Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Gerardus W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| |
Collapse
|
8
|
The Utility of Whole Exome Sequencing in Diagnosing Pediatric Neurological Disorders. Balkan J Med Genet 2021; 23:17-24. [PMID: 33816068 PMCID: PMC8009565 DOI: 10.2478/bjmg-2020-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Pediatric neurological disorders have a wide spectrum of clinical presentations and can be challenging to diagnose. Whole exome sequencing (WES) is increasingly becoming an integral diagnostic tool in medicine. It is cost-effective and has high diagnostic yield, especially in consanguineous populations. This study aims to review WES results and its value in diagnosing neurological disorders. A retrospective chart review was performed for WES results between the period of January 2018 to November 2019. Whole exome sequencing was requested for children with unexplained neurological signs and symptoms such as epilepsy, developmental delay, visual impairment, spasticity, hypotonia and magnetic resonance imaging (MRI) brain changes. It was conducted for children in a pediatric neurology clinic of a tertiary center at Jeddah, Saudi Arabia. Twenty-six children with undiagnosed neurological conditions were identified and underwent WES diagnosis. Nineteen patients (73.0%) of the cohort were diagnosed with pathogenic variants, likely pathogenic variants or variants of unknown significance (VUS). Consanguinity was positive in 18 families of the cohort (69.0%). Seven patients showed homozygous mutations. Five patients had heterozygous mutations. There were six patients with VUS and six patients had negative WES results. Whole exome sequencing showed a high diagnostic rate in this group of children with variable neurological disorders.
Collapse
|
9
|
Zelesniack E, Oubaid V, Harendza S. Defining competence profiles of different medical specialties with the requirement-tracking questionnaire - a pilot study to provide a framework for medial students' choice of postgraduate training. BMC MEDICAL EDUCATION 2021; 21:46. [PMID: 33435986 PMCID: PMC7801870 DOI: 10.1186/s12909-020-02479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The medical specialties are characterised by a great diversity in their daily work which requires different sets of competences. A requirement analysis would help to establish competence profiles of the different medical specialities. The aim of this pilot study was to define competence profiles for individual medical specialties. This could provide a framework as support for medical graduates who wish to choose a medical specialty for their postgraduate training. METHODS In February 2020, physicians were invited via the State Chamber of Physicians' monthly journal to electronically fill out the requirement tracking (R-Track) questionnaire. It contains 63 aspects assigned to six areas of competence: "Mental abilities", "Sensory abilities", "Psychomotor and multitasking abilities", "Social interactive competences", "Motivation", and "Personality traits". The expression of the different aspects was assessed on a 5-point Likert scale (1: "very low" to 5: "very high"). Sociodemographic data and information about the current workplace (hospital or practice) were also collected. RESULTS In total, 195 practicing physicians from 19 different specialities followed the invitation by the State Chamber of Physicians to participate in this survey. For almost all medical specialties, the competence area "Motivation" reached rank 1. "Psychomotor and multitasking abilities" received high ranks among specialties performing surgical activities, while "Social interactive competences" and "Personality traits" were highly rated by specialties with an intense level of patient-physician-interaction. "Mental abilities" were only rated highly by radiologists (rank 2) and physiologists (rank 3) while "Sensory abilities" were generally rated very low with the expression (rank 4) for anaesthesiology and ENT. CONCLUSIONS In this pilot study, a first outline of competences profiles for 17 medical specialties were defined. The specific "Motivation" for a medical specialty seemed to play the greatest role for most specialties. This first specialty specific competence framework could provide a first insight into specific competences required by medical specialties and could serve medical graduate as a decision aid when looking for a medical specialty for their postgraduate training.
Collapse
Affiliation(s)
- Elena Zelesniack
- III. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
| | | | - Sigrid Harendza
- III. Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
| |
Collapse
|
10
|
Michaels-Igbokwe C, McInnes B, MacDonald KV, Currie GR, Omar F, Shewchuk B, Bernier FP, Marshall DA. (Un)standardized testing: the diagnostic odyssey of children with rare genetic disorders in Alberta, Canada. Genet Med 2020; 23:272-279. [PMID: 32989270 DOI: 10.1038/s41436-020-00975-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE We provide a description of the diagnostic odyssey for a cohort of children seeking diagnosis of a rare genetic disorder in terms of the time from initial consultation to most recent visit or receipt of diagnosis, the number of tests per patient, and the types of tests received. METHODS Retrospective chart review of 299 children seen at the Alberta Children's Hospital (ACH) Genetics Clinic (GC) for whom the result of at least one single-gene test, gene panel, or chromosome microarray analysis (CMA) was recorded. RESULTS Of 299 patients, 90 (30%) received a diagnosis in the period of the review. Patients had an average of 5.4 tests each; 236 (79%) patients received CMA; 172 (58%) patients received single-gene tests and 34 (11%) received gene panels; 167 (56%) underwent imaging/electrical activity studies. The mean observation period was 898 days (95% confidence interval [CI] 791, 1004). Among patients with visits recorded prior to visiting ACH GC, 43% of the total observation time occurred prior to the GC. CONCLUSION As genomic technologies expand, the nature of the diagnostic odyssey will change. This study has outlined the current standard of care in the ACH GC, providing a baseline against which future changes can be assessed.
Collapse
Affiliation(s)
- Christine Michaels-Igbokwe
- Cumming School of Medicine, Department of Paediatrics, University of Calgary, Calgary, AB, Canada. .,Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada.
| | - Brenda McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Karen V MacDonald
- Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Gillian R Currie
- Cumming School of Medicine, Department of Paediatrics, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada.,O'Brien Institute for Public Health, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Fadya Omar
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brittany Shewchuk
- Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deborah A Marshall
- Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada.,O'Brien Institute for Public Health, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
11
|
International consensus recommendations on the diagnostic work-up for malformations of cortical development. Nat Rev Neurol 2020; 16:618-635. [PMID: 32895508 PMCID: PMC7790753 DOI: 10.1038/s41582-020-0395-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2020] [Indexed: 12/22/2022]
Abstract
Malformations of cortical development (MCDs) are neurodevelopmental disorders that result from abnormal development of the cerebral cortex in utero. MCDs place a substantial burden on affected individuals, their families and societies worldwide, as these individuals can experience lifelong drug-resistant epilepsy, cerebral palsy, feeding difficulties, intellectual disability and other neurological and behavioural anomalies. The diagnostic pathway for MCDs is complex owing to wide variations in presentation and aetiology, thereby hampering timely and adequate management. In this article, the international MCD network Neuro-MIG provides consensus recommendations to aid both expert and non-expert clinicians in the diagnostic work-up of MCDs with the aim of improving patient management worldwide. We reviewed the literature on clinical presentation, aetiology and diagnostic approaches for the main MCD subtypes and collected data on current practices and recommendations from clinicians and diagnostic laboratories within Neuro-MIG. We reached consensus by 42 professionals from 20 countries, using expert discussions and a Delphi consensus process. We present a diagnostic workflow that can be applied to any individual with MCD and a comprehensive list of MCD-related genes with their associated phenotypes. The workflow is designed to maximize the diagnostic yield and increase the number of patients receiving personalized care and counselling on prognosis and recurrence risk.
Collapse
|
12
|
Mazzarotto F, Olivotto I, Walsh R. Advantages and Perils of Clinical Whole-Exome and Whole-Genome Sequencing in Cardiomyopathy. Cardiovasc Drugs Ther 2020; 34:241-253. [DOI: 10.1007/s10557-020-06948-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
13
|
Fahr P, Buchanan J, Wordsworth S. A Review of Health Economic Studies Comparing Traditional and Massively Parallel Sequencing Diagnostic Pathways for Suspected Genetic Disorders. PHARMACOECONOMICS 2020; 38:143-158. [PMID: 31741314 DOI: 10.1007/s40273-019-00856-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Genetic disorders are clinically diverse and genetically heterogeneous, and are traditionally diagnosed based on an iterative phenotype-guided genetic assessment. However, such diagnostic approaches are long (diagnostic odysseys are common), misdiagnoses occur frequently, and diagnostic rates are low. Massively parallel sequencing (MPS) technologies may improve diagnostic rates and reduce the time to diagnosis for patients with suspected genetic disorders; however, MPS technologies are expensive and the health economic evidence base to support their use is limited. Several studies have compared the costs of traditional and MPS diagnostic pathways for patients with suspected genetic disorders, however costing methods and diagnostic scenarios are heterogeneous across studies. We conducted a literature review to identify and summarise information on these costing methods and diagnostic scenarios. Relevant studies were identified in MEDLINE, EMBASE, EconLit, University of York Centre for Reviews and Dissemination and the Cochrane Library, from 2010 to 2018. Twenty-four articles were included in the review. We observed considerable heterogeneity across studies with respect to the selection of items of resource use used to derive total diagnostic pathway cost estimates. We also observed structural differences in the diagnostic scenarios used to compare the traditional and MPS diagnostic pathways. There is a need for guidelines on the costing of diagnostic pathways to encourage the use of consistent methods. More micro-costing studies that evaluate diagnostic service delivery are also required. Greater homogeneity in costing approaches would facilitate more reliable comparisons between studies and improve the transferability of cost estimates across countries.
Collapse
Affiliation(s)
- Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| |
Collapse
|
14
|
Papandreou A, Danti FR, Spaull R, Leuzzi V, Mctague A, Kurian MA. The expanding spectrum of movement disorders in genetic epilepsies. Dev Med Child Neurol 2020; 62:178-191. [PMID: 31784983 DOI: 10.1111/dmcn.14407] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
An ever-increasing number of neurogenetic conditions presenting with both epilepsy and atypical movements are now recognized. These disorders within the 'genetic epilepsy-dyskinesia' spectrum are clinically and genetically heterogeneous. Increased clinical awareness is therefore necessary for a rational diagnostic approach. Furthermore, careful interpretation of genetic results is key to establishing the correct diagnosis and initiating disease-specific management strategies in a timely fashion. In this review we describe the spectrum of movement disorders associated with genetically determined epilepsies. We also propose diagnostic strategies and putative pathogenic mechanisms causing these complex syndromes associated with both seizures and atypical motor control. WHAT THIS PAPER ADDS: Implicated genes encode proteins with very diverse functions. Pathophysiological mechanisms by which epilepsy and movement disorder phenotypes manifest are often not clear. Early diagnosis of treatable disorders is essential and next generation sequencing may be required.
Collapse
Affiliation(s)
- Apostolos Papandreou
- Molecular Neurosciences, Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Federica Rachele Danti
- Molecular Neurosciences, Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Robert Spaull
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | - Amy Mctague
- Molecular Neurosciences, Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Neurology, Great Ormond Street Hospital, London, UK
| |
Collapse
|
15
|
Doble B, Schofield D, Evans CA, Groza T, Mattick JS, Field M, Roscioli T. Impacts of genomics on the health and social costs of intellectual disability. J Med Genet 2020; 57:479-486. [PMID: 31980565 DOI: 10.1136/jmedgenet-2019-106445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND This study provides an integrated assessment of the economic and social impacts of genomic sequencing for the detection of monogenic disorders resulting in intellectual disability (ID). METHODS Multiple knowledge bases were cross-referenced and analysed to compile a reference list of monogenic disorders associated with ID. Multiple literature searches were used to quantify the health and social costs for the care of people with ID. Health and social expenditures and the current cost of whole-exome sequencing and whole-genome sequencing were quantified in relation to the more common causes of ID and their impact on lifespan. RESULTS On average, individuals with ID incur annual costs in terms of health costs, disability support, lost income and other social costs of US$172 000, accumulating to many millions of dollars over a lifetime. CONCLUSION The diagnosis of monogenic disorders through genomic testing provides the opportunity to improve the diagnosis and management, and to reduce the costs of ID through informed reproductive decisions, reductions in unproductive diagnostic tests and increasingly targeted therapies.
Collapse
Affiliation(s)
- Brett Doble
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia .,Programme in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Deborah Schofield
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,GenImpact, School of Economics, Faculty of Business and Economics, Macquarie University, Sydney, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Tudor Groza
- Pryzm Health, Gold Coast, Queensland, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Mike Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia.,NSW Health Pathology East Laboratory, Prince of Wales Private Hospital, Randwick, New South Wales, Australia
| |
Collapse
|
16
|
Niu X, Amendola LM, Hart R, Bennette CS, Heagerty P, Horike-Pyne M, Trinidad SB, Rosenthal EA, Comstock B, Nefcy C, Hisama FM, Bennett RL, Grady WM, Gallego CJ, Tarczy-Hornoch P, Fullerton SM, Burke W, Regier DA, Dorschner MO, Shirts BH, Robertson PD, Nickerson DA, Patrick DL, Jarvik GP, Veenstra DL. Clinical exome sequencing vs. usual care for hereditary colorectal cancer diagnosis: A pilot comparative effectiveness study. Contemp Clin Trials 2019; 84:105820. [PMID: 31400517 PMCID: PMC6741782 DOI: 10.1016/j.cct.2019.105820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/26/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Clinical exome sequencing (CES) provides the advantage of assessing genetic variation across the human exome compared to a traditional stepwise diagnostic approach or multi-gene panels. Comparative effectiveness research methods offer an approach to better understand the patient-centered and economic outcomes of CES. PURPOSE To evaluate CES compared to usual care (UC) in the diagnostic work-up of inherited colorectal cancer/polyposis (CRCP) in a randomized controlled trial (RCT). METHODS The primary outcome was clinical sensitivity for the diagnosis of inherited CRCP; secondary outcomes included psychosocial outcomes, family communication, and healthcare resource utilization. Participants were surveyed 2 and 4 weeks after results return and at 3-month intervals up to 1 year. RESULTS Evolving outcome measures and standard of care presented critical challenges. The majority of participants in the UC arm received multi-gene panels [94.73%]. Rates of genetic findings supporting the diagnosis of hereditary CRCP were 7.5% [7/93] vs. 5.4% [5/93] in the CES and UC arms, respectively (P = 0.28). Differences in privacy concerns after receiving CRCP results were identified (0.88 in UC vs 0.38 in CES, P = 0.05); however, healthcare resource utilization, family communication and psychosocial outcomes were similar between the two arms. More participants with positive results (17.7%) intended to change their life insurance 1 month after the first return visit compared to participants returned a variant of uncertain significance (9.1%) or negative result (4.8%) (P = 0.09). CONCLUSION Our results suggest that CES provides similar clinical benefits to multi-gene panels in the diagnosis of hereditary CRCP.
Collapse
Affiliation(s)
- Xin Niu
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Ragan Hart
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | | | - Patrick Heagerty
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Martha Horike-Pyne
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Bryan Comstock
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chris Nefcy
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Fuki M Hisama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Robin L Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98101, USA
| | - Carlos J Gallego
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Comparative Health Outcomes, Economics and Policy Institute (CHOICE), University of Washington, Seattle, WA 98195, USA
| | - Peter Tarczy-Hornoch
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Michael O Dorschner
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Donald L Patrick
- Department of Health Services, University of Washington, Seattle, WA 98195, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David L Veenstra
- Comparative Health Outcomes, Economics and Policy Institute (CHOICE), University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
17
|
The cost trajectory of the diagnostic care pathway for children with suspected genetic disorders. Genet Med 2019; 22:292-300. [DOI: 10.1038/s41436-019-0635-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022] Open
|
18
|
The value of diagnostic testing for parents of children with rare genetic diseases. Genet Med 2019; 21:2798-2806. [PMID: 31239560 DOI: 10.1038/s41436-019-0583-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/01/2019] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Exome sequencing (ES) can rapidly identify disease-causing variants responsible for rare, single-gene diseases, and potentially reduce the duration of the diagnostic odyssey. Our study examines how parents and families value ES. METHODS We developed a discrete choice experiment (DCE) survey that was administered to parents of children with rare diseases. The DCE included 14 choice tasks with 6 attributes and 3 alternatives. A valuation-space model was used to estimate willingness to pay, willingness to wait for test results, and minimum acceptable chance of a diagnosis for changes in each attribute. RESULTS There were n = 319 respondents of whom 89% reported their child had genetic testing, and 66% reported their child had a diagnosis. Twenty-six percent reported that their child had been offered ES. Parents were willing to pay CAD$6590 (US$4943), wait 5.2 years to obtain diagnostic test results, and accept a reduction of 3.1% in the chance of a diagnosis for ES compared with operative procedures. CONCLUSION Timely access to ES could reduce the diagnostic odyssey and associated costs. Before ES is incorporated routinely into care for patients with rare diseases in Canada and more broadly, there must be a clear understanding of its value to patients and families.
Collapse
|
19
|
Schofield D, Rynehart L, Shresthra R, White SM, Stark Z. Long-term economic impacts of exome sequencing for suspected monogenic disorders: diagnosis, management, and reproductive outcomes. Genet Med 2019; 21:2586-2593. [DOI: 10.1038/s41436-019-0534-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
|
20
|
Mu W, Schiess N, Orthmann-Murphy JL, El-Hattab AW. The utility of whole exome sequencing in diagnosing neurological disorders in adults from a highly consanguineous population. J Neurogenet 2019; 33:21-26. [PMID: 30724636 DOI: 10.1080/01677063.2018.1555249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is increasing evidence that whole exome sequencing (WES) has a high diagnostic yield and is cost-efficient for individuals with neurological phenotypes. However, there is limited data on the use of WES in non-Western populations, including populations with a high rate of consanguinity. Retrospective chart review was performed on 24 adults with undiagnosed neurological symptoms evaluated in genetics and neurology clinics in a tertiary care facility on the Arabian Peninsula, and had WES between 2014 and 2016. Definitive diagnoses were made in 13/24 (54%) of cases. Of these, 5/13 (38%) revealed novel pathogenic variants. Of the known 19/24 (79%) consanguineous cases, diagnostic rate was slightly higher, 11/19 (58%) as compared to 2/5 (40%) among non-consanguineous cases. Autosomal recessive disorders comprised 10/13 (77%) of molecular diagnoses, all found to be due to homozygous pathogenic variants among consanguineous cases. WES in this cohort of adults with neurological symptoms had a high diagnostic rate likely due to high consanguinity rates in this population, as evidenced by the high diagnostic rate of homozygous pathogenic variants.
Collapse
Affiliation(s)
- Weiyi Mu
- a Institute of Genetic Medicine , Johns Hopkins University , Baltimore , MD , USA
| | - Nicoline Schiess
- b Department of Neurology , Johns Hopkins University , Baltimore , MD , USA
| | - Jennifer L Orthmann-Murphy
- b Department of Neurology , Johns Hopkins University , Baltimore , MD , USA.,c Department of Neurology , Hospital of the University of Pennsylvania , Philadelphia , PA , USA
| | - Ayman W El-Hattab
- d Division of Clinical Genetics and Metabolic Disorder , Tawam Hospital , Al-Ain , United Arab Emirates
| |
Collapse
|
21
|
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. Am J Hum Genet 2018; 103:58-73. [PMID: 29961570 DOI: 10.1016/j.ajhg.2018.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.
Collapse
|
22
|
Vrijenhoek T, Middelburg EM, Monroe GR, van Gassen KLI, Geenen JW, Hövels AM, Knoers NV, van Amstel HKP, Frederix GWJ. Whole-exome sequencing in intellectual disability; cost before and after a diagnosis. Eur J Hum Genet 2018; 26:1566-1571. [PMID: 29959382 DOI: 10.1038/s41431-018-0203-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/03/2018] [Accepted: 05/22/2018] [Indexed: 02/02/2023] Open
Abstract
Clinical application of whole-exome and whole-genome sequencing (WES and WGS) has led to an increasing interest in how it could drive healthcare decisions. As with any healthcare innovation, implementation of next-generation sequencing in the clinic raises questions on affordability and costing impact for society as a whole. We retrospectively analyzed medical records of 370 patients with ID who had undergone WES at various stages of their diagnostic trajectory. We collected all medical interventions performed on these patients at the University Medical Center Utrecht (UMCU), Utrecht, the Netherlands. We categorized the patients according to their WES-based preliminary diagnosis ("yes", "no", and "uncertain"), and assessed the per-patient healthcare activities and corresponding costs before (pre) and after (post) genetic diagnosis. The WES-specific diagnostic yield among the 370 patients was 35% (128 patients). Pre-WES costs were €7.225 on average. Highest average costs were observed for laboratory-based tests, including genetics, followed by consults. Compared to pre-WES costs, the post-WES costs were on average 80% lower per patient, irrespective of the WES-based diagnostic outcome. Application of WES results in a considerable reduction of healthcare costs, not just in current settings, but even more so when applied earlier in the diagnostic trajectory (genetics-first). In such context, WES may replace less cost-effective traditional technologies without compromising the diagnostic yield. Moreover, WES appears to harbor an intrinsic "end-of-trajectory" effect; regardless of the diagnosis, downstream medical interventions decrease substantially in both number and costs.
Collapse
Affiliation(s)
- Terry Vrijenhoek
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Eline M Middelburg
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Glen R Monroe
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Joost W Geenen
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anke M Hövels
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Nine V Knoers
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Gerardus W J Frederix
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands. .,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
| |
Collapse
|
23
|
Suleiman J, Al Hashem AM, Tabarki B, Al-Thihli K, Bi W, El-Hattab AW. PPP1R21 homozygous null variants associated with developmental delay, muscle weakness, distinctive facial features, and brain abnormalities. Clin Genet 2018; 94:351-355. [PMID: 29808498 DOI: 10.1111/cge.13387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/19/2023]
Abstract
We present 3 children with homozygous null variants in the PPP1R21 gene. A 3-year-old girl had profound developmental delay, hypotonia and weakness, poor feeding, recurrent chest infections and respiratory failure, rotatory nystagmus, absent reflexes, and a homozygous nonsense variant c.2089C>T (p.Arg697*). A 2-year-old boy had profound developmental delay, weakness and hypotonia, recurrent chest infections and respiratory distress, undescended testes, rotatory nystagmus, hyporeflexia, and a homozygous nonsense variant c.427C>T (p.Arg143*). An 11-year-old girl with profound developmental delay, weakness and hypotonia, stereotypic movements, growth failure, hyporeflexia, and a homozygous frameshift variant c.87_88delAG (p.Gly30Cysfs*4). In addition, these children shared common facial features (thick eyebrows, hypertelorism, broad nasal bridge, short nose with upturned nasal tip and broad low-hanging columella, thick lips, low-set ears, and coarse facies with excessive facial hair), and brain abnormalities (cerebellar vermis hypoplasia, ventricular dilatation, and reduced white matter volume). Although PPP1R21 has not yet been linked to human disease, the consistency in the phenotype of individuals from unrelated families, the nature of the variants which result in truncated proteins, and the expected vital role for PPP1R21 in cellular function, all support that PPP1R21 is a novel disease-associated gene responsible for the phenotype observed in these individuals.
Collapse
Affiliation(s)
- J Suleiman
- Division of Neurology, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates.,Department of Pediatrics, College of Medicine and Health sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - A M Al Hashem
- Division of Genetics, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - B Tabarki
- Division of Neurology, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - K Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - W Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - A W El-Hattab
- Division of Genetic and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates
| |
Collapse
|
24
|
Economic evaluation of genomic sequencing in the paediatric population: a critical review. Eur J Hum Genet 2018; 26:1241-1247. [PMID: 29795475 DOI: 10.1038/s41431-018-0175-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/06/2018] [Accepted: 04/26/2018] [Indexed: 11/08/2022] Open
Abstract
Systematic evidence is critical to the formulation of national health policy to provide public funding for the integration of genomic sequencing into routine clinical care. The purpose of this review is to present systematic evidence on the economic evaluation of genomic sequencing conducted for paediatric patients in clinical care, and to identify any gaps in the methodology of economic evaluations. We undertook a critical review of the empirical evidence from economic evaluations of genomic sequencing among paediatric patients searching five electronic databases. Our inclusion criteria were limited to literature published in the English language between 2010 and 2017 in OECD countries. Articles that met our inclusion criteria were assessed using a recognised checklist for a well-designed economic evaluation. We found 11 full-text articles that met our inclusion criteria. Our analysis found that genomic sequencing markedly increased the diagnostic rate to 16-79%, but lowered the cost by 11-64% compared to the standard diagnostic pathway. Only five recent studies in paediatric clinical cohorts met most of the criteria for a well-designed economic evaluation and demonstrated cost-effectiveness of genomic sequencing in paediatric clinical cohorts of patients. Our review identified the need for improvement in the rigour of the methodologies used to provide robust evidence for the formulation of health policy on public funding to integrate genomic sequencing into routine clinical care. Nonetheless, there is emerging evidence of the cost-effectiveness of genomic sequencing over usual care for paediatric patients.
Collapse
|
25
|
Dragojlovic N, Kim E, Elliott AM, Friedman JM, Lynd LD. Evaluating the use of parental reports to estimate health care resource utilization in children with suspected genetic disorders. J Eval Clin Pract 2018; 24:416-422. [PMID: 29603523 DOI: 10.1111/jep.12876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE A key step in evaluating the cost-effectiveness of diagnostic genome-wide sequencing (GWS) services is to measure the cost of prior and subsequent diagnosis-related health care resource utilization by patients. The majority of patients using diagnostic GWS services are children, and parental surveys are often used to complement utilization data abstracted from medical records. The objective of this study was to evaluate the validity of parental reports for children with very high levels of resource utilization. METHOD Primary caregivers of children enrolled in the CAUSES Research Clinic, a diagnostic GWS programme at B.C. Children's Hospital, completed an online survey. Parent-reported health care encounters for the 6-month period prior to survey completion were compared to utilization data abstracted from electronic medical records (EMR). The association between demographic characteristics and the probability of survey completion was tested using logistic regression. Agreement between parent-reported and EMR data was evaluated using Cohen's kappa, prevalence- and bias-adjusted kappa (PABAK), and the intraclass correlation coefficient (ICC). RESULTS There were no major differences in demographic characteristics or resource utilization levels between families that completed the survey and those who did not. Agreement between parental reports and EMR data was high for hospitalizations (κ = 0.71; PABAK = 0.89; ICC = 0.77) but lower for outpatient physician visits (κ = 0.21; PABAK = 0.48; ICC = 0.27). CONCLUSIONS Parental surveys are a valuable tool for estimating health care resource utilization during a 6-month recall period for children with suspected genetic disorders but are best used to complement utilization data collected from other sources.
Collapse
Affiliation(s)
- Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ellen Kim
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | -
- British Columbia Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), 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
| |
Collapse
|
26
|
Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genet Med 2018; 20:1122-1130. [PMID: 29446766 DOI: 10.1038/gim.2017.247] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022] Open
Abstract
PURPOSE We conducted a systematic literature review to summarize the current health economic evidence for whole-exome sequencing (WES) and whole-genome sequencing (WGS). METHODS Relevant studies were identified in the EMBASE, MEDLINE, Cochrane Library, EconLit and University of York Centre for Reviews and Dissemination databases from January 2005 to July 2016. Publications were included in the review if they were economic evaluations, cost studies, or outcome studies. RESULTS Thirty-six studies met our inclusion criteria. These publications investigated the use of WES and WGS in a variety of genetic conditions in clinical practice, the most common being neurological or neurodevelopmental disorders. Study sample size varied from a single child to 2,000 patients. Cost estimates for a single test ranged from $555 to $5,169 for WES and from $1,906 to $24,810 for WGS. Few cost analyses presented data transparently and many publications did not state which components were included in cost estimates. CONCLUSION The current health economic evidence base to support the more widespread use of WES and WGS in clinical practice is very limited. Studies that carefully evaluate the costs, effectiveness, and cost-effectiveness of these tests are urgently needed to support their translation into clinical practice.
Collapse
|
27
|
Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, Cohn RD, Scherer SW, Ungar WJ. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur J Hum Genet 2017; 25:1303-1312. [PMID: 29158552 PMCID: PMC5865210 DOI: 10.1038/s41431-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Accepted: 09/09/2017] [Indexed: 01/14/2023] Open
Abstract
The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.
Collapse
Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Jasmin Bhawra
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Canada
| | - Kate Tsiplova
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Nasim Monfared
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Sarah Bowdin
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - D James Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Christian R Marshall
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Raveen Basran
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Cheryl Shuman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Shinya Ito
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Courtney Hum
- Prenatal Diagnosis and Medical Genetics Program, Sinai Health System, Toronto, Canada
| | - Marta Girdea
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
| |
Collapse
|
28
|
Tan TY, Dillon OJ, Stark Z, Schofield D, Alam K, Shrestha R, Chong B, Phelan D, Brett GR, Creed E, Jarmolowicz A, Yap P, Walsh M, Downie L, Amor DJ, Savarirayan R, McGillivray G, Yeung A, Peters H, Robertson SJ, Robinson AJ, Macciocca I, Sadedin S, Bell K, Oshlack A, Georgeson P, Thorne N, Gaff C, White SM. Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions. JAMA Pediatr 2017; 171:855-862. [PMID: 28759686 PMCID: PMC5710405 DOI: 10.1001/jamapediatrics.2017.1755] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
IMPORTANCE Optimal use of whole-exome sequencing (WES) in the pediatric setting requires an understanding of who should be considered for testing and when it should be performed to maximize clinical utility and cost-effectiveness. OBJECTIVES To investigate the impact of WES in sequencing-naive children suspected of having a monogenic disorder and evaluate its cost-effectiveness if WES had been available at different time points in their diagnostic trajectory. DESIGN, SETTING, AND PARTICIPANTS This prospective study was part of the Melbourne Genomics Health Alliance demonstration project. At the ambulatory outpatient clinics of the Victorian Clinical Genetics Services at the Royal Children's Hospital, Melbourne, Australia, children older than 2 years suspected of having a monogenic disorder were prospectively recruited from May 1 through November 30, 2015, by clinical geneticists after referral from general and subspecialist pediatricians. All children had nondiagnostic microarrays and no prior single-gene or panel sequencing. EXPOSURES All children underwent singleton WES with targeted phenotype-driven analysis. MAIN OUTCOMES AND MEASURES The study examined the clinical utility of a molecular diagnosis and the cost-effectiveness of alternative diagnostic trajectories, depending on timing of WES. RESULTS Of 61 children originally assessed, 44 (21 [48%] male and 23 [52%] female) aged 2 to 18 years (mean age at initial presentation, 28 months; range, 0-121 months) were recruited, and a diagnosis was achieved in 23 (52%) by singleton WES. The diagnoses were unexpected in 8 of 23 (35%), and clinical management was altered in 6 of 23 (26%). The mean duration of the diagnostic odyssey was 6 years, with each child having a mean of 19 tests and 4 clinical genetics and 4 nongenetics specialist consultations, and 26 (59%) underwent a procedure while under general anesthetic for diagnostic purposes. Economic analyses of the diagnostic trajectory identified that WES performed at initial tertiary presentation resulted in an incremental cost savings of A$9020 (US$6838) per additional diagnosis (95% CI, A$4304-A$15 404 [US$3263-US$11 678]) compared with the standard diagnostic pathway. Even if WES were performed at the first genetics appointment, there would be an incremental cost savings of A$5461 (US$4140) (95% CI, A$1433-A$10 557 [US$1086- US$8004]) per additional diagnosis compared with the standard diagnostic pathway. CONCLUSIONS AND RELEVANCE Singleton WES in children with suspected monogenic conditions has high diagnostic yield, and cost-effectiveness is maximized by early application in the diagnostic pathway. Pediatricians should consider early referral of children with undiagnosed syndromes to clinical geneticists.
Collapse
Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | - Zornitza Stark
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Deborah Schofield
- Murdoch Childrens Research Institute, Melbourne, Australia,Faculty of Pharmacy, University of Sydney, Sydney, Australia,Garvan Institute of Medical Research, Sydney, Australia
| | - Khurshid Alam
- Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | - Belinda Chong
- Victorian Clinical Genetics Services, Melbourne, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Melbourne, Australia
| | - Gemma R. Brett
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Emma Creed
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Anna Jarmolowicz
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Patrick Yap
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Maie Walsh
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Lilian Downie
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - David J. Amor
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Heidi Peters
- Department of Paediatrics, University of Melbourne, Melbourne, Australia,The Royal Children’s Hospital, Melbourne, Australia
| | - Susan J. Robertson
- Murdoch Childrens Research Institute, Melbourne, Australia,The Royal Children’s Hospital, Melbourne, Australia
| | | | - Ivan Macciocca
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute, Melbourne, Australia
| | - Katrina Bell
- Murdoch Childrens Research Institute, Melbourne, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | | | - Clara Gaff
- Department of Paediatrics, University of Melbourne, Melbourne, Australia,Melbourne Genomics Health Alliance, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Susan M. White
- Victorian Clinical Genetics Services, Melbourne, Australia,Murdoch Childrens Research Institute, Melbourne, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| |
Collapse
|
29
|
HEADROOM BEYOND THE QUALITY- ADJUSTED LIFE-YEAR: THE CASE OF COMPLEX PEDIATRIC NEUROLOGY. Int J Technol Assess Health Care 2017; 33:5-10. [DOI: 10.1017/s0266462317000046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objectives: The headroom method was introduced for the very early evaluation of the potential value of new technologies. It allows for establishing a ceiling price for technologies to still be cost-effective by combining the maximum effect a technology might yield, the maximum willingness-to-pay (WTP) for this effect, and potential downstream expenses and savings. Although the headroom method is QALY-based, not all innovations are expected to result in QALY gain.Methods: This study explores the feasibility and usefulness of the headroom method in the evaluation of technologies that are unlikely to result in QALY gain. This will be illustrated with the diagnostic trajectory of complex pediatric neurology (CPN).Results: Our headroom analysis showed a large room for improvement in the current diagnostic trajectory of CPN in terms of diagnostic yield. Combining this with a maximum WTP value for an additional diagnosis and the potential downstream expenses and savings, resulted in a total headroom of €15,028. This indicates that a new technology in this particular diagnostic trajectory, might be cost-effective as long as its costs do not exceed €15,028.Conclusions: The headroom method seems a useful tool in the very early evaluation of medical technologies, also in cases when immediate QALY gain is unlikely. It allows for allocating healthcare resources to those technologies that are most promising. It should be kept in mind, however, that the headroom assumes an optimistic scenario, and for that reason cannot guarantee future cost-effectiveness. It might be most useful for ruling out those technologies that are unlikely to be cost-effective.
Collapse
|
30
|
Oei K, Hayeems RZ, Ungar WJ, Cohn RD, Cohen E. Genetic Testing among Children in a Complex Care Program. CHILDREN-BASEL 2017; 4:children4050042. [PMID: 28531152 PMCID: PMC5448000 DOI: 10.3390/children4050042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/20/2017] [Accepted: 05/16/2017] [Indexed: 11/16/2022]
Abstract
Little is known about the pattern of genetic testing and frequency of genetic diagnoses among children enrolled in structured complex care programs (CCPs). Such information may inform the suitability of emerging genome diagnostics for this population. The objectives were to describe the proportion of children with undiagnosed genetic conditions despite genetic testing and measure the testing period, types and costs of genetic tests used. A retrospective analysis of 420 children enrolled in Toronto’s Hospital for Sick Children’s CCP from January 2010 until June 2014 was conducted. Among those who underwent genetic testing (n = 319; 76%), a random sample of 20% (n = 63) was further analyzed. A genetic diagnosis was confirmed in 48% of those who underwent testing. Those with no genetic diagnosis underwent significantly more genetic tests than those with a confirmed genetic diagnosis [median interquartile range (IQR): six tests (4–9) vs. three tests (2–4), p = 0.002], more sequence-level tests and a longer, more expensive testing period than those with a genetic diagnosis [median (IQR): length of testing period: 4.12 years (1.73–8.42) vs. 0.35 years (0.12–3.04), p < 0.001; genetic testing costs C$8496 ($4399–$12,480) vs. C$2614 ($1605–$4080), p < 0.001]. A genetic diagnosis was not established for 52% of children. Integrating genome-wide sequencing into clinical care may improve diagnostic efficiency and yield in this population.
Collapse
Affiliation(s)
- Krista Oei
- Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
- Division of Paediatric Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| | - Robin Z Hayeems
- Child Health Evaluative Studies, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
- Institute of Health Policy and Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada.
| | - Wendy J Ungar
- Child Health Evaluative Studies, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
- Institute of Health Policy and Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada.
| | - Ronald D Cohn
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada.
- Program in Genetics and Genomic Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| | - Eyal Cohen
- Division of Paediatric Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
- Child Health Evaluative Studies, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
- Institute of Health Policy and Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada.
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada.
| |
Collapse
|
31
|
Walsh M, Bell KM, Chong B, Creed E, Brett GR, Pope K, Thorne NP, Sadedin S, Georgeson P, Phelan DG, Day T, Taylor JA, Sexton A, Lockhart PJ, Kiers L, Fahey M, Macciocca I, Gaff CL, Oshlack A, Yiu EM, James PA, Stark Z, Ryan MM. Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy. Ann Clin Transl Neurol 2017; 4:318-325. [PMID: 28491899 PMCID: PMC5420808 DOI: 10.1002/acn3.409] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Objective To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. Methods Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. Results Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2–68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months–62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. Conclusions This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes.
Collapse
Affiliation(s)
- Maie Walsh
- Murdoch Childrens Research Institute Melbourne Australia.,Royal Melbourne Hospital Melbourne Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute Melbourne Australia
| | - Belinda Chong
- Murdoch Childrens Research Institute Melbourne Australia
| | - Emma Creed
- Royal Melbourne Hospital Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Gemma R Brett
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Kate Pope
- Murdoch Childrens Research Institute Melbourne Australia
| | - Natalie P Thorne
- Melbourne Genomics Health Alliance Melbourne Australia.,Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute Melbourne Australia
| | | | - Dean G Phelan
- Murdoch Childrens Research Institute Melbourne Australia
| | - Timothy Day
- Royal Melbourne Hospital Melbourne Australia
| | | | | | - Paul J Lockhart
- Murdoch Childrens Research Institute Melbourne Australia.,Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia
| | | | | | - Ivan Macciocca
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
| | - Paul A James
- Royal Melbourne Hospital Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Zornitza Stark
- Murdoch Childrens Research Institute Melbourne Australia
| | - Monique M Ryan
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
| | | |
Collapse
|
32
|
A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Genet Med 2017; 19:1055-1063. [PMID: 28333917 PMCID: PMC5589982 DOI: 10.1038/gim.2017.1] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022] Open
Abstract
Purpose: Implementation of novel genetic diagnostic tests is generally driven by technological advances because they promise shorter turnaround times and/or higher diagnostic yields. Other aspects, including impact on clinical management or cost-effectiveness, are often not assessed in detail prior to implementation. Methods: We studied the clinical utility of whole-exome sequencing (WES) in complex pediatric neurology in terms of diagnostic yield and costs. We analyzed 150 patients (and their parents) presenting with complex neurological disorders of suspected genetic origin. In a parallel study, all patients received both the standard diagnostic workup (e.g., cerebral imaging, muscle biopsies or lumbar punctures, and sequential gene-by-gene–based testing) and WES simultaneously. Results: Our unique study design allowed direct comparison of diagnostic yield of both trajectories and provided insight into the economic implications of implementing WES in this diagnostic trajectory. We showed that WES identified significantly more conclusive diagnoses (29.3%) than the standard care pathway (7.3%) without incurring higher costs. Exploratory analysis of WES as a first-tier diagnostic test indicates that WES may even be cost-saving, depending on the extent of other tests being omitted. Conclusion: Our data support such a use of WES in pediatric neurology for disorders of presumed genetic origin. Genet Med advance online publication 23 March 2017
Collapse
|
33
|
Exploring the feasibility of delivering standardized genomic care using ophthalmology as an example. Genet Med 2017; 19:1032-1039. [DOI: 10.1038/gim.2017.9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/13/2017] [Indexed: 01/13/2023] Open
|
34
|
Weymann D, Laskin J, Roscoe R, Schrader KA, Chia S, Yip S, Cheung WY, Gelmon KA, Karsan A, Renouf DJ, Marra M, Regier DA. The cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers. Mol Genet Genomic Med 2017; 5:251-260. [PMID: 28546995 PMCID: PMC5441418 DOI: 10.1002/mgg3.281] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/18/2017] [Accepted: 02/08/2017] [Indexed: 12/21/2022] Open
Abstract
Background Limited data exist on the real‐world costs of applying whole‐genome analysis (WGA) in a clinical setting. We estimated the costs of applying WGA to guide treatments for patients with advanced cancers and characterized how costs evolve over time. Methods The setting is the British Columbia Cancer Agency Personalized OncoGenomics (POG) program in British Columbia, Canada. Cost data were obtained for patients who enrolled in the program from 2012 to 2015. We estimated mean WGA costs using bootstrapping. We applied time series analysis and produced 10‐year forecasts to determine when costs are expected to reach critical thresholds. Results The mean cost of WGA over the study period was CDN$34,886 per patient (95% CI: $34,051, $35,721). Over time, WGA costs decreased, driven by a reduction in costs of sequencing. Yet, costs of other components of WGA increased. Forecasting showed WGA costs may not reach critical thresholds within the next 10 years. Conclusion WGA costs decreased over the studied time horizon, but expenditures needed to realize WGA remain significant. Future research exploring costs and benefits of WGA‐guided cancer care are crucial to guide health policy.
Collapse
Affiliation(s)
- Deirdre Weymann
- Canadian Centre for Applied Research in Cancer Control (ARCC)Cancer Control ResearchBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Janessa Laskin
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Robyn Roscoe
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Kasmintan A Schrader
- Department of Medical GeneticsFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada.,Department of Molecular OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Stephen Chia
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Stephen Yip
- Department of Pathology & Laboratory MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada.,Department of PathologyBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Winson Y Cheung
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Karen A Gelmon
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Aly Karsan
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada.,Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of Pathology & Laboratory MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Daniel J Renouf
- Division of Medical OncologyBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of MedicineFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Marco Marra
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada.,Department of Medical GeneticsFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control (ARCC)Cancer Control ResearchBC Cancer AgencyVancouverBritish ColumbiaCanada.,School of Population and Public HealthFaculty of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| |
Collapse
|
35
|
Domínguez-Carral J, López-Pisón J, Macaya A, Bueno Campaña M, García-Pérez MA, Natera-de Benito D. Genetic testing among Spanish pediatric neurologists: Knowledge, attitudes and practices. Eur J Med Genet 2016; 60:124-129. [PMID: 27890788 DOI: 10.1016/j.ejmg.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/16/2016] [Accepted: 11/22/2016] [Indexed: 01/01/2023]
Abstract
Advances in genetic testing applied to child neurology have enabled the development of genetic tests with greater sensitivity in elucidating an etiologic diagnosis for common neurological conditions. The objective of the current study was to examine child neurologists' perspectives and insights into genetic testing. We surveyed 118 Spanish child neurologists, exploring their knowledge, attitudes, and practices concerning genetic tests. All of them had requested at least one genetic test in the past six months. Global developmental delay or intellectual disability in absence of a strong specific etiologic suspicion and autism spectrum disorders were the disorders for which genetic testing was most frequently requested. The most commonly requested genetic test was CGH-array. Overall, child neurologist perception of readiness for making genetic-related decisions was not bad, although many would like to have a greater support from geneticists and were interested in increasing the time dedicated to genetics within their continuing education program. These data have important implications for future practice, research, and education.
Collapse
Affiliation(s)
- J Domínguez-Carral
- Department of Pediatrics, Hospital Universitario de Torrejón, Madrid, Spain
| | - J López-Pisón
- Department of Pediatric Neurology, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - A Macaya
- Department of Pediatric Neurology, Hospital Universitario Vall d´Hebron, Barcelona, Spain
| | - M Bueno Campaña
- Department of Pediatrics, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - M A García-Pérez
- Department of Pediatrics, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - D Natera-de Benito
- Department of Pediatrics, Hospital Universitario de Fuenlabrada, Madrid, Spain.
| |
Collapse
|
36
|
van Nimwegen KJM, Kievit W, van der Wilt GJ, Schieving JH, Willemsen MAAP, Donders ART, Verhaak CM, Grutters JPC. Parental quality of life in complex paediatric neurologic disorders of unknown aetiology. Eur J Paediatr Neurol 2016; 20:723-31. [PMID: 27321953 DOI: 10.1016/j.ejpn.2016.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/13/2016] [Accepted: 05/17/2016] [Indexed: 02/05/2023]
Abstract
Complex paediatric neurology (CPN) patients generally present with non-specific symptoms, such as developmental delay, impaired movement and epilepsy. The diagnostic trajectory in these disorders is usually complicated and long-lasting, and may be burdensome to the patients and their parents. Additionally, as caring for a chronically ill child can be stressful and demanding, parents of these patients may experience impaired health-related quality of life (HRQoL). This study aims to assess parental HRQoL and factors related to it in CPN. Physical and mental HRQoL of 120 parents was measured and compared to the general population using the SF-12 questionnaire. Parents also completed this questionnaire for the measurement of patient HRQoL. Additional questionnaires were used to measure parental uncertainty (Visual Analogue Scale) and worry phenomena (Penn State Worry Questionnaire), and to obtain socio-demographic data. A linear mixed model with random effect was used to investigate which of these variables were associated with parental HRQoL. As compared to the general population, HRQoL of these parents appeared diminished. Fathers showed both lowered physical (51.76, p < 0.05) and mental (49.41, p < 0.01) HRQoL, whereas mothers only showed diminished mental (46.46, p < 0.01) HRQoL. Patient HRQoL and parental worry phenomena were significantly correlated with overall and mental parental HRQoL. The reduction in parental mental HRQoL is alarming, also because children strongly rely on their parents and parental mental health is known to influence children's health. Awareness of these problems among clinicians, and supportive care if needed are important to prevent exacerbation of the problems.
Collapse
Affiliation(s)
- K J M van Nimwegen
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands.
| | - W Kievit
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands.
| | - G J van der Wilt
- Radboud University Medical Center, Donders Centre for Neuroscience, Department for Health Evidence, Nijmegen, The Netherlands.
| | - J H Schieving
- Radboud University Medical Center, Department of Neurology, Nijmegen, The Netherlands.
| | - M A A P Willemsen
- Radboud University Medical Center, Department of Neurology, Nijmegen, The Netherlands.
| | - A R T Donders
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands.
| | - C M Verhaak
- Radboud University Medical Center, Department of Medical Psychology, Nijmegen, The Netherlands.
| | - J P C Grutters
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands.
| |
Collapse
|
37
|
Chennagiri N, White EJ, Frieden A, Lopez E, Lieber DS, Nikiforov A, Ross T, Batorsky R, Hansen S, Lip V, Luquette LJ, Mauceli E, Margulies D, Milos PM, Napolitano N, Nizzari MM, Yu T, Thompson JF. Orthogonal NGS for High Throughput Clinical Diagnostics. Sci Rep 2016; 6:24650. [PMID: 27090146 PMCID: PMC4836299 DOI: 10.1038/srep24650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/04/2016] [Indexed: 11/11/2022] Open
Abstract
Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Va Lip
- Claritas Genomics, Cambridge MA, USA
| | | | | | - David Margulies
- Claritas Genomics, Cambridge MA, USA
- Harvard Medical School, Boston MA, USA
- Boston Children’s Hospital, Boston MA, USA
| | | | | | | | | | | |
Collapse
|
38
|
Monroe GR, Frederix GW, Savelberg SMC, de Vries TI, Duran KJ, van der Smagt JJ, Terhal PA, van Hasselt PM, Kroes HY, Verhoeven-Duif NM, Nijman IJ, Carbo EC, van Gassen KL, Knoers NV, Hövels AM, van Haelst MM, Visser G, van Haaften G. Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability. Genet Med 2016; 18:949-56. [DOI: 10.1038/gim.2015.200] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/30/2015] [Indexed: 11/09/2022] Open
|
39
|
Hehir-Kwa JY, Pfundt R, Veltman JA. Exome sequencing and whole genome sequencing for the detection of copy number variation. Expert Rev Mol Diagn 2015; 15:1023-32. [PMID: 26088785 DOI: 10.1586/14737159.2015.1053467] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many laboratories now use genomic microarrays as their first-tier diagnostic test for copy number variation (CNV) detection. In addition, whole exome sequencing is increasingly being offered as a diagnostic test for heterogeneous disorders. Although mostly used for the detection of point mutations and small insertion-deletions, exome sequencing can also be used to call CNVs, allowing combined small and large variant analysis. Whole genome sequencing in addition to these advantages also offers the potential to characterize CNVs to unprecedented levels of accuracy, providing position and orientation information. In this review, we discuss the clinical potential of CNV identification in whole exome sequencing and whole genome sequencing data and the implications this has on diagnostic laboratories.
Collapse
Affiliation(s)
- Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | |
Collapse
|