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Piñeros-Fernández MC, Morte B, García-Giménez JL. Utility of exome sequencing for the diagnosis of pediatric-onset neuromuscular diseases beyond diagnostic yield: a narrative review. Neurol Sci 2024; 45:1455-1464. [PMID: 37989827 PMCID: PMC10942921 DOI: 10.1007/s10072-023-07210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Diagnosis of neuromuscular diseases (NMD) can be challenging because of the heterogeneity of this group of diseases. This review aimed to describe the diagnostic yield of whole exome sequencing (WES) for pediatric-onset neuromuscular disease diagnosis, as well as other benefits of this approach in patient management since WES can contribute to appropriate treatment selection in NMD patients. WES increases the possibility of reaching a conclusive genetic diagnosis when other technologies have failed and even exploring new genes not previously associated with a specific NMD. Moreover, this strategy can be useful when a dual diagnosis is suspected in complex congenital anomalies and undiagnosed cases.
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Affiliation(s)
- Martha Cecilia Piñeros-Fernández
- Servicio de Neurología Pediátrica, Hospital Pediátrico, Fundación Cardio Infantil-LaCardio, Bogotá, Colombia
- Unidad Pediátrica, Los Cobos Medical Center, Bogotá, Colombia
- Consulta Externa Especializada, Virrey Solís IPS, Bogotá, Colombia
| | - Beatriz Morte
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, València, Spain.
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Pennings M, Meijer RPP, Gerrits M, Janssen J, Pfundt R, de Leeuw N, Gilissen C, Gardeitchik T, Schouten M, Voermans N, van de Warrenburg B, Kamsteeg EJ. Copy number variants from 4800 exomes contribute to ~7% of genetic diagnoses in movement disorders, muscle disorders and neuropathies. Eur J Hum Genet 2023; 31:654-662. [PMID: 36781956 PMCID: PMC10250492 DOI: 10.1038/s41431-023-01312-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Various groups of neurological disorders, including movement disorders and neuromuscular diseases, are clinically and genetically heterogeneous. Diagnostic panel-based exome sequencing is a routine test for these disorders. Despite the success rates of exome sequencing, it results in the detection of causative sequence variants in 'only' 25-30% of cases. Copy number variants (CNVs), i.e. deletion or duplications, explain 10-20% of individuals with multisystemic phenotypes, such as co-existing intellectual disability, but may also have a role in disorders affecting a single system (organ), like neurological disorders with normal intelligence. In this study, CNVs were extracted from clinical exome sequencing reports of 4800 probands primarily with a movement disorder, myopathy or neuropathy. In 88 (~2%) probands, phenotype-matching CNVs were detected, representing ~7% of genetically confirmed cases. CNVs varied from involvement of over 100 genes to single exons and explained X-linked, autosomal dominant, or - recessive disorders, the latter due to either a homozygous CNV or a compound heterozygous CNV with a sequence variant on the other allele. CNVs were detected affecting genes where deletions or duplications are established as a common mechanism, like PRKN (in Parkinson's disease), DMD (in Duchenne muscular dystrophy) and PMP22 (in neuropathies), but also genes in which no intragenic CNVs have been reported to date. Analysis of CNVs as part of panel-based exome sequencing for genetically heterogeneous neurological diseases provides an additional diagnostic yield of ~2% without extra laboratory costs. Therefore it is recommended to perform CNV analysis for movement disorders, muscle disease, neuropathies, or any other single-system disorder.
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Affiliation(s)
- Maartje Pennings
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Rowdy P P Meijer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Monique Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jannie Janssen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Meyke Schouten
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicol Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.
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Chen PS, Chao CC, Tsai LK, Huang HY, Chien YH, Huang PH, Hwu WL, Hsieh ST, Lee NC, Hsueh HW, Yang CC. Diagnostic Challenges of Neuromuscular Disorders after Whole Exome Sequencing. J Neuromuscul Dis 2023:JND230013. [PMID: 37066920 DOI: 10.3233/jnd-230013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
BACKGROUND Whole-exome sequencing (WES) facilitates the diagnosis of hereditary neuromuscular disorders. To achieve an accurate diagnosis, physicians should interpret the genetic report carefully along with clinical information and examinations. We described our experience with (1) clinical validation in patients with variants found using WES and (2) a diagnostic approach for those with negative findings from WES. METHODS WES was performed on patients with the clinical impression of hereditary neuromuscular disorders. Information on clinical manifestations, neurological examination, electrodiagnostic studies, histopathology of muscle and nerve, and laboratory tests were collected. RESULTS Forty-one patients (Male/Female: 18/23, age of onset: 34.5±15.9) accepted WES and were categorized into four scenarios: (1) patients with a positive WES result, (2) patients with an inconclusive WES result but supporting clinical data, (3) negative findings from WES, but a final diagnosis after further work-up, and (4) undetermined etiology from WES and in further work-ups. The yield rate of the initial WES was 63.4% (26/41). Among these, seventeen patients had positive WES result, while the other nine patients had inconclusive WES result but supporting clinical data. Notably, in the fifteen patients with equivocal or negative findings from WES, four patients (26.7%) achieved a diagnosis after further workup: tumor-induced osteomalacia, metabolic myopathy with pathogenic variants in mitochondrial DNA, microsatellite expansion disease, and vasculitis-related neuropathy. The etiologies remained undetermined in eleven patients (myopathy: 7, neuropathy: 4) after WES and further workup. CONCLUSIONS It is essential to design genotype-guided molecular studies to correlate the identified variants with their clinical features. For patients who had negative findings from WES, acquired diseases, mitochondrial DNA disorders and microsatellite expansion diseases should be considered.
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Affiliation(s)
- Pin-Shiuan Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Chao Chao
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Kai Tsai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-Yi Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Hsin Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
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Kim YG, Kwon H, Park JH, Nam SH, Ha C, Shin S, Heo WY, Kim HJ, Chung KW, Jang JH, Kim JW, Choi BO. Whole-genome sequencing in clinically diagnosed Charcot-Marie-Tooth disease undiagnosed by whole-exome sequencing. Brain Commun 2023; 5:fcad139. [PMID: 37180992 PMCID: PMC10174204 DOI: 10.1093/braincomms/fcad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/16/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023] Open
Abstract
Whole-genome sequencing is the most comprehensive form of next-generation sequencing method. We aimed to assess the additional diagnostic yield of whole-genome sequencing in patients with clinically diagnosed Charcot-Marie-Tooth disease when compared with whole-exome sequencing, which has not been reported in the literature. Whole-genome sequencing was performed on 72 families whose genetic cause of clinically diagnosed Charcot-Marie-Tooth disease was not revealed after the whole-exome sequencing and 17p12 duplication screening. Among the included families, 14 (19.4%) acquired genetic diagnoses that were compatible with their phenotypes. The most common factor that led to the additional diagnosis in the whole-genome sequencing was genotype-driven analysis (four families, 4/14), in which a wider range of genes, not limited to peripheral neuropathy-related genes, were analysed. Another four families acquired diagnosis due to the inherent advantage of whole-genome sequencing such as better coverage than the whole-exome sequencing (two families, 2/14), structural variants (one family, 1/14) and non-coding variants (one family, 1/14). In conclusion, an evident gain in diagnostic yield was obtained from whole-genome sequencing of the whole-exome sequencing-negative cases. A wide range of genes, not limited to inherited peripheral neuropathy-related genes, should be targeted during whole-genome sequencing.
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Affiliation(s)
- Young-gon Kim
- Correspondence to: Jong-Won Kim, MD, PhD Department of Laboratory Medicine and Genetics, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
| | | | - Jong-ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Soo Hyun Nam
- Cell and Gene Therapy Institute (CGTI), Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Won Young Heo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Hye Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Byung-Ok Choi
- Correspondence may also be sent to: Byung-Ok Choi, MD, PhD Department of Neurology, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
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Huq AJ, Thompson B, Bennett MF, Bournazos A, Bommireddipalli S, Gorelik A, Schultz J, Sexton A, Purvis R, West K, Cotter M, Valente G, Hughes A, Riaz M, Walsh M, Farrand S, Loi SM, Kilpatrick T, Brodtmann A, Darby D, Eratne D, Walterfang M, Delatycki MB, Storey E, Fahey M, Cooper S, Lacaze P, Masters CL, Velakoulis D, Bahlo M, James PA, Winship I. Clinical impact of whole-genome sequencing in patients with early-onset dementia. J Neurol Neurosurg Psychiatry 2022; 93:jnnp-2021-328146. [PMID: 35906014 DOI: 10.1136/jnnp-2021-328146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND In the clinical setting, identification of the genetic cause in patients with early-onset dementia (EOD) is challenging due to multiple types of genetic tests required to arrive at a diagnosis. Whole-genome sequencing (WGS) has the potential to serve as a single diagnostic platform, due to its superior ability to detect common, rare and structural genetic variation. METHODS WGS analysis was performed in 50 patients with EOD. Point mutations, small insertions/deletions, as well as structural variants (SVs) and short tandem repeats (STRs), were analysed. An Alzheimer's disease (AD)-related polygenic risk score (PRS) was calculated in patients with AD. RESULTS Clinical genetic diagnosis was achieved in 7 of 50 (14%) of the patients, with a further 8 patients (16%) found to have established risk factors which may have contributed to their EOD. Two pathogenic variants were identified through SV analysis. No expanded STRs were found in this study cohort, but a blinded analysis with a positive control identified a C9orf72 expansion accurately. Approximately 37% (7 of 19) of patients with AD had a PRS equivalent to >90th percentile risk. DISCUSSION WGS acts as a single genetic test to identify different types of clinically relevant genetic variations in patients with EOD. WGS, if used as a first-line clinical diagnostic test, has the potential to increase the diagnostic yield and reduce time to diagnosis for EOD.
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Affiliation(s)
- Aamira J Huq
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Bryony Thompson
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Adam Bournazos
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Alexandra Gorelik
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Joshua Schultz
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Rebecca Purvis
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Kirsty West
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Megan Cotter
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Giulia Valente
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Andrew Hughes
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Moeen Riaz
- Public Health and Preventative Medicine, Monash University Faculty of Medicine, Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Maie Walsh
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Sarah Farrand
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Samantha M Loi
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Trevor Kilpatrick
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Amy Brodtmann
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia
- Florey Neurosciences Institutes, University of Melbourne, Carlton South, Victoria, Australia
| | - David Darby
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia
- Mental Health Research Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Dhamidhu Eratne
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Mark Walterfang
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Elsdon Storey
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Neuroscience, Alfred Health, Melbourne, Victoria, Australia
| | - Michael Fahey
- Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Sandra Cooper
- Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Paul Lacaze
- Public Health and Preventative Medicine, Monash University Faculty of Medicine, Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Dennis Velakoulis
- Neuropsychiatry Unit, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Paul A James
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
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Van Der Merwe N, Ramesar R, De Vries J. Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings. Front Genet 2022; 13:864822. [PMID: 35754817 PMCID: PMC9216214 DOI: 10.3389/fgene.2022.864822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA. Semi-structured interviews were conducted, and the transcripts analysed using the framework approach for data analysis. Current roadblocks for the clinical adoption of WES in SA include a lack of standardised guidelines; complexities relating to variant interpretation due to lack of functional studies and underrepresentation of people of African ancestry in the reference genome, population and variant databases; lack of resources and skilled personnel for variant confirmation and follow-up. Suggestions to overcome these barriers include obtaining funding and buy-in from the private and public sectors and medical insurance companies; the generation of a locally relevant reference genome; training of health professionals in the field of genomics and bioinformatics; and multidisciplinary collaboration. Participants emphasised the importance of upscaling the accessibility to and training of GCs, as well as upskilling of clinicians and genetic nurses for return of genetic data in collaboration with GCs and medical geneticists. Future research could focus on exploring the development of stakeholder partnerships for increased access to trained specialists as well as community engagement and education, alongside the development of guidelines for result disclosure.
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Affiliation(s)
- Nicole Van Der Merwe
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina De Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
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Lavelle TA, Feng X, Keisler M, Cohen JT, Neumann PJ, Prichard D, Schroeder BE, Salyakina D, Espinal PS, Weidner SB, Maron JL. Cost-effectiveness of exome and genome sequencing for children with rare and undiagnosed conditions. Genet Med 2022; 24:1349-1361. [PMID: 35396982 DOI: 10.1016/j.gim.2022.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to estimate the cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children. METHODS We modeled costs, diagnoses, and quality-adjusted life years (QALYs) for diagnostic strategies for critically ill infants (aged <1 year) and children (aged <18 years) with suspected genetic conditions: (1) standard of care (SOC) testing, (2) ES, (3) GS, (4) SOC followed by ES, (5) SOC followed by GS, (6) ES followed by GS, and (7) SOC followed by ES followed by GS. We calculated the 10-year incremental cost per additional diagnosis, and lifetime incremental cost per QALY gained, from a health care perspective. RESULTS First-line GS costs $15,048 per diagnosis vs SOC for infants and $27,349 per diagnosis for children. If GS is unavailable, ES represents the next most efficient option compared with SOC ($15,543 per diagnosis for infants and $28,822 per diagnosis for children). Other strategies provided the same or fewer diagnoses at a higher incremental cost per diagnosis. Lifetime results depend on the patient's assumed long-term prognosis after diagnosis. For infants, GS ranged from cost-saving (vs all alternatives) to $18,877 per QALY (vs SOC). For children, GS (vs SOC) ranged from $119,705 to $490,047 per QALY. CONCLUSION First-line GS may be the most cost-effective strategy for diagnosing infants with suspected genetic conditions. For all children, GS may be cost-effective under certain assumptions. ES is nearly as efficient as GS and hence is a viable option when GS is unavailable.
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Affiliation(s)
- Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA.
| | - Xue Feng
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Marlena Keisler
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Joshua T Cohen
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Peter J Neumann
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | | | | | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Paula S Espinal
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Samuel B Weidner
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Jill L Maron
- Women & Infants Hospital of Rhode Island, Care New England Health System, Providence, RI
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8
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Xie D, Duan R, Li C, Xie Z, Wang A, Xiong L, Wei J, Xi H, Fang J, Yan H, Wang J, Zhang Y, Mao X, Wang J, Wang H. Study on the Economic Burden of Neurodevelopmental Diseases on Patients With Genetic Diagnosis. Front Public Health 2022; 10:887796. [PMID: 35615033 PMCID: PMC9126321 DOI: 10.3389/fpubh.2022.887796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To study the burden of neurodevelopmental diseases (NDDs) via cost-of-illness analysis of Chinese patients with genetic diagnosis. Methods We recruited NDD patients (0–18 years old) with genetic diagnosis (GD) from September 1, 2020 to January 30, 2021. We gathered basic information on the details of diagnosis, as well as the direct medical cost, direct non-healthcare cost and indirect cost before and after receiving GD. We corrected the cost for time biases by calculating the cost per day for each patient. Results For the 502 patients with NDDs, the mean age was 4.08 ± 3.47. The household income was 0.6 (0.4, 1.0) 10,000 CNY per-month on average. The direct medical cost, direct non-healthcare cost and indirect cost were 12.27 (7.36, 22.23) 10,000 CNY, 1.45 (0.73, 2.69)10,000 CNY and 14.14(4.80, 28.25) 10,000 CNY per patient, respectively. Every patient received 1.20 (0.34, 3.60) 10,000 CNY on average (15.91%) from insurance. The daily total cost after receiving GD were ~62.48% lower than those before GD (191.59 CNY vs. 71.45 CNY). The descend range of lab cost (95.77%, P < 0.05) was the largest, followed by drugs (91.39%, P < 0.05), hospitalization (90.85%, P < 0.05), and consultation (57.41%, P < 0.05). The cost of rehabilitation kept slightly increasing but there were no significant differences (P > 0.05). The daily direct medical cost of each patient fell by 75.26% (P < 0.05) from 311.79 CNY to 77.14 CNY when the diagnostic age was younger than 1, and declined by 49.30% (P < 0.05) and 8.97% (P > 0.05) when the diagnostic age was 1–3 and older than 3, respectively. Conclusions Early genetic diagnosis is crucial for to reducing the burden of disease because of the amount of money spent was lower when they are diagnosed at younger age. Patients with NDDs can incur a heavy economic burden, especially in rehabilitation cost and indirect cost, because the insurance coverage for patients is low, so it is urgent for governments to pay more attention to these issues.
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Affiliation(s)
- Donghua Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Department of Neurology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Li
- Children Health Hospital of Shenzhen City, Shenzhen, China
| | - Zhiqun Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Aihua Wang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Lili Xiong
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Jianhui Wei
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Hui Xi
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Junqu Fang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Junyu Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiao Mao
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- *Correspondence: Xiao Mao
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
- Jingmin Wang
| | - Hua Wang
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- Hua Wang
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9
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Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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10
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Grunseich C, Sarkar N, Lu J, Owen M, Schindler A, Calabresi PA, Sumner CJ, Roda RH, Chaudhry V, Lloyd TE, Crawford TO, Subramony SH, Oh SJ, Richardson P, Tanji K, Kwan JY, Fischbeck KH, Mankodi A. Improving the efficacy of exome sequencing at a quaternary care referral centre: novel mutations, clinical presentations and diagnostic challenges in rare neurogenetic diseases. J Neurol Neurosurg Psychiatry 2021; 92:1186-1196. [PMID: 34103343 PMCID: PMC8522445 DOI: 10.1136/jnnp-2020-325437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/10/2021] [Accepted: 05/05/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND We used a multimodal approach including detailed phenotyping, whole exome sequencing (WES) and candidate gene filters to diagnose rare neurological diseases in individuals referred by tertiary neurology centres. METHODS WES was performed on 66 individuals with neurogenetic diseases using candidate gene filters and stringent algorithms for assessing sequence variants. Pathogenic or likely pathogenic missense variants were interpreted using in silico prediction tools, family segregation analysis, previous publications of disease association and relevant biological assays. RESULTS Molecular diagnosis was achieved in 39% (n=26) including 59% of childhood-onset cases and 27% of late-onset cases. Overall, 37% (10/27) of myopathy, 41% (9/22) of neuropathy, 22% (2/9) of MND and 63% (5/8) of complex phenotypes were given genetic diagnosis. Twenty-seven disease-associated variants were identified including ten novel variants in FBXO38, LAMA2, MFN2, MYH7, PNPLA6, SH3TC2 and SPTLC1. Single-nucleotide variants (n=10) affected conserved residues within functional domains and previously identified mutation hot-spots. Established pathogenic variants (n=16) presented with atypical features, such as optic neuropathy in adult polyglucosan body disease, facial dysmorphism and skeletal anomalies in cerebrotendinous xanthomatosis, steroid-responsive weakness in congenital myasthenia syndrome 10. Potentially treatable rare diseases were diagnosed, improving the quality of life in some patients. CONCLUSIONS Integrating deep phenotyping, gene filter algorithms and biological assays increased diagnostic yield of exome sequencing, identified novel pathogenic variants and extended phenotypes of difficult to diagnose rare neurogenetic disorders in an outpatient clinic setting.
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Affiliation(s)
- Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Nathan Sarkar
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Joyce Lu
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Mallory Owen
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Alice Schindler
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter A Calabresi
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charlotte J Sumner
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ricardo H Roda
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vinay Chaudhry
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas E Lloyd
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas O Crawford
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - S H Subramony
- Department of Neurology, University of Florida, Gainesville, Florida, USA
| | - Shin J Oh
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Perry Richardson
- Department of Neurology, George Washington University, Washington, District of Columbia, USA
| | - Kurenai Tanji
- Division of Neuropathology, Columbia University Medical Center, New York, New York, USA
| | - Justin Y Kwan
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Ami Mankodi
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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11
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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12
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Nunes Gonçalves JP, Leoni TB, Martins MP, Peluzzo TM, Dourado MET, Saute JAM, Paranhos Miranda Covaleski AP, Bulle de Oliveira AS, Claudino R, Marques W, Nucci A, França MC. Genetic epidemiology of familial ALS in Brazil. Neurobiol Aging 2021; 102:227.e1-227.e4. [PMID: 33618928 DOI: 10.1016/j.neurobiolaging.2021.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/03/2020] [Accepted: 01/09/2021] [Indexed: 01/11/2023]
Abstract
Many genes associated with familial forms of the amyotrophic lateral sclerosis (fALS) have been identified in European and North American cohorts. However, little is known about the genetic bases of fALS in Latin America and Brazil, in particular. To address this question, we recruited 107 patients with fALS from 93 unrelated families from Southeastern, Southern, and Northeastern regions of the country. A 3-step diagnostic approach was used: 1) Triplet repeat primed polymerase chain reaction to search for C9orf72 expansions, then 2) fragment digestion to search for the c.166 C>T VAPB variant, and finally, 3) whole exome sequencing for those who tested negative. We identified the genetic cause for fALS in 70% of the families. VAPB and C9orf72 were the most frequent genes (30% and 22%, respectively), followed by SOD1, TARDBP, ANXA11, and FUS. Five novel variants in known ALS genes were found, including the SOD1 Val120Leu and ANXA11 Asp40Tyr, which were seen in 2 unrelated families each. In conclusion, VAPB and then C9orf72 are the genes most commonly related to fALS in Brazil.
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Affiliation(s)
- João Pedro Nunes Gonçalves
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL
| | - Tauana Bernardes Leoni
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL
| | - Melina Pazian Martins
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL
| | - Thiago Mazzo Peluzzo
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL
| | - Mario Emílio T Dourado
- Department of Integrative Medicine, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Jonas Alex M Saute
- Department of Internal Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Rinaldo Claudino
- Department of Neurology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Wilson Marques
- Department of Neurosciences and Behavior Sciences, Ribeirão Preto School of Medicine, University of São Paulo (HCFMRP-USP), Ribeirão Preto, Brazil
| | - Anamarli Nucci
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL
| | - Marcondes C França
- Departments of Neurology and Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, BRAZIL.
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13
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Widening the lens of actionability: A qualitative study of primary care providers' views and experiences of managing secondary genomic findings. Eur J Hum Genet 2021; 30:595-603. [PMID: 33776058 PMCID: PMC9091250 DOI: 10.1038/s41431-021-00876-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/22/2022] Open
Abstract
Most secondary genomic findings (SFs) fall in the scope of primary care practice. However, primary care providers' (PCPs) capacity to manage these findings is not well understood. We explored PCPs' views and experiences of managing SFs through a qualitative study. PCPs participated in semi-structured interviews about SFs from a patient in their practice or a hypothetical patient. The interpretive descriptive methodology was used to analyze transcripts thematically through constant comparison. Fifteen family physicians from Ontario, Canada participated (ten females; 6-40 years in practice across community and academic settings). PCPs made sense of SFs through the lens of actionability: they actively looked for clinical relevance by considering a wide range of immediate and future actions, including referrals, genetic testing, screening, lifestyle changes, counseling about family planning, informing family members, future medication choice, increased vigilance/surveillance, and managing results in the electronic medical record. PCPs saw clinical actionability as the main benefit mitigating the potential harms of learning SFs, namely patient anxiety and unnecessary investigations. PCPs conceptualized actionability more broadly than it is traditionally defined in medical genetics. Further research will be needed to determine if PCPs' emphasis on actionability conflicts with patients' expectations of SFs and if it leads to overutilization of healthcare resources.
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14
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The clinical utility of exome sequencing and extended bioinformatic analyses in adolescents and adults with a broad range of neurological phenotypes: an Australian perspective. J Neurol Sci 2020; 420:117260. [PMID: 33310205 DOI: 10.1016/j.jns.2020.117260] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/21/2022]
Abstract
Currently there is no secured ongoing funding in Australia for next generation sequencing (NGS) such as exome sequencing (ES) for adult neurological disorders. Studies have focused on paediatric populations in research or highly specialised settings, utilised standard NGS pipelines focusing only on small insertions, deletions and single nucleotide variants, and not explored impacts on management in detail. This prospective multi-site study performed ES and an extended bioinformatics repeat expansion analysis pipeline, on patients with broad phenotypes (ataxia, dementia, dystonia, spastic paraparesis, motor neuron disease, Parkinson's disease and complex/not-otherwise-specified), with symptom onset between 2 and 60 years. Genomic data analysis was phenotype-driven, using virtual gene panels, reported according to American College of Medical Genetics and Genomics guidelines. One-hundred-and-sixty patients (51% female) were included, median age 52 years (range 14-79) and median 9 years of symptoms. 34/160 (21%) patients received a genetic diagnosis. Highest diagnostic rates were in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified (10/38, 26%) and ataxia (7/28, 25%) groups. Findings were considered 'possible/uncertain' in 21/160 patients. Repeat expansion detection identified an unexpected diagnosis of Huntington disease in an ataxic patient with negative ES. Impacts on management, such as more precise and tailored care, were seen in most diagnosed patients (23/34, 68%). ES and a novel bioinformatics analysis pipepline had a substantial diagnostic yield (21%) and management impacts for most diagnosed patients, in heterogeneous, complex, mainly adult-onset neurological disorders in real-world settings in Australia, providing evidence for NGS and complementary multiple, new technologies as valuable diagnostic tools.
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15
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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.
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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
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16
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Ramchand J, Wallis M, Macciocca I, Lynch E, Farouque O, Martyn M, Phelan D, Chong B, Lockwood S, Weintraub R, Thompson T, Trainer A, Zentner D, Vohra J, Chetrit M, Hare DL, James P. Prospective Evaluation of the Utility of Whole Exome Sequencing in Dilated Cardiomyopathy. J Am Heart Assoc 2020; 9:e013346. [PMID: 31931689 PMCID: PMC7033851 DOI: 10.1161/jaha.119.013346] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background Dilated cardiomyopathy may be heritable but shows extensive genetic heterogeneity. The utility of whole exome sequencing as a first-line genetic test for patients with dilated cardiomyopathy in a contemporary "real-world" setting has not been specifically established. Using whole exome sequencing with rigorous, evidence-based variant interpretation, we aimed to identify the prevalence of a molecular diagnosis in patients with dilated cardiomyopathy in a clinical setting. Methods and Results Whole exome sequencing was performed in eligible patients (n=83) with idiopathic or familial dilated cardiomyopathy. Variants were prioritized for curation in up to 247 genes and classified using American College of Medical Genetics and Genomics-based criteria. Ten (12%) had a pathogenic or likely pathogenic variant. Eight (10%) participants had truncating TTN variants classified as variants of uncertain significance. Five (6%) participants had variants of unknown significance according to strict American College of Medical Genetics and Genomics criteria but classified as either pathogenic or likely pathogenic by other clinical laboratories. Pathogenic or likely pathogenic variants were found in 8 genes (all within tier 1 genes), 2 (20%) of which are not included in a standard commercially available dilated cardiomyopathy panel. Using our bioinformatics pipeline, there was an average of 0.74 variants of uncertain significance per case with ≈0.75 person-hours needed to interpret each of these variants. Conclusions Whole exome sequencing is an effective diagnostic tool for patients with dilated cardiomyopathy. With stringent classification using American College of Medical Genetics and Genomics criteria, the rate of detection of pathogenic variants is lower than previous reports. Efforts to improve adherence to these guidelines will be important to prevent erroneous misclassification of nonpathogenic variants in dilated cardiomyopathy genetic testing and inappropriate cascade screening.
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Affiliation(s)
- Jay Ramchand
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Mathew Wallis
- Department of Genetics Austin Health Heidelberg Victoria Australia
| | - Ivan Macciocca
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Elly Lynch
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia.,Melbourne Genomics Health Alliance Melbourne Victoria Australia
| | - Omar Farouque
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance Melbourne Victoria Australia.,Department of Paediatrics University of Melbourne Parkville Victoria Australia.,Murdoch Children's Research Institute Parkville Victoria Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Siobhan Lockwood
- Monash Cardiovascular Research Centre and Monash Heart Monash University and Monash Health Melbourne Australia
| | - Robert Weintraub
- Victorian Clinical Genetics Services Murdoch Children's Research Institute Royal Children's Hospital Flemington Victoria Australia
| | - Tina Thompson
- Genetic Medicine Melbourne Health Parkville Victoria Australia
| | - Alison Trainer
- Genetic Medicine Melbourne Health Parkville Victoria Australia
| | - Dominica Zentner
- Department of Cardiology Melbourne Health Parkville Victoria Australia.,Genetic Medicine Melbourne Health Parkville Victoria Australia.,Royal Melbourne Hospital Clinical School Faculty of Medicine Dentistry and Health Sciences University of Melbourne Parkville Victoria Australia
| | - Jitendra Vohra
- Department of Cardiology Melbourne Health Parkville Victoria Australia.,Genetic Medicine Melbourne Health Parkville Victoria Australia.,Royal Melbourne Hospital Clinical School Faculty of Medicine Dentistry and Health Sciences University of Melbourne Parkville Victoria Australia
| | | | - David L Hare
- Department of Medicine Austin Health The University of Melbourne Heidelberg Victoria Australia.,Department of Cardiology Austin Health Heidelberg Victoria Australia
| | - Paul James
- Genetic Medicine Melbourne Health Parkville Victoria Australia
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17
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Reuter CM, Kohler JN, Bonner D, Zastrow D, Fernandez L, Dries A, Marwaha S, Davidson J, Brokamp E, Herzog M, Hong J, Macnamara E, Rosenfeld JA, Schoch K, Spillmann R, Loscalzo J, Krier J, Stoler J, Sweetser D, Palmer CG, Phillips JA, Shashi V, Adams DA, Yang Y, Ashley EA, Fisher PG, Mulvihill JJ, Bernstein JA, Wheeler MT. Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. J Genet Couns 2019; 28:1107-1118. [PMID: 31478310 PMCID: PMC6901723 DOI: 10.1002/jgc4.1161] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. METHODS We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. RESULTS Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). CONCLUSIONS These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.
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Affiliation(s)
- Chloe M. Reuter
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jennefer N. Kohler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Annika Dries
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jean Davidson
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Matthew Herzog
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
| | - Joyce Hong
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Kelly Schoch
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Rebecca Spillmann
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | | | - Joseph Loscalzo
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joel Krier
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joan Stoler
- Division of Genetics, Boston Children’s Hospital, Boston, MA
| | - David Sweetser
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Christina G.S. Palmer
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
- Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA
- Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - David A. Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Euan A. Ashley
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Paul G. Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - John J. Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Jonathan A. Bernstein
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T. Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
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18
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Next-generation sequencing in Charcot-Marie-Tooth disease: opportunities and challenges. Nat Rev Neurol 2019; 15:644-656. [PMID: 31582811 DOI: 10.1038/s41582-019-0254-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 01/08/2023]
Abstract
Charcot-Marie-Tooth disease and the related disorders hereditary motor neuropathy and hereditary sensory neuropathy, collectively termed CMT, are the commonest group of inherited neuromuscular diseases, and they exhibit wide phenotypic and genetic heterogeneity. CMT is usually characterized by distal muscle atrophy, often with foot deformity, weakness and sensory loss. In the past decade, next-generation sequencing (NGS) technologies have revolutionized genomic medicine and, as these technologies are being applied to clinical practice, they are changing our diagnostic approach to CMT. In this Review, we discuss the application of NGS technologies, including disease-specific gene panels, whole-exome sequencing, whole-genome sequencing (WGS), mitochondrial sequencing and high-throughput transcriptome sequencing, to the diagnosis of CMT. We discuss the growing challenge of variant interpretation and consider how the clinical phenotype can be combined with genetic, bioinformatic and functional evidence to assess the pathogenicity of genetic variants in patients with CMT. WGS has several advantages over the other techniques that we discuss, which include unparalleled coverage of coding, non-coding and intergenic areas of both nuclear and mitochondrial genomes, the ability to identify structural variants and the opportunity to perform genome-wide dense homozygosity mapping. We propose an algorithm for incorporating WGS into the CMT diagnostic pathway.
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Nicastro E, Di Giorgio A, Marchetti D, Barboni C, Cereda A, Iascone M, D'Antiga L. Diagnostic Yield of an Algorithm for Neonatal and Infantile Cholestasis Integrating Next-Generation Sequencing. J Pediatr 2019; 211:54-62.e4. [PMID: 31160058 DOI: 10.1016/j.jpeds.2019.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/15/2019] [Accepted: 04/09/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To evaluate the performance of a diagnostic protocol for neonatal/infantile cholestasis in which the main clinical patterns steered the early use of different genetic testing strategies. STUDY DESIGN An observational study was conducted between 2012 and 2017 in a tertiary care setting on a prospective cohort of children with cholestasis occurring at ≤1 year of age and persisting ≥6 weeks, to measure the detection rate of underlying monogenic diseases. After the exclusion of biliary atresia, a clinically driven genetic testing was performed, entailing 3 different approaches with different wideness: confirmatory single-gene testing; focused virtual panels; and wide search through trio whole-exome sequencing. RESULTS We enrolled 125 children (66 female, median age 2 months); 96 (77%) patients had hypocholic stools and were evaluated rapidly to exclude biliary atresia, which was the final diagnosis in 74 (59%). Overall, 50 patients underwent genetic testing, 6 with single confirmatory gene testing, 38 through panels, and 6 with trio whole-exome sequencing because of complex phenotype. The genetic testing detection rate was 60%: the final diagnosis was Alagille syndrome in 11, progressive familial intrahepatic cholestasis type 2 in 6, alpha-1-antitrypsin deficiency in 3, and progressive familial intrahepatic cholestasis type 3 in 2; a further 7 genetic conditions were identified in 1 child each. Overall, only 18 of 125 (14%) remained with an indeterminate etiology. CONCLUSIONS This protocol combining clinical and genetic assessment proved to be an effective diagnostic tool for neonatal/infantile cholestasis, identifying inherited disorders with a high detection rate. It also could allow a noninvasive diagnosis in children presenting with colored stools.
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Affiliation(s)
- Emanuele Nicastro
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy.
| | - Angelo Di Giorgio
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Marchetti
- Medical Genetics Laboratory, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Chiara Barboni
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Clinical Genetics, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Maria Iascone
- Medical Genetics Laboratory, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Lorenzo D'Antiga
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
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20
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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21
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Taylor N, Best S, Martyn M, Long JC, North KN, Braithwaite J, Gaff C. A transformative translational change programme to introduce genomics into healthcare: a complexity and implementation science study protocol. BMJ Open 2019; 9:e024681. [PMID: 30842113 PMCID: PMC6429849 DOI: 10.1136/bmjopen-2018-024681] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/21/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Translating scientific advances in genomic medicine into evidence-based clinical practice is challenging. Studying the natural translation of genomics into 'early-adopting' health system sectors is essential. We will (a) examine 29 health systems (Australian and Melbourne Genomics Health Alliance flagships) integrating genomics into practice and (b) combine this learning to co-design and test an evidence-based generalisable toolkit for translating genomics into healthcare. METHODS AND ANALYSIS Twenty-nine flagships integrating genomics into clinical settings are studied as complex adaptive systems to understand emergent and self-organising behaviours among inter-related actors and processes. The Effectiveness-Implementation Hybrid approach is applied to gather information on the delivery and potential for real-world implementation. Stages '1' and '2a' (representing hybrid model 1) are the focus of this protocol. The Translation Science to Population Impact (TSci Impact) framework is used to study policy decisions and service provision, and the Theoretical Domains Framework (TDF) is used to understand individual level behavioural change; both frameworks are applied across stages 1 and 2a. Stage 1 synthesises interview data from 32 participants involved in developing the genomics clinical practice systems and approaches across five 'demonstration-phase' (early adopter) flagships. In stage 2a, stakeholders are providing quantitative and qualitative data on process mapping, clinical audits, uptake and sustainability (TSci Impact), and psychosocial and environmental determinants of change (TDF). Findings will be synthesised before codesigning an intervention toolkit to facilitate implementation of genomic testing. Study methods to simultaneously test the comparative effectiveness of genomic testing and the implementation toolkit (stage 2b), and the refined implementation toolkit while simply observing the genomics intervention (stage 3) are summarised. ETHICS AND DISSEMINATION Ethical approval has been granted. The results will be disseminated in academic forums and used to refine interventions to translate genomics evidence into healthcare. Non-traditional academic dissemination methods (eg, change in guidelines or government policy) will also be employed.
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Affiliation(s)
- Natalie Taylor
- Cancer Council New South Wales, Woolloomooloo, New South Wales, Australia
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
- Faculty of Health Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Best
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics and Medicine, University of Melbourne, Melbourne, UK
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
| | - Kathryn N North
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
- Australian Genomics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
- Department of Paediatrics and Medicine, University of Melbourne, Melbourne, UK
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22
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Martyn M, Kanga-Parabia A, Lynch E, James PA, Macciocca I, Trainer AH, Halliday J, Keogh L, Wale J, Winship I, Bogwitz M, Valente G, Walsh M, Downie L, Amor D, Wallis M, Cunningham F, Burgess M, Brown NJ, Jarmolowicz A, Lunke S, Goranitis I, Gaff CL. A novel approach to offering additional genomic findings-A protocol to test a two-step approach in the healthcare system. J Genet Couns 2019; 28:388-397. [DOI: 10.1002/jgc4.1102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Melissa Martyn
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Anaita Kanga-Parabia
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Paul A. James
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Ivan Macciocca
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Alison H. Trainer
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Jane Halliday
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | | | - Janney Wale
- Melbourne Genomics Health Alliance; Melbourne Australia
| | | | | | | | - Maie Walsh
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Lilian Downie
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - David Amor
- University of Melbourne; Melbourne Australia
- Royal Children’s Hospital; Melbourne Australia
| | | | - Fiona Cunningham
- Murdoch Children’s Research Institute; Melbourne Australia
- Monash Health; Melbourne Australia
| | | | - Natasha J. Brown
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
- Austin Health; Melbourne Australia
- Royal Children’s Hospital; Melbourne Australia
| | - Anna Jarmolowicz
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Sebastian Lunke
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Ilias Goranitis
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Clara L. Gaff
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
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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.
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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
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24
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Affiliation(s)
- David R Adams
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
| | - Christine M Eng
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
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25
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Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102072. [PMID: 30248891 PMCID: PMC6210164 DOI: 10.3390/ijerph15102072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022]
Abstract
The time required to reach a correct diagnosis is a key concern for rare disease (RD) patients. Diagnostic delay can be intolerably long, often described as an “odyssey” and, for some, a diagnosis may remain frustratingly elusive. The International Rare Disease Research Consortium proposed, as ultimate goal for 2017–2027, to enable all people with a suspected RD to be diagnosed within one year of presentation, if the disorder is known. Subsequently, unsolved cases would enter a globally coordinated diagnostic and research pipeline. In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic tools to increase the chance of a timely and accurate diagnosis. The success of this approach is evident in the Orphanet database. From 2010 to March 2017 over 600 new RDs and roughly 3600 linked genes have been described and identified. However, combination of -omics and phenotype data, as well as international sharing of this information, has raised ethical concerns. Values to be assessed include not only patient autonomy but also family implications, beneficence, non-maleficence, justice, solidarity and reciprocity, which must be respected and promoted and, at the same time, balanced among each other. In this work we suggest that, to maximize patients’ involvement in the search for a diagnosis and identification of new causative genes, undiagnosed patients should have the possibility to: (1) actively participate in the description of their phenotype; (2) choose the level of visibility of their profile in matchmaking databases; (3) express their preferences regarding return of new findings, in particular which level of Variant of Unknown Significance (VUS) significance should be considered relevant to them. The quality of the relationship between individual patients and physicians, and between the patient community and the scientific community, is critically important for optimizing the use of available data and enabling international collaboration in order to provide a diagnosis, and the attached support, to unsolved cases. The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.
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26
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Stark Z, Schofield D, Martyn M, Rynehart L, Shrestha R, Alam K, Lunke S, Tan TY, Gaff CL, White SM. Does genomic sequencing early in the diagnostic trajectory make a difference? A follow-up study of clinical outcomes and cost-effectiveness. Genet Med 2018; 21:173-180. [DOI: 10.1038/s41436-018-0006-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
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27
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Howell KB, Eggers S, Dalziel K, Riseley J, Mandelstam S, Myers CT, McMahon JM, Schneider A, Carvill GL, Mefford HC, Scheffer IE, Harvey AS. A population-based cost-effectiveness study of early genetic testing in severe epilepsies of infancy. Epilepsia 2018; 59:1177-1187. [PMID: 29750358 DOI: 10.1111/epi.14087] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The severe epilepsies of infancy (SEI) are a devastating group of disorders that pose a major care and economic burden on society; early diagnosis is critical for optimal management. This study sought to determine the incidence and etiologies of SEI, and model the yield and cost-effectiveness of early genetic testing. METHODS A population-based study was undertaken of the incidence, etiologies, and cost-effectiveness of a whole exome sequencing-based gene panel (targeted WES) in infants with SEI born during 2011-2013, identified through electroencephalography (EEG) and neonatal databases. SEI was defined as seizure onset before age 18 months, frequent seizures, epileptiform EEG, and failure of ≥2 antiepileptic drugs. Medical records, investigations, MRIs, and EEGs were analyzed, and genetic testing was performed if no etiology was identified. Economic modeling was performed to determine yield and cost-effectiveness of investigation of infants with unknown etiology at epilepsy onset, incorporating targeted WES at different stages of the diagnostic pathway. RESULTS Of 114 infants with SEI (incidence = 54/100 000 live births/y), the etiology was determined in 76 (67%): acquired brain injuries (n = 14), focal cortical dysplasias (n = 14), other brain malformations (n = 17), channelopathies (n = 11), chromosomal (n = 9), metabolic (n = 6), and other genetic (n = 5) disorders. Modeling showed that incorporating targeted WES increased diagnostic yield compared to investigation without targeted WES (48/86 vs 39/86). Early targeted WES had lower total cost ($677 081 U.S. dollars [USD] vs $738 136 USD) than late targeted WES. A pathway with early targeted WES and limited metabolic testing yielded 7 additional diagnoses compared to investigation without targeted WES (46/86 vs 39/86), with lower total cost ($455 597 USD vs $661 103 USD), lower cost per diagnosis ($9904 USD vs $16 951 USD), and a dominant cost-effectiveness ratio. SIGNIFICANCE Severe epilepsies occur in 1 in 2000 infants, with the etiology identified in two-thirds, most commonly malformative. Early use of targeted WES yields more diagnoses at lower cost. Early genetic diagnosis will enable timely administration of precision medicines, once developed, with the potential to improve long-term outcome.
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Affiliation(s)
- Katherine B Howell
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Stefanie Eggers
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kim Dalziel
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Melbourne School of Global and Population Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica Riseley
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Mandelstam
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Medical Imaging, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Radiology, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jacinta M McMahon
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Amy Schneider
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Ingrid E Scheffer
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - A Simon Harvey
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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28
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Abstract
PURPOSE OF REVIEW Charcot-Marie-Tooth disease (CMT) and related neuropathies represent a heterogeneous group of hereditary disorders. The present review will discuss the most recent advances in the field. RECENT FINDINGS Knowledge of CMT epidemiology and frequency of the main associated genes is increasing, with an overall prevalence estimated at 10-28/100 000. In the last years, the huge number of newly uncovered genes, thanks to next-generation sequencing techniques, is challenging the current classification of CMT. During the last 18 months other genes have been associated with CMT, such as PMP2, MORC2, NEFH, MME, and DGAT2. For the most common forms of CMT, numerous promising compounds are under study in cellular and animal models, mainly targeting either the protein degradation pathway or the protein overexpression. Consequently, efforts are devoted to develop responsive outcome measures and biomarkers for this overall slowly progressive disorder, with quantitative muscle MRI resulting the most sensitive-to-change measure. SUMMARY This is a rapidly evolving field where better understanding of pathophysiology is paving the way to develop potentially effective treatments, part of which will soon be tested in patients. Intense research is currently devoted to prepare clinical trials and develop responsive outcome measures.
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AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss. Genet Med 2018; 20:1600-1608. [PMID: 29595809 DOI: 10.1038/gim.2018.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/13/2018] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Hereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes. METHODS A tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes. RESULTS ES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis. CONCLUSION The tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.
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Meeting the challenges of implementing rapid genomic testing in acute pediatric care. Genet Med 2018. [DOI: 10.1038/gim.2018.37] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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31
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Saghira C, Bis DM, Stanek D, Strickland A, Herrmann DN, Reilly MM, Scherer SS, Shy ME, Züchner S. Variant pathogenicity evaluation in the community-driven Inherited Neuropathy Variant Browser. Hum Mutat 2018; 39:635-642. [PMID: 29473246 DOI: 10.1002/humu.23412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 12/13/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) is an umbrella term for inherited neuropathies affecting an estimated one in 2,500 people. Over 120 CMT and related genes have been identified and clinical gene panels often contain more than 100 genes. Such a large genomic space will invariantly yield variants of uncertain clinical significance (VUS) in nearly any person tested. This rise in number of VUS creates major challenges for genetic counseling. Additionally, fewer individual variants in known genes are being published as the academic merit is decreasing, and most testing now happens in clinical laboratories, which typically do not correlate their variants with clinical phenotypes. For CMT, we aim to encourage and facilitate the global capture of variant data to gain a large collection of alleles in CMT genes, ideally in conjunction with phenotypic information. The Inherited Neuropathy Variant Browser provides user-friendly open access to currently reported variation in CMT genes. Geneticists, physicians, and genetic counselors can enter variants detected by clinical tests or in research studies in addition to genetic variation gathered from published literature, which are then submitted to ClinVar biannually. Active participation of the broader CMT community will provide an advance over existing resources for interpretation of CMT genetic variation.
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Affiliation(s)
- Cima Saghira
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida
- Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | - Dana M Bis
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida
- Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | - David Stanek
- Department of Paediatric Neurology, Charles University, Prague, Czech Republic
| | - Alleene Strickland
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida
- Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | - David N Herrmann
- Department of Neurology, University of Rochester, Rochester, New York
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | - Steven S Scherer
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael E Shy
- Department of Neurology, University of Iowa, Iowa City, Iowa
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida
- Hussman Institute for Human Genomics, University of Miami, Miami, Florida
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32
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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Affiliation(s)
- T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J D Wagner
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - M Tétreault
- Department of Human Genetics, McGill University, Montréal, Canada
| | - L Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - S Baker
- Department of Medicine, McMaster University Medical Centre, Hamilton, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - P R Bourque
- Department of Medicine, University of Ottawa, Ottawa, Canada
| | - J S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - C Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - A M Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - F Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - C J Curry
- Department of Pediatrics, University of California, San Francisco, California
| | - G Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G A Horvath
- Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada
| | - E Bareke
- Department of Human Genetics, McGill University, Montréal, Canada
| | - M Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | | | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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