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Kooshavar D, Amor DJ, Boggs K, Baker N, Barnett C, de Silva MG, Edwards S, Fahey MC, Marum JE, Snell P, Bozaoglu K, Pope K, Mohammad SS, Riney K, Sachdev R, Scheffer IE, Schenscher S, Silberstein J, Smith N, Tom M, Ware TL, Lockhart PJ, Leventer RJ. Diagnostic utility of exome sequencing followed by research reanalysis in human brain malformations. Brain Commun 2024; 6:fcae056. [PMID: 38444904 PMCID: PMC10914449 DOI: 10.1093/braincomms/fcae056] [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: 05/29/2023] [Revised: 12/13/2023] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
This study aimed to determine the diagnostic yield of singleton exome sequencing and subsequent research-based trio exome analysis in children with a spectrum of brain malformations seen commonly in clinical practice. We recruited children ≤ 18 years old with a brain malformation diagnosed by magnetic resonance imaging and consistent with an established list of known genetic causes. Patients were ascertained nationally from eight tertiary paediatric centres as part of the Australian Genomics Brain Malformation Flagship. Chromosome microarray was required for all children, and those with pathogenic copy number changes were excluded. Cytomegalovirus polymerase chain reaction on neonatal blood spots was performed on all children with polymicrogyria with positive patients excluded. Singleton exome sequencing was performed through a diagnostic laboratory and analysed using a clinical exome sequencing pipeline. Undiagnosed patients were followed up in a research setting, including reanalysis of the singleton exome data and subsequent trio exome sequencing. A total of 102 children were recruited. Ten malformation subtypes were identified with the commonest being polymicrogyria (36%), pontocerebellar hypoplasia (14%), periventricular nodular heterotopia (11%), tubulinopathy (10%), lissencephaly (10%) and cortical dysplasia (9%). The overall diagnostic yield for the clinical singleton exome sequencing was 36%, which increased to 43% after research follow-up. The main source of increased diagnostic yield was the reanalysis of the singleton exome data to include newly discovered gene-disease associations. One additional diagnosis was made by trio exome sequencing. The highest phenotype-based diagnostic yields were for cobblestone malformation, tubulinopathy and lissencephaly and the lowest for cortical dysplasia and polymicrogyria. Pathogenic variants were identified in 32 genes, with variants in 6/32 genes occurring in more than one patient. The most frequent genetic diagnosis was pathogenic variants in TUBA1A. This study shows that over 40% of patients with common brain malformations have a genetic aetiology identified by exome sequencing. Periodic reanalysis of exome data to include newly identified genes was of greater value in increasing diagnostic yield than the expansion to trio exome. This study highlights the genetic and phenotypic heterogeneity of brain malformations, the importance of a multidisciplinary approach to diagnosis and the large number of patients that remain without a genetic diagnosis despite clinical exome sequencing and research reanalysis.
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Affiliation(s)
- Daniz Kooshavar
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David J Amor
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Kirsten Boggs
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
- Department of Clinical Genetics, The Children’s Hospital Westmead, Westmead, NSW 2145, Australia
- Australian Genomics, Parkville, VIC 3052, Australia
| | - Naomi Baker
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Christopher Barnett
- SA Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Michelle G de Silva
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Australian Genomics, Parkville, VIC 3052, Australia
| | - Samantha Edwards
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | | | - Penny Snell
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Kiymet Bozaoglu
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Kate Pope
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Shekeeb S Mohammad
- Department of Neurology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Kate Riney
- Neurosciences Unit, Queensland Children’s Hospital, South Brisbane, QLD 4101, Australia
- Faculty of Medicine, University of Queensland, St Lucia, QLD 4072, Australia
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Ingrid E Scheffer
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health and Florey Institute, Heidelberg, VIC 3084, Australia
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Sarah Schenscher
- Paediatric and Reproductive Genetics Unit, Women’s and Children’s Hospital, Adelaide, SA 5006Australia
| | - John Silberstein
- Department of Neurology, Princess Margaret Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Smith
- Department of Neurology and Clinical Neurophysiology, Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia
| | - Melanie Tom
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Herston, QLD 4029Australia
| | - Tyson L Ware
- Department of Paediatrics, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Paul J Lockhart
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard J Leventer
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC 3052, Australia
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2
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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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3
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Lauretta ML, Jarmolowicz A, Amor DJ, Best S, Morgan AT. An Investigation of Barriers and Enablers for Genetics in Speech-Language Pathology Explored Through a Case Study of Childhood Apraxia of Speech. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2023:1-15. [PMID: 37713535 DOI: 10.1044/2023_jslhr-22-00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
PURPOSE Advancements in genetic testing and analysis have allowed improved identification of the genetic basis of childhood apraxia of speech, a rare speech presentation. This study aimed to understand speech-language pathologists' (SLPs') consideration of incorporation of genetics in clinical practice using a theory-informed qualitative approach. METHOD Semistructured interviews were conducted with 12 pediatric SLPs using a behavior change theory (Theoretical Domains Framework [TDF]) within a case study describing a child with complex co-occurring features, including childhood apraxia of speech. Interviews focused on three stages of the patient journey (prereferral, referral, and postreferral). Interviews were analyzed to identify barriers and enablers to considering incorporation of genetics in current clinical practice. Barriers and enablers were grouped and mapped onto a contextually relevant TDF-coded analysis framework. RESULTS Barriers were identified across several TDF domains, through all stages of the patient journey. Lack of confidence, relevance, and level of experience were most common prereferral, and connection to and awareness of genetics services and contextual factors were barriers in the referral stage. Perception of professional role, knowledge, and beliefs about effects on families were barriers postreferral. Associated enablers were also identified, including seeing value in genetic diagnosis, support from other health care professionals, supervision, and relationships with genetics services. CONCLUSIONS Results of this qualitative study highlight barriers and enablers to incorporating genetics into speech-language pathology clinical practice. These findings will assist in the development of theory-informed implementation strategies to support SLPs into the future. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.24112800.
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Affiliation(s)
| | - Anna Jarmolowicz
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Victorian Comprehensive Cancer Centre Alliance, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, St. Lucia, Australia
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4
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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5
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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6
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Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
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7
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Oliver KL, Trivisano M, Mandelstam SA, De Dominicis A, Francis DI, Green TE, Muir AM, Chowdhary A, Hertzberg C, Goldhahn K, Metreau J, Prager C, Pinner J, Cardamone M, Myers KA, Leventer RJ, Lesca G, Bahlo M, Hildebrand MS, Mefford HC, Kaindl AM, Specchio N, Scheffer IE. WWOX developmental and epileptic encephalopathy: Understanding the epileptology and the mortality risk. Epilepsia 2023; 64:1351-1367. [PMID: 36779245 PMCID: PMC10952634 DOI: 10.1111/epi.17542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
OBJECTIVE WWOX is an autosomal recessive cause of early infantile developmental and epileptic encephalopathy (WWOX-DEE), also known as WOREE (WWOX-related epileptic encephalopathy). We analyzed the epileptology and imaging features of WWOX-DEE, and investigated genotype-phenotype correlations, particularly with regard to survival. METHODS We studied 13 patients from 12 families with WWOX-DEE. Information regarding seizure semiology, comorbidities, facial dysmorphisms, and disease outcome were collected. Electroencephalographic (EEG) and brain magnetic resonance imaging (MRI) data were analyzed. Pathogenic WWOX variants from our cohort and the literature were coded as either null or missense, allowing individuals to be classified into one of three genotype classes: (1) null/null, (2) null/missense, (3) missense/missense. Differences in survival outcome were estimated using the Kaplan-Meier method. RESULTS All patients experienced multiple seizure types (median onset = 5 weeks, range = 1 day-10 months), the most frequent being focal (85%), epileptic spasms (77%), and tonic seizures (69%). Ictal EEG recordings in six of 13 patients showed tonic (n = 5), myoclonic (n = 2), epileptic spasms (n = 2), focal (n = 1), and migrating focal (n = 1) seizures. Interictal EEGs demonstrated slow background activity with multifocal discharges, predominantly over frontal or temporo-occipital regions. Eleven of 13 patients had a movement disorder, most frequently dystonia. Brain MRIs revealed severe frontotemporal, hippocampal, and optic atrophy, thin corpus callosum, and white matter signal abnormalities. Pathogenic variants were located throughout WWOX and comprised both missense and null changes including five copy number variants (four deletions, one duplication). Survival analyses showed that patients with two null variants are at higher mortality risk (p-value = .0085, log-rank test). SIGNIFICANCE Biallelic WWOX pathogenic variants cause an early infantile developmental and epileptic encephalopathy syndrome. The most common seizure types are focal seizures and epileptic spasms. Mortality risk is associated with mutation type; patients with biallelic null WWOX pathogenic variants have significantly lower survival probability compared to those carrying at least one presumed hypomorphic missense pathogenic variant.
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Affiliation(s)
- Karen L. Oliver
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Population Health and Immunity DivisionWalter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Marina Trivisano
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
| | - Simone A. Mandelstam
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthMelbourneVictoriaAustralia
- Department of Radiology, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Angela De Dominicis
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
- Department of Biomedicine and PreventionUniversity of Rome “Tor Vergata”RomeItaly
| | - David I. Francis
- Victorian Clinical Genetics ServicesMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Timothy E. Green
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
| | - Alison M. Muir
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Apoorva Chowdhary
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Christoph Hertzberg
- Zentrum für Sozialpädiatrie und Neuropädiatrie (DBZ)Vivantes Hospital NeukoellnBerlinGermany
| | - Klaus Goldhahn
- Department of Pediatrics and Neuropediatrics, DRK Klinikum WestendBerlinGermany
| | - Julia Metreau
- Department of Pediatric NeurologyHôpital Bicêtre, Assistance Publique Hopitaux de ParisLe Kremlin‐BicêtreFrance
| | - Christine Prager
- Center for Chronically Sick Children (SPZ)Charité‐Universitätsmedizin BerlinBerlinGermany
- Department of Pediatric NeurologyCharité–Universitätsmedizin BerlinBerlinGermany
| | - Jason Pinner
- Sydney Children's HospitalRandwickNew South WalesAustralia
- School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Michael Cardamone
- Sydney Children's HospitalRandwickNew South WalesAustralia
- School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Kenneth A. Myers
- Division of Child Neurology, Department of PediatricsMcGill UniversityMontrealQuebecCanada
- Research Institute of the McGill University Health CentreMontrealQuebecCanada
- Department of Neurology and NeurosurgeryMontreal Children's Hospital, McGill UniversityMontrealQuebecCanada
| | - Richard J. Leventer
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of NeurologyRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University HospitalUniversité Claude Bernard Lyon 1, member of the European Reference Network EpiCARELyonFrance
| | - Melanie Bahlo
- Population Health and Immunity DivisionWalter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michael S. Hildebrand
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Heather C. Mefford
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Center for Pediatric Neurological Disease ResearchSt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Angela M. Kaindl
- Center for Chronically Sick Children (SPZ)Charité‐Universitätsmedizin BerlinBerlinGermany
- Department of Pediatric NeurologyCharité–Universitätsmedizin BerlinBerlinGermany
- Institute of Cell Biology and NeurobiologyCharité–Universitätsmedizin BerlinBerlinGermany
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
| | - Ingrid E. Scheffer
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthMelbourneVictoriaAustralia
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8
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O’Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ARXIV 2023:arXiv:2301.07363v1. [PMID: 36713248 PMCID: PMC9882576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order and emerging technologies, such as optical genome mapping and long-read DNA or RNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to a consortium such as GREGoR, which is focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H. Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M. Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Michael H. Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010 USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Philip M. Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emily E. Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emmanuèle C. Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
- Center for Genetics Medicine Research, Children’s National Research and Innovation Campus, Washington, DC, USA
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle WA 98195 USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephen B. Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Matthew T. Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Seth I. Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children’s National Hospital, Washington, DC 20010 USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005 USA
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195 USA
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9
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Martinussen J, Chalk M, Elliott J, Gallacher L. Receiving Genomic Sequencing Results through the Victorian Undiagnosed Disease Program: Exploring Parental Experiences. J Pers Med 2022; 12:jpm12081250. [PMID: 36013198 PMCID: PMC9410238 DOI: 10.3390/jpm12081250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases cumulatively affect a significant number of people, and for many, a diagnosis remains elusive. The Victorian Undiagnosed Disease Program (UDP-Vic) utilizes deep phenotyping, advanced genomic sequencing and functional studies to diagnose children with rare diseases for which previous clinical testing has been non-diagnostic. Whereas the diagnostic outcomes of undiagnosed disease programs have been well-described, here, we explore how parents experience participation in the UDP-Vic and the impact of receiving both diagnostic and non-diagnostic genomic sequencing results for their children. Semi-structured interviews ranging in length from 25 to 105 min were conducted with 21 parents of children in the program. Ten participants were parents of children who received a diagnosis through the program, and eleven were parents of children who remain undiagnosed. Although the experiences of families varied, five shared themes emerged from the data: (1) searching for a diagnosis, (2) varied impact of receiving a result, (3) feelings of relief and disappointment, (4) seeking connection and (5) moving towards acceptance. The findings demonstrate the shared experience of parents of children with rare disease both before and after a genomic sequencing result. The results have implications for genetic counselors and clinicians offering genomic sequencing and supporting families of children with rare diseases.
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Affiliation(s)
- Jo Martinussen
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Michal Chalk
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
| | - Lyndon Gallacher
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
- Correspondence:
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