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Baynam G, Gomez R, Jain R. Stigma associated with genetic testing for rare diseases-causes and recommendations. Front Genet 2024; 15:1335768. [PMID: 38638122 PMCID: PMC11024281 DOI: 10.3389/fgene.2024.1335768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
Rare disease (RD) is a term used to describe numerous, heterogeneous diseases that are geographically disparate. Approximately 400 million people worldwide live with an RD equating to roughly 1 in 10 people, with 71.9% of RDs having a genetic origin. RDs present a distinctive set of challenges to people living with rare diseases (PLWRDs), their families, healthcare professionals (HCPs), healthcare system, and societies at large. The possibility of inheriting a genetic disease has a substantial social and psychological impact on affected families. In addition to other concerns, PLWRDs and their families may feel stigmatized, experience guilt, feel blamed, and stress about passing the disease to future generations. Stigma can affect all stages of the journey of PLWRDs and their families, from pre-diagnosis to treatment access, care and support, and compliance. It adversely impacts the quality of life of RD patients. To better explore the impact of stigma associated with genetic testing for RDs, we conducted a literature search on PubMed and Embase databases to identify articles published on stigma and RDs from January 2013 to February 2023. There is a dearth of literature investigating the dynamics of stigma and RD genetic testing. The authors observed that the research into the implications of stigma for patient outcomes in low- and middle-income countries (LMICs) and potential interventions is limited. Herein, the authors present a review of published literature on stigma with a focus on RD genetic testing, the associated challenges, and possible ways to address these.
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Affiliation(s)
- Gareth Baynam
- Undiagnosed Diseases Program -WA, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, Australia
- Rare Care Centre, Perth Children’s Hospital, Subiaco, WA, Australia
| | - Roy Gomez
- Emerging Asia Medical Lead–Specialty Care, Pfizer, Singapore, Singapore
| | - Ritu Jain
- Nanyang Technological University, Singapore, Singapore
- DEBRA International, Asia Pacific Alliance of Rare Disease Organizations, Singapore, Singapore
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Moynihan D, Monaco S, Ting TW, Narasimhalu K, Hsieh J, Kam S, Lim JY, Lim WK, Davila S, Bylstra Y, Balakrishnan ID, Heng M, Chia E, Yeo KK, Goh BK, Gupta R, Tan T, Baynam G, Jamuar SS. Cluster analysis and visualisation of electronic health records data to identify undiagnosed patients with rare genetic diseases. Sci Rep 2024; 14:5056. [PMID: 38424111 PMCID: PMC10904843 DOI: 10.1038/s41598-024-55424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
Rare genetic diseases affect 5-8% of the population but are often undiagnosed or misdiagnosed. Electronic health records (EHR) contain large amounts of data, which provide opportunities for analysing and mining. Data mining, in the form of cluster analysis and visualisation, was performed on a database containing deidentified health records of 1.28 million patients across 3 major hospitals in Singapore, in a bid to improve the diagnostic process for patients who are living with an undiagnosed rare disease, specifically focusing on Fabry Disease and Familial Hypercholesterolaemia (FH). On a baseline of 4 patients, we identified 2 additional patients with potential diagnosis of Fabry disease, suggesting a potential 50% increase in diagnosis. Similarly, we identified > 12,000 individuals who fulfil the clinical and laboratory criteria for FH but had not been diagnosed previously. This proof-of-concept study showed that it is possible to perform mining on EHR data albeit with some challenges and limitations.
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Affiliation(s)
| | | | - Teck Wah Ting
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Kaavya Narasimhalu
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- Department of Neurology, National Neuroscience Institute (Singapore General Hospital), Singapore, Singapore
| | - Jenny Hsieh
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- Department of Internal Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sylvia Kam
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Jiin Ying Lim
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Laboratory of Genome Variation Analytics, Genome Institute of Singapore, Singapore, Singapore
| | - Sonia Davila
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Yasmin Bylstra
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Iswaree Devi Balakrishnan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
- National Heart Centre Singapore, Singapore, Singapore
| | - Mark Heng
- SingHealth Office of Insights and Analytics, Singapore, Singapore
| | - Elian Chia
- SingHealth Office of Insights and Analytics, Singapore, Singapore
| | | | - Bee Keow Goh
- Data Analytics Office, KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Tele Tan
- Curtin University, Perth, Australia
| | - Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, Perth, WA, Australia
- Western Australian Register of Developmental Anomalies, Perth, WA, Australia
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore.
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
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Bhattacharjee R, Jolly LA, Corbett MA, Wee IC, Rao SR, Gardner AE, Ritchie T, van Hugte EJH, Ciptasari U, Piltz S, Noll JE, Nazri N, van Eyk CL, White M, Fornarino D, Poulton C, Baynam G, Collins-Praino LE, Snel MF, Nadif Kasri N, Hemsley KM, Thomas PQ, Kumar R, Gecz J. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment. Nat Commun 2024; 15:1210. [PMID: 38331934 PMCID: PMC10853216 DOI: 10.1038/s41467-024-45121-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mouse brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Overall, we suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and the patient, and DNA damage-associated functional alterations are at the root of THOC2 syndrome.
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Affiliation(s)
- Rudrarup Bhattacharjee
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Mark A Corbett
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ing Chee Wee
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sushma R Rao
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alison E Gardner
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tarin Ritchie
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Sandra Piltz
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jacqueline E Noll
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide and Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Nazzmer Nazri
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Melissa White
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Dani Fornarino
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Lyndsey E Collins-Praino
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Kim M Hemsley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Paul Q Thomas
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Raman Kumar
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
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Baynam G, Julkowska D, Bowdin S, Hermes A, McMaster CR, Prichep E, Richer É, van der Westhuizen FH, Repetto GM, Malherbe H, Reichardt JKV, Arbour L, Hudson M, du Plessis K, Haendel M, Wilcox P, Lynch SA, Rind S, Easteal S, Estivill X, Caron N, Chongo M, Thomas Y, Letinturier MCV, Vorster BC. Advancing diagnosis and research for rare genetic diseases in Indigenous peoples. Nat Genet 2024; 56:189-193. [PMID: 38332370 DOI: 10.1038/s41588-023-01642-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Affiliation(s)
- Gareth Baynam
- Rare Care Centre and Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.
- Faculty of Health and Medicine, Division of Pediatrics, University of Western Australia, Perth, Western Australia, Australia.
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
- Faculty of Medicine, University of Notre Dame, Fremantle, Western Australia, Australia.
- Faculty of Science and Engineering, Spatial Sciences, Curtin University, Perth, Western Australia, Australia.
- Faculty of Medicine, Notre Dame University, Perth, Western Australia, Australia.
- School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia.
| | - Daria Julkowska
- IRDiRC Scientific Secretariat, French National Institute of Health and Medical Research (Inserm), Paris, France
| | - Sarah Bowdin
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | - Azure Hermes
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christopher R McMaster
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute of Genetics, Canadian Institutes of Health Research, Halifax, Nova Scotia, Canada
| | - Elissa Prichep
- Platform on Shaping the Future of Health and Healthcare, World Economic Forum, New York, NY, USA
| | - Étienne Richer
- Institute of Genetics, Canadian Institutes of Health Research, Halifax, Nova Scotia, Canada
| | | | - Gabriela M Repetto
- Facultad de Medicina, Center for Genetics and Genomics, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Helen Malherbe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Rare Diseases South Africa, Johannesburg, South Africa
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Victoria, British Columbia, Canada
| | - Maui Hudson
- Faculty of Maori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Melissa Haendel
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Sally Ann Lynch
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Ireland
- Academic Centre on Rare Diseases, University College Dublin, Dublin, Ireland
| | - Shamir Rind
- Western Australian Register of Developmental Anomalies, Perth, Western Australia, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xavier Estivill
- Quantitative Genomics Medicine Laboratories (qgenomics), Esplugues de Llobregat, Barcelona, Spain
| | - Nadine Caron
- UBC Centre for Excellence in Indigenous Health, Vancouver, British Columbia, Canada
- UBC Northern Medical Program and Department of Surgery, Prince George, British Columbia, Canada
| | - Meck Chongo
- UBC Centre for Excellence in Indigenous Health, Vancouver, British Columbia, Canada
| | - Yarlalu Thomas
- Western Australian Register of Developmental Anomalies, Perth, Western Australia, Australia
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Groza T, Caufield H, Gration D, Baynam G, Haendel MA, Robinson PN, Mungall CJ, Reese JT. An evaluation of GPT models for phenotype concept recognition. BMC Med Inform Decis Mak 2024; 24:30. [PMID: 38297371 PMCID: PMC10829255 DOI: 10.1186/s12911-024-02439-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVE Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. MATERIALS AND METHODS The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. RESULTS The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. CONCLUSION Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.
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Affiliation(s)
- Tudor Groza
- Rare Care Centre, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.
- Telethon Kids Institute, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.
- School of Electrical Engineering, Computing and Mathematical Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia.
- SingHealth Duke-NUS Institute of Precision Medicine, 5 Hospital Drive Level 9, Singapore, 169609, Singapore.
| | - Harry Caufield
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dylan Gration
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, 374 Bagot Road, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
- Telethon Kids Institute, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, 374 Bagot Road, Subiaco, WA, 6008, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Melissa A Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, 06032, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Justin T Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Farley KO, Forbes CA, Shaw NC, Kuzminski E, Ward M, Baynam G, Lassmann T, Fear VS. CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction. HGG Adv 2024; 5:100257. [PMID: 38007613 PMCID: PMC10787298 DOI: 10.1016/j.xhgg.2023.100257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
An estimated 3.5%-5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases are difficult to diagnose, with some affected individuals experiencing diagnostic delays of 5-30 years. Next-generation sequencing has improved clinical diagnostic rates to 33%-48%. In a majority of cases, novel variants potentially causing the disease are discovered. These variants require functional validation in specialist laboratories, resulting in a diagnostic delay. In the interim, the finding is classified as a genetic variant of uncertain significance (VUS) and the affected individual remains undiagnosed. A VUS (PTCHD1 c. 2489T>G) was identified in a child with autistic behavior, global developmental delay, and hypotonia. Loss of function mutations in PTCHD1 are associated with autism spectrum disorder and intellectual disability; however, the molecular function of PTCHD1 and its role in neurodevelopmental disease is unknown. Here, we apply CRISPR gene editing and induced pluripotent stem cell (iPSC) neural disease modeling to assess the variant. During differentiation from iPSCs to neural progenitors, we detect subtle but significant gene signatures in synaptic transmission and muscle contraction pathways. Our work supports the causal link between the genetic variant and the child's phenotype, providing evidence for the variant to be considered a pathogenic variant according to the American College of Medical Genetics and Genomics guidelines. In addition, our study provides molecular data on the role of PTCHD1 in the context of other neurodevelopmental disorders.
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Affiliation(s)
- Kathryn O Farley
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicole C Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Emma Kuzminski
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA 6008, Australia; Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia; Rare Care Centre, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Timo Lassmann
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
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7
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Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos A, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon S, Castellanos F, Caufield JH, Chan LE, Chute C, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He Y(O, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus M, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts A, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res 2024; 52:D1333-D1346. [PMID: 37953324 PMCID: PMC10767975 DOI: 10.1093/nar/gkad1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.
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Affiliation(s)
| | | | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Joel Anderton
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Anita M Bagley
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Eduard Bakštein
- National Institute of Mental Health, Klecany, Czech Republic
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27517, USA
| | - Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Michael Berk
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Holli Bertram
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Somer Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David F Bodenstein
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | | | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Jolana Čady
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, NY, NY, USA
| | | | - Seth J Carbon
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - J Harry Caufield
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Jaime Cruz-Rojo
- UDISGEN (Dysmorphology and Genetics Unit), 12 de Octubre Hospital, Madrid, Spain
| | - Noémi Dahan-Oliel
- Department of Clinical Research, Shriners Hospitals for Children, Montreal, Quebec, Canada
| | - Jon R Davids
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Maud de Dieuleveult
- Département I&D, AP-HP, Banque Nationale de Données Maladies Rares, Paris, France
| | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - J Raymond DePaulo
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Beata Derfalvi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Ferdinand Dhombres
- Fetal Medicine Department, Armand Trousseau Hospital, Sorbonne University, GRC26, INSERM, Limics, Paris, France
| | - Claudia Diaz-Byrd
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bruno Donadille
- St Antoine Hospital, Reference Center for Rare Growth Endocrine Disorders, Sorbonne University, AP-HP, INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | | | - Reem Elfeky
- Department of Immunology, GOS Hospital for Children NHS Foundation Trust, University College London, London, UK
| | - Shahim Essaid
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Giovanna Fico
- Bipolar and Depressive Disorders Unit, Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain
| | - Helen V Firth
- Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Yun Freudenberg-Hua
- Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | | | - Davera L Gabriel
- School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Gore Moses
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian Green
- SNOMED International, London W2 6BD, UK
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Tudor Groza
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Julia Guthrie
- Department of Structural and Computational Biology, University of Vienna; Max Perutz Labs, Vienna, Austria
| | - Benjamin Gyori
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marc Hanauer
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Kateřina Hanušová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | | | - Harshad Hegde
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingo Helbig
- Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kateřina Holasová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Charles Tapley Hoyt
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Eric Hurwitz
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Lisa Joseph
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Kamyar Keramatian
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Bryan King
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Megan L Kraus
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carlo Kroll
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Maaike Kusters
- Immunology, NIHR Great Ormond Street Hospital BRC, London, UK
| | - Markus S Ladewig
- Department of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany
| | - David Lagorce
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Pablo Lapunzina
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Bryan Laraway
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | | | - Caterina Lucano
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Marzieh Majd
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Victor Martinez-Glez
- Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Sabadell, Spain
| | - Toby H McHenry
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Julie A McMurry
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela Mihulová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Caitlin E Millett
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Philip B Mitchell
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW, Australia
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Kenji Narutomi
- Okinawa Prefectural Nanbu Medical Center & Children's Medical Center
| | - Shahrzad Nematollahi
- School of Physical and Occupational Therapy, McGill University, Montreal, Quebec, Canada
| | - Julian Nevado
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Andrew A Nierenberg
- Dauten Family Center for Bipolar Treatment Innovation, Massachusetts General Hospital, Boston, MA, USA
| | - Nikola Novák Čajbiková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - John I Nurnberger
- Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Daniel Olson
- Data Collaboration Center, Data Science, Critical Path Institute, Tucson, AZ, USA
| | - Abigail Ortiz
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia
| | - Guiomar Perez de Nanclares
- Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital, Vitoria-Gasteiz, Spain
| | - Amy Peters
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Tim Putman
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christina K Rapp
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Ana Rath
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren Rekerle
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | - Suzy Roy
- SNOMED International, London W2 6BD, UK
| | - Stephan J Sanders
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Catharina Schuetz
- Universitätsklinikum Carl Gustav Carus, Medizinische Fakultät, TU, Dresden, Germany
| | - Eva C Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, Germany
| | - Thomas G Schulze
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Martin Schwarz
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Katie Scott
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center UKS, Homburg/Saar, Germany
| | | | - Morgan N Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric S Simon
- Eisenberg Family Depression Center, University of Michigan, Ann Arbor, MI, USA
| | - Balwinder Singh
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jake T Smolinsky
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Sarah Sperry
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | | | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robin Steinhaus
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Rebecca Strawbridge
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | | | - Polina Talapova
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | | | - Pavel Tesner
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | | | - Markéta Vlčková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Anita Walden
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kai Wang
- Chinese HPO Consortium, Beijing, China
| | - Ron Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | | | | | - Lisa D Wiggins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrew E Williams
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | - Chen Wu
- Chinese HPO Consortium, Beijing, China
| | - Margot J Wyrwoll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Hui Xiong
- Chinese HPO Consortium, Beijing, China
| | - Nefize Yalin
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Yasunori Yamamoto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Japan
| | - Lakshmi N Yatham
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Anastasia K Yocum
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Allan H Young
- Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham, Kent, London SE5 8AF, UK
| | - Zafer Yüksel
- Department of Human Genetics, Bioscientia Healthcare GmbH, Ingelheim, Germany
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andreas Zankl
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Ignacio Zarante
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Miroslav Zvolský
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Sabrina Toro
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Melissa A Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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8
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Fear VS, Forbes CA, Shaw NC, Farley KO, Mantegna JL, Htun JP, Syn G, Viola H, Cserne Szappanos H, Hool L, Ward M, Baynam G, Lassmann T. Gene editing and cardiac disease modelling for the interpretation of genetic variants of uncertain significance in congenital heart disease. Stem Cell Res Ther 2023; 14:345. [PMID: 38049901 PMCID: PMC10696868 DOI: 10.1186/s13287-023-03592-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Genomic sequencing in congenital heart disease (CHD) patients often discovers novel genetic variants, which are classified as variants of uncertain significance (VUS). Functional analysis of each VUS is required in specialised laboratories, to determine whether the VUS is disease causative or not, leading to lengthy diagnostic delays. We investigated stem cell cardiac disease modelling and transcriptomics for the purpose of genetic variant classification using a GATA4 (p.Arg283Cys) VUS in a patient with CHD. METHODS We performed high efficiency CRISPR gene editing with homology directed repair in induced pluripotent stem cells (iPSCs), followed by rapid clonal selection with amplicon sequencing. Genetic variant and healthy matched control cells were compared using cardiomyocyte disease modelling and transcriptomics. RESULTS Genetic variant and healthy cardiomyocytes similarly expressed Troponin T (cTNNT), and GATA4. Transcriptomics analysis of cardiomyocyte differentiation identified changes consistent with the patient's clinical human phenotype ontology terms. Further, transcriptomics revealed changes in calcium signalling, and cardiomyocyte adrenergic signalling in the variant cells. Functional testing demonstrated, altered action potentials in GATA4 genetic variant cardiomyocytes were consistent with patient cardiac abnormalities. CONCLUSIONS This work provides in vivo functional studies supportive of a damaging effect on the gene or gene product. Furthermore, we demonstrate the utility of iPSCs, CRISPR gene editing and cardiac disease modelling for genetic variant interpretation. The method can readily be applied to other genetic variants in GATA4 or other genes in cardiac disease, providing a centralised assessment pathway for patient genetic variant interpretation.
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Affiliation(s)
- Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia.
- Centre for Child Health Research, University of Western Australia, Crawley, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Nicole C Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Kathryn O Farley
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Jessica L Mantegna
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Jasmin P Htun
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Genevieve Syn
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Helena Viola
- University of Western Australia, Crawley, Australia
| | | | - Livia Hool
- University of Western Australia, Crawley, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Timo Lassmann
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Centre for Child Health Research, University of Western Australia, Crawley, Australia
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9
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Reis ALM, Rapadas M, Hammond JM, Gamaarachchi H, Stevanovski I, Ayuputeri Kumaheri M, Chintalaphani SR, Dissanayake DSB, Siggs OM, Hewitt AW, Llamas B, Brown A, Baynam G, Mann GJ, McMorran BJ, Easteal S, Hermes A, Jenkins MR, Patel HR, Deveson IW. The landscape of genomic structural variation in Indigenous Australians. Nature 2023; 624:602-610. [PMID: 38093003 PMCID: PMC10733147 DOI: 10.1038/s41586-023-06842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
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Affiliation(s)
- Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Hasindu Gamaarachchi
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Meutia Ayuputeri Kumaheri
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Sanjog R Chintalaphani
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Duminda S B Dissanayake
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Owen M Siggs
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Bastien Llamas
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Alex Brown
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Gareth Baynam
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Genetic Services of Western Australia, Western Australian Department of Health, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Western Australia, Australia
| | - Graham J Mann
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Brendan J McMorran
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Misty R Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
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10
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Silcocks M, Farlow A, Hermes A, Tsambos G, Patel HR, Huebner S, Baynam G, Jenkins MR, Vukcevic D, Easteal S, Leslie S. Indigenous Australian genomes show deep structure and rich novel variation. Nature 2023; 624:593-601. [PMID: 38093005 PMCID: PMC10733150 DOI: 10.1038/s41586-023-06831-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama-Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000-35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.
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Affiliation(s)
- Matthew Silcocks
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia
| | - Ashley Farlow
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgia Tsambos
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sharon Huebner
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gareth Baynam
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital and Rare Care Centre, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Misty R Jenkins
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
| | - Damjan Vukcevic
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen Leslie
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia.
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia.
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11
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Martin T, McIntyre S, Waight E, Baynam G, Watson L, Langdon K, Woolfenden S, Smithers‐Sheedy H, Sherwood J. Prevalence and trends for Aboriginal and Torres Strait Islander children living with cerebral palsy: A birds-eye view. Dev Med Child Neurol 2023; 65:1475-1485. [PMID: 37147854 PMCID: PMC10952932 DOI: 10.1111/dmcn.15617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/07/2023]
Abstract
AIM To provide a birds-eye view of the trends of cerebral palsy (CP) for Australian Aboriginal and Torres Strait Islander children and young adults. METHOD Data were obtained for this population-based observational study from the Australian Cerebral Palsy Register (ACPR), birth years 1995 to 2014. The Indigenous status of children was classified by maternal Aboriginal and Torres Strait Islander or non-Indigenous status. Descriptive statistics were calculated for socio-demographic and clinical characteristics. Prenatal/perinatal and post-neonatal birth prevalence was calculated per 1000 live births and per 10 000 live births respectively, and Poisson regression used to assess trends. RESULTS Data from the ACPR were available for 514 Aboriginal and Torres Strait Islander individuals with CP. Most children could walk independently (56%) and lived in urban or regional areas (72%). One in five children lived in socioeconomically disadvantaged remote/very remote areas. The birth prevalence of prenatal/perinatal CP declined after the mid-2000s from a high of 4.8 (95% confidence interval 3.2-7.0) to 1.9 per 1000 live births (95% confidence interval 1.1-3.2) (2013-2014), with marked declines observed for term births and teenage mothers. INTERPRETATION The birth prevalence of CP in Aboriginal and Torres Strait Islander children in Australia declined between the mid-2000s and 2013 to 2014. This birds-eye view provides key stakeholders with new knowledge to advocate for sustainable funding for accessible, culturally safe, antenatal and CP services. WHAT THIS PAPER ADDS Birth prevalence of cerebral palsy (CP) is beginning to decline for Aboriginal and Torres Strait Islanders. Recent CP birth prevalence for Aboriginal and Torres Strait Islanders is 1.9 per 1000 live births. Most children with CP live in more populated areas rather than remote or very remote areas. One in five Aboriginal and Torres Strait Islander children with CP live in socioeconomically disadvantaged remote areas.
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Affiliation(s)
- Tanya Martin
- School of Nursing and MidwiferyThe University of SydneyCamperdownNew South WalesAustralia
| | - Sarah McIntyre
- Cerebral Palsy Alliance/Research Institute, Specialty of Child & Adolescent HealthThe University of SydneyCamperdownNew South WalesAustralia
| | - Emma Waight
- Cerebral Palsy Alliance/Research Institute, Specialty of Child & Adolescent HealthThe University of SydneyCamperdownNew South WalesAustralia
| | - Gareth Baynam
- Department of Health, Western Australian Register of Developmental AnomaliesGovernment of Western AustraliaPerthWestern AustraliaAustralia
| | - Linda Watson
- Department of Health, Western Australian Register of Developmental AnomaliesGovernment of Western AustraliaPerthWestern AustraliaAustralia
| | | | - Susan Woolfenden
- Discipline of Paediatrics, School of Clinical MedicineUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Women, Children and their FamiliesSydney Local Health DistrictSydneyNew South WalesAustralia
| | - Hayley Smithers‐Sheedy
- Cerebral Palsy Alliance/Research Institute, Specialty of Child & Adolescent HealthThe University of SydneyCamperdownNew South WalesAustralia
| | - Juanita Sherwood
- Jumbunna Institute for Indigenous Education and ResearchUniversity of Technology SydneySydneyNew South WalesAustralia
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Baxter MF, Hansen M, Gration D, Groza T, Baynam G. Surfacing undiagnosed disease: consideration, counting and coding. Front Pediatr 2023; 11:1283880. [PMID: 38027298 PMCID: PMC10646190 DOI: 10.3389/fped.2023.1283880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
The diagnostic odyssey for people living with rare diseases (PLWRD) is often prolonged for myriad reasons including an initial failure to consider rare disease and challenges to systemically and systematically identifying and tracking undiagnosed diseases across the diagnostic journey. This often results in isolation, uncertainty, a delay to targeted treatments and increase in risk of complications with significant consequences for patient and family wellbeing. This article aims to highlight key time points to consider a rare disease diagnosis along with elements to consider in the potential operational classification for undiagnosed rare diseases during the diagnostic odyssey. We discuss the need to create a coding framework that traverses all stages of the diagnostic odyssey for PLWRD along with the potential benefits this will have to PLWRD and the wider community.
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Affiliation(s)
- Megan F. Baxter
- Emergency Department, Perth Children’s Hospital, Perth, WA, Australia
- School of Medicine and Dentistry, Griffith University, Gold Coast, QLD, Australia
| | - Michele Hansen
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia
| | - Dylan Gration
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia
| | - Tudor Groza
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Rare Care Centre, Perth Children’s Hospital, Perth, WA, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia
- Rare Care Centre, Perth Children’s Hospital, Perth, WA, Australia
- Undiagnosed Diseases Program, WA, Genetic Services of WA, Perth, WA, Australia
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13
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Sciascia S, Roccatello D, Salvatore M, Carta C, Cellai LL, Ferrari G, Lumaka A, Groft S, Alanay Y, Azam M, Baynam G, Cederroth H, Cutiongco-de la Paz EM, Dissanayake VHW, Giugliani R, Gonzaga-Jauregui C, Hettiarachchi D, Kvlividze O, Landoure G, Makay P, Melegh B, Ozbek U, Puri RD, Romero VI, Scaria V, Jamuar SS, Shotelersuk V, Gahl WA, Wiafe SA, Bodamer O, Posada M, Taruscio D. Unmet needs in countries participating in the undiagnosed diseases network international: an international survey considering national health care and economic indicators. Front Public Health 2023; 11:1248260. [PMID: 37822540 PMCID: PMC10562568 DOI: 10.3389/fpubh.2023.1248260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/08/2023] [Indexed: 10/13/2023] Open
Abstract
Background Patients, families, the healthcare system, and society as a whole are all significantly impacted by rare diseases (RDs). According to various classifications, there are currently up to 9,000 different rare diseases that have been recognized, and new diseases are discovered every month. Although very few people are affected by each uncommon disease individually, millions of people are thought to be impacted globally when all these conditions are considered. Therefore, RDs represent an important public health concern. Although crucial for clinical care, early and correct diagnosis is still difficult to achieve in many nations, especially those with low and middle incomes. Consequently, a sizeable amount of the overall burden of RD is attributable to undiagnosed RD (URD). Existing barriers and policy aspects impacting the care of patients with RD and URD remain to be investigated. Methods To identify unmet needs and opportunities for patients with URD, the Developing Nations Working Group of the Undiagnosed Diseases Network International (DNWG-UDNI) conducted a survey among its members, who were from 20 different nations. The survey used a mix of multiple choice and dedicated open questions covering a variety of topics. To explore reported needs and analyze them in relation to national healthcare economical aspects, publicly available data on (a) World Bank ranking; (b) Current health expenditure per capita; (c) GDP per capita; (d) Domestic general government health expenditure (% of GDP); and (e) Life expectancy at birth, total (years) were incorporated in our study. Results This study provides an in-depth evaluation of the unmet needs for 20 countries: low-income (3), middle-income (10), and high-income (7). When analyzing reported unmet needs, almost all countries (N = 19) indicated that major barriers still exist when attempting to improve the care of patients with UR and/or URD; most countries report unmet needs related to the availability of specialized care and dedicated facilities. However, while the countries ranked as low income by the World Bank showed the highest prevalence of referred unmet needs across the different domains, no specific trend appeared when comparing the high, upper, and low-middle income nations. No overt trend was observed when separating countries by current health expenditure per capita, GDP per capita, domestic general government health expenditure (% of GDP) and life expectancy at birth, total (years). Conversely, both the GDP and domestic general government health expenditure for each country impacted the presence of ongoing research. Conclusion We found that policy characteristics varied greatly with the type of health system and country. No overall pattern in terms of referral for unmet needs when separating countries by main economic or health indicators were observed. Our findings highlight the importance of identifying actionable points (e.g., implemented orphan drug acts or registries where not available) in order to improve the care and diagnosis of RDs and URDs on a global scale.
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Affiliation(s)
- Savino Sciascia
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, ASL Città di Torino and University of Turin, Turin, Italy
| | - Dario Roccatello
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, ASL Città di Torino and University of Turin, Turin, Italy
| | - Marco Salvatore
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Carta
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Laura L. Cellai
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Gianluca Ferrari
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Aimè Lumaka
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Service de Génétique Humaine, University Hospitals of Liège, Liège, Belgium
| | - Stephen Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yasemin Alanay
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Türkiye
| | - Maleeha Azam
- COMSATS University Islamabad, Islamabad, Pakistan
| | - Gareth Baynam
- Rare Care, Clinical Center of Expertise for Rare and Undiagnosed Diseases, Perth Children's Hospital, Perth, WA, Australia
| | | | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Roberto Giugliani
- House of Rares, Medical Genetics Service, HCPA, Department Genetics UFRGS and DASA, Porto Alegre, Brazil
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Universidad Nacional Autonoma de Mexico, Juriquilla, Queretaro, Mexico
| | - Dineshani Hettiarachchi
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Oleg Kvlividze
- Georgian Foundation for Genetic and Rare Diseases (GeRaD), School of Medicine, New Vision University, Tbilisi, Georgia
| | - Guida Landoure
- Faculté de Médecine et d'Odontostomatologie, l'Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Prince Makay
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Béla Melegh
- Department of Medical Genetics, School of Medicine, University of Pécs, Pécs, Hungary
| | - Ugur Ozbek
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Türkiye
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saumya S. Jamuar
- Genetics Service, Department of Pediatrics, KK Women’s and Children’s Hospital and Pediatric ACP, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital and Chulalongkorn University, Bangkok, Thailand
| | - William A. Gahl
- National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, United States
| | | | - Olaf Bodamer
- Division of Genetics and Genomics, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Manuel Posada
- Rare Diseases Research Institute (IIER), SpainUDP, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Domenica Taruscio
- National Center for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
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14
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Nevin SM, McGill BC, Kelada L, Hilton G, Maack M, Elvidge KL, Farrar MA, Baynam G, Katz NT, Donovan L, Grattan S, Signorelli C, Bhattacharya K, Nunn K, Wakefield CE. The psychosocial impact of childhood dementia on children and their parents: a systematic review. Orphanet J Rare Dis 2023; 18:277. [PMID: 37679855 PMCID: PMC10486052 DOI: 10.1186/s13023-023-02859-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/20/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Childhood dementias are a group of rare and ultra-rare paediatric conditions clinically characterised by enduring global decline in central nervous system function, associated with a progressive loss of developmentally acquired skills, quality of life and shortened life expectancy. Traditional research, service development and advocacy efforts have been fragmented due to a focus on individual disorders, or groups classified by specific mechanisms or molecular pathogenesis. There are significant knowledge and clinician skill gaps regarding the shared psychosocial impacts of childhood dementia conditions. This systematic review integrates the existing international evidence of the collective psychosocial experiences of parents of children living with dementia. METHODS We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We systematically searched four databases to identify original, peer-reviewed research reporting on the psychosocial impacts of childhood dementia, from the parent perspective. We synthesised the data into three thematic categories: parents' healthcare experiences, psychosocial impacts, and information and support needs. RESULTS Nineteen articles met review criteria, representing 1856 parents. Parents highlighted extensive difficulties connecting with an engaged clinical team and navigating their child's rare, life-limiting, and progressive condition. Psychosocial challenges were manifold and encompassed physical, economic, social, emotional and psychological implications. Access to coordinated healthcare and community-based psychosocial supports was associated with improved parent coping, psychological resilience and reduced psychological isolation. Analysis identified a critical need to prioritize access to integrated family-centred psychosocial supports throughout distinct stages of their child's condition trajectory. CONCLUSION This review will encourage and guide the development of evidence-based and integrated psychosocial resources to optimise quality of life outcomes for of children with dementia and their families.
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Affiliation(s)
- Suzanne M Nevin
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia.
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia.
| | - Brittany C McGill
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Lauren Kelada
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Gail Hilton
- Childhood Dementia Initiative, Sydney, NSW, Australia
| | - Megan Maack
- Childhood Dementia Initiative, Sydney, NSW, Australia
| | | | - Michelle A Farrar
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Department of Neurology, Sydney Children's Hospital, Randwick, Australia
| | - Gareth Baynam
- Faculty of Health and Medical Sciences, Division of Paediatrics, University of Western Australia, Western Australia, Australia
- Rare Care Centre, Perth Children's Hospital, Perth, WA, Australia
- Telethon Kids Institute, Perth, WA, Australia
| | - Naomi T Katz
- Victorian Paediatric Palliative Care Program, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Leigh Donovan
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Sarah Grattan
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
| | - Christina Signorelli
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospitals' Network, Randwick and Westmead, Australia
- Faculty of Medicine and Health, Discipline of Genomics, Sydney University, Westmead, Australia
| | - Kenneth Nunn
- Department of Psychological Medicine, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Claire E Wakefield
- School of Clinical Medicine, UNSW Medicine and Health, Discipline of Paediatrics and Child Health, Sydney, Australia
- Behavioral Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
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15
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MacArthur C, Hansen M, Baynam G, Bower C, Kelty E. Trends in prenatal diagnosis of congenital anomalies in Western Australia between 1980 and 2020: A population-based study. Paediatr Perinat Epidemiol 2023; 37:596-606. [PMID: 37143205 PMCID: PMC10947594 DOI: 10.1111/ppe.12983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Advances in screening and diagnostics have changed the way in which we identify and diagnose congenital anomalies. OBJECTIVE To examine changes in rates of prenatal diagnosis of congenital anomalies over time and by demographic characteristics. METHODS We undertook a population-based retrospective cohort study of all children born in Western Australia between 1980 and 2020 and diagnosed with a congenital anomaly. Age at diagnosis (prenatal, neonatal, infancy, early childhood or childhood) prevalence (all-type and type-specific), and prevalence ratios (PR) were calculated. We fit joinpoint regression models to describe the average annual percentage change (APC) in prenatal diagnosis over time, and log-binomial regression models to estimate the association between prenatal diagnosis and demographic characteristics. RESULTS Prenatal diagnosis prevalence between the first (1980-1989: 28.3 per 10,000 births) and last (2005-2014: 156.1 per 10,000 births) decades of the study increased 5.5-fold (95% confidence interval [CI] 5.0, 5.9). Substantial increases were observed for cardiovascular (PR 10.7, 95% CI 8.0, 14.6), urogenital (PR 10.5, 95% CI: 8.7, 12.6) and chromosomal anomalies (PR 7.0, 95% CI 5.9, 8.3). Prenatal diagnosis was positively associated with the birth year (adjusted risk ratio [RR] 1.04, 95% CI 1.03, 1.04), advanced maternal age (RR 1.14, 95% CI 1.11, 1.18), multiple anomalies (RR 2.86, 95% CI 2.77, 2.96) and major anomalies (RR 3.75, 95% CI 3.36, 4.19), and inversely associated with remoteness (RR 0.89, 95% CI: 0.83, 0.95) and Aboriginality (RR 0.90, 95% CI 0.83, 0.97). CONCLUSIONS Increases in prenatal diagnosis of congenital anomalies were observed in Western Australia from 1980 to 2020, reflecting advances in screening. Prenatal diagnosis was less common in remote regions and in Aboriginal children, strengthening calls for increased provision of antenatal care services for these populations.
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Affiliation(s)
- Cassandra MacArthur
- School of Population and Global HealthThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Michele Hansen
- Telethon Kids InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Gareth Baynam
- Western Australian Register of Developmental AnomaliesKing Edward Memorial HospitalPerthWestern AustraliaAustralia
- Faculty of Health and Medicine, Institute and Division of PaediatricsUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Rare Care, Clinical Centre of Expertise for Rare and Undiagnosed DiseasesPerth Children's HospitalPerthWestern AustraliaAustralia
| | - Carol Bower
- Telethon Kids InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Erin Kelty
- School of Population and Global HealthThe University of Western AustraliaCrawleyWestern AustraliaAustralia
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16
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Kaur M, Blair J, Devkota B, Fortunato S, Clark D, Lawrence A, Kim J, Do W, Semeo B, Katz O, Mehta D, Yamamoto N, Schindler E, Al Rawi Z, Wallace N, Wilde JJ, McCallum J, Liu J, Xu D, Jackson M, Rentas S, Tayoun AA, Zhe Z, Abdul-Rahman O, Allen B, Angula MA, Anyane-Yeboa K, Argente J, Arn PH, Armstrong L, Basel-Salmon L, Baynam G, Bird LM, Bruegger D, Ch'ng GS, Chitayat D, Clark R, Cox GF, Dave U, DeBaere E, Field M, Graham JM, Gripp KW, Greenstein R, Gupta N, Heidenreich R, Hoffman J, Hopkin RJ, Jones KL, Jones MC, Kariminejad A, Kogan J, Lace B, Leroy J, Lynch SA, McDonald M, Meagher K, Mendelsohn N, Micule I, Moeschler J, Nampoothiri S, Ohashi K, Powell CM, Ramanathan S, Raskin S, Roeder E, Rio M, Rope AF, Sangha K, Scheuerle AE, Schneider A, Shalev S, Siu V, Smith R, Stevens C, Tkemaladze T, Toimie J, Toriello H, Turner A, Wheeler PG, White SM, Young T, Loomes KM, Pipan M, Harrington AT, Zackai E, Rajagopalan R, Conlin L, Deardorff MA, McEldrew D, Pie J, Ramos F, Musio A, Kline AD, Izumi K, Raible SE, Krantz ID. Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms. Am J Med Genet A 2023; 191:2113-2131. [PMID: 37377026 PMCID: PMC10524367 DOI: 10.1002/ajmg.a.63247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/29/2023]
Abstract
Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.
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Affiliation(s)
- Maninder Kaur
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin Blair
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Sierra Fortunato
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Audrey Lawrence
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jiwoo Kim
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wonwook Do
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Benjamin Semeo
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Olivia Katz
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Devanshi Mehta
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nobuko Yamamoto
- Division of Otolaryngology, National Center for Child Health and Development, Tokyo, Japan
| | - Emma Schindler
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zayd Al Rawi
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Wallace
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Jennifer McCallum
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinglan Liu
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Dongbin Xu
- Hematologics Inc, Seattle, Washington, USA
| | - Marie Jackson
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Zhang Zhe
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Bill Allen
- Fullerton Genetics Center, Mission Health, Asheville, North Carolina, USA
| | - Moris A Angula
- Department of Pediatrics, NYU Langone Hospital-Long Island, Mineola, New York, USA
| | - Kwame Anyane-Yeboa
- Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jesús Argente
- Hospital Infantil Universitario Niño Jesús & Universidad Autónoma de Madrid, Madrid, Spain
- CIBER Fisiopatología de la obesidad y nutrición (CIBEROBN) and IMDEA Food Institute, Madrid, Spain
| | - Pamela H Arn
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, Florida, USA
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital, Raphael Recanati Genetics Institute, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Rare Care Centre, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Division of Genetics & Dysmophology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Daniel Bruegger
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for SickKids, University of Toronto, Toronto, Ontario, Canada
| | - Robin Clark
- Department of Pediatrics, Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Gerald F Cox
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Usha Dave
- R & D MILS International India, Mumbai, India
| | - Elfrede DeBaere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Karen W Gripp
- Nemours Children's Health, Wilmington, Delaware, USA
| | - Robert Greenstein
- University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Neerja Gupta
- Division of Genetics, Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Randy Heidenreich
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Jodi Hoffman
- Department of Pediatrics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth L Jones
- Division of Dysmorphology & Teratology, Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
| | - Marilyn C Jones
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Division of Genetics & Dysmophology, Rady Children's Hospital San Diego, San Diego, California, USA
| | | | - Jillene Kogan
- Division of Genetics, Advocate Children's Hospital, Park Ridge, Illinois, USA
| | - Baiba Lace
- Children's Clinical University Hospital, Riga, Latvia
| | - Julian Leroy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sally Ann Lynch
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - Marie McDonald
- Duke University Medical Center, Durham, North Carolina, USA
| | - Kirsten Meagher
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Mendelsohn
- Complex Health Solutions, United Healthcare, Minneapolis, Minnesota, USA
| | - Ieva Micule
- Children's Clinical University Hospital, Riga, Latvia
| | - John Moeschler
- Department of Pediatrics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Kaoru Ohashi
- Department of Medical Genetics, BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Cynthia M Powell
- Division of Genetics and Metabolism, Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Subhadra Ramanathan
- Department of Pediatrics, Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Salmo Raskin
- Genetika-Centro de aconselhamento e laboratório de genética, Curitiba, Brazil
| | - Elizabeth Roeder
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Marlene Rio
- Department of Genetics, Hôpital Necker-Enfants Malades, Paris, France
| | - Alan F Rope
- Genome Medical, South San Francisco, California, USA
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adele Schneider
- Department of Pediatrics and Oculogenetics, Wills Eye Hospital, Philadelphia, Pennsylvania, USA
| | - Stavit Shalev
- Rappaport Faculty of Medicine, Technion, The Genetics Institute, Emek Medical Center, Afula, Haifa, Israel
| | - Victoria Siu
- London Health Sciences Centre, London, Ontario, Canada
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, Maine, USA
| | - Cathy Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, T.C. Thompson Children's Hospital, Chattanooga, Tennessee, USA
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - John Toimie
- Clinical Genetics Service, Laboratory Medicine Building, Southern General Hospital, Glasgow, UK
| | - Helga Toriello
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan, USA
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
- Division of Genetics, Arnold Palmer Hospital, Orlando, Florida, USA
| | | | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Terri Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Research to Prevent Blindness Inc, New York, New York, USA
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary Pipan
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Behavioral Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ann Tokay Harrington
- Center for Rehabilitation, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramakrishnan Rajagopalan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew A Deardorff
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Deborah McEldrew
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Juan Pie
- Laboratorio de Genética Clínica y Genómica Funcional, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Feliciano Ramos
- Unidad de Genética Clínica, Servicio de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Zaragoza, Spain
- Departamento de Pediatría, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Antonio Musio
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa
| | - Antonie D Kline
- Greater Baltimore Medical Centre, Harvey Institute of Human Genetics, Baltimore, Maryland, USA
| | - Kosuke Izumi
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sarah E Raible
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian D Krantz
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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17
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Junaid M, Slack-Smith L, Wong K, Hewitt T, Glasson E, Bourke J, Baynam G, Calache H, Leonard H. Hospitalizations from Birth to 28 Years in a Population Cohort of Individuals Born with Five Rare Craniofacial Anomalies in Western Australia. J Pediatr 2023; 259:113418. [PMID: 37030611 DOI: 10.1016/j.jpeds.2023.113418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
OBJECTIVE To describe trends, age-specific patterns, and factors influencing hospitalizations for 5 rare craniofacial anomalies (CFAs). METHODS Data on livebirths (1983-2010; n = 721 019) including rare CFA (craniofacial microsomia, mandibulofacial dysostosis, Pierre Robin sequence, Van der Woude syndrome, and frontonasal dysplasia), episodes of death, and demographic and perinatal factors were identified from the Western Australian Register of Developmental Anomalies, Death Registrations and Midwives Notification System. Information on incident craniofacial and noncraniofacial related admissions, length of hospital stay, and intensive care and emergency-related admissions were identified using principal diagnosis and procedural codes were extracted from the Hospital Morbidity Data Collection and linked to other data sources. Associations of hospitalizations by age groups as well as demographic and perinatal factors were expressed as incidence rate ratio (IRR). RESULTS The incident hospitalizations were 3 times as high for rare CFA (IRR 3.22-3.72) throughout childhood into adolescence than those without. Children with rare CFA had 3-4 times as many potentially preventable hospitalizations until 18 years of age than those without. Specifically, respiratory infections (IRR 2.13-2.35), ear infections (IRR 7.92-26.28), and oral health-related conditions contributed for most noncraniofacial admissions until the adolescence period. A greater incidence of noncraniofacial related hospitalizations was observed among Indigenous children, births with intrauterine growth restrictions, and families with high socioeconomic disadvantage. CONCLUSIONS Throughout childhood, individuals with rare CFA had greater hospital service use, specifically for potentially preventable conditions, than those without. These population-level findings can inform new preventive strategies and early disease management targeted toward reducing preventable hospitalizations.
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Affiliation(s)
- Mohammed Junaid
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia; Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia.
| | - Linda Slack-Smith
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia; Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia
| | - Kingsley Wong
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia
| | - Timothy Hewitt
- Department of Plastic and Reconstructive Surgery, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Emma Glasson
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia
| | - Jenny Bourke
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia
| | - Gareth Baynam
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia; Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, Western Australia, Australia
| | - Hanny Calache
- Deakin Health Economics, Institute of Health Transformation, School of Health and Social Development, Faculty of Health, Deakin University, Geelong, Victoria, Australia; Department of Dentistry and Oral Health, La Trobe Rural Health School, La Trobe University, Bendigo, Victoria, Australia
| | - Helen Leonard
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, Nedlands, Western Australia, Australia; UWA Centre of Child Health Research, University of Western Australia, Nedlands, Western Australia, Australia
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18
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Junaid M, Slack-Smith L, Wong K, Hewitt T, Bourke J, Baynam G, Calache H, Leonard H. Patterns, trends, and factors influencing hospitalizations for craniosynostosis in Western Australia. A population-based study. Eur J Pediatr 2023; 182:2379-2392. [PMID: 36899143 PMCID: PMC10175457 DOI: 10.1007/s00431-023-04922-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Understanding hospital service use among children with a diagnosis of craniosynostosis (CS) is important to improve services and outcomes. This study aimed to describe population-level trends, patterns, and factors influencing hospitalizations for craniosynostosis in Western Australia. Data on live births (1990-2010; n = 554,624) including craniosynostosis, episodes of death, demographic, and perinatal factors were identified from the midwives, birth defects, hospitalizations, and death datasets. Information on craniosynostosis and non-craniosynostosis-related admissions, cumulative length of hospital stay (cLoS), intensive care unit, and emergency department-related admissions were extracted from the hospitalization dataset and linked to other data sources. These associations were examined using negative binomial regression presented as annual percent change and associations of hospitalizations by age groups, demographic, and perinatal factors were expressed as incidence rate ratio (IRR). We found an increasing trend in incident hospitalizations but a marginal decline in cLoS for craniosynostosis over the observed study period. Perinatal conditions, feeding difficulties, nervous system anomalies, respiratory, and other infections contributed to majority of infant non-CS-related admissions.Respiratory infections accounted for about twice the number of admissions for individuals with CS (IRRs 1.94-2.34) across all observed age groups. Higher incidence of non-CS hospitalizations was observed among females, with associated anomalies, to families with highest socioeconomic disadvantage and living in remote areas of the state. Conclusion: Marginal reduction in the cLoS for CS-related admissions observed over the 21-year period are potentially indicative of improved peri-operative care. However, higher incidence of respiratory infection-related admissions for syndromic synostosis is concerning and requires investigation.
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Affiliation(s)
- Mohammed Junaid
- School of Population and Global Health, The University of Western Australia, Clifton Street Building, Clifton Street, Nedlands, 6009, WA, Australia. .,Telethon Kids Institute, The University of Western Australia, Northern Entrance, 15 Hospital Avenue, Nedlands, WA, Australia.
| | - Linda Slack-Smith
- School of Population and Global Health, The University of Western Australia, Clifton Street Building, Clifton Street, Nedlands, 6009, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Northern Entrance, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Kingsley Wong
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Timothy Hewitt
- Department of Plastic and Reconstructive Surgery, Perth Children's Hospital, Nedlands, WA, Australia
| | - Jenny Bourke
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Hanny Calache
- Deakin Health Economics, Institute of Health Transformation, School of Health and Social Development, Faculty of Health, Deakin University, Geelong, VIC, Australia.,Department of Dentistry and Oral Health, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Helen Leonard
- Telethon Kids Institute, The University of Western Australia, Northern Entrance, 15 Hospital Avenue, Nedlands, WA, Australia
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Jamuar S, Palmer R, Dawkins H, Lee DW, Helmholz P, Baynam G. 3D facial analysis for rare disease diagnosis and treatment monitoring: Proof-Of-Concept plan for hereditary angioedema. PLOS Digit Health 2023; 2:e0000090. [PMID: 36947507 PMCID: PMC10032512 DOI: 10.1371/journal.pdig.0000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/24/2023] [Indexed: 03/23/2023]
Abstract
Rare diseases pose a diagnostic conundrum to even the most experienced clinicians around the world. The technology could play an assistive role in hastening the diagnosis process. Data-driven methodologies can identify distinctive disease features and create a definitive diagnostic spectrum. The healthcare professionals in developed and developing nations would benefit immensely from these approaches resulting in quicker diagnosis and enabling early care for the patients. Hereditary Angioedema is one such rare disease that requires a lengthy diagnostic cascade ensuing massive patient inconvenience and cost burden on the healthcare system. It is hypothesized that facial analysis with advanced imaging and algorithmic association can create an ideal diagnostic peer to the clinician while assimilating signs and symptoms in the hospital. 3D photogrammetry has been applied to diagnose rare diseases in various cohorts. The facial features are captured at a granular level in utmost finer detail. A validated and proven algorithm-powered software provides recommendations in real-time. Thus, paving the way for quick and early diagnosis to well-trained or less trained clinicians in different settings around the globe. The generated evidence indicates the strong applicability of 3 D photogrammetry in association with proprietary Cliniface software to Hereditary Angioedema for aiding in the diagnostic process. The approach, mechanism, and beneficial impact have been sketched out appropriately herein. This blueprint for hereditary angioedema may have far-reaching consequences beyond disease diagnosis to benefit all the stakeholders in the healthcare arena including research and new drug development.
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Affiliation(s)
- Saumya Jamuar
- Genetics Service, KK Women's and Children's Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Richard Palmer
- School of Earth and Planetary Sciences, Curtin University, Perth, Australia
| | - Hugh Dawkins
- School of Medicine, The University of Notre Dame Australia, Sydney
- Division of Genetics, School of Biomedical Sciences, University of Western Australia
| | - Dae-Wook Lee
- APAC Rare Disease Medical Affairs, Takeda Pharmaceuticals (Asia Pacific) Pte Ltd, Singapore (at the time of manuscript development)
| | - Petra Helmholz
- School of Earth and Planetary Sciences, Curtin University, Perth, Australia
| | - Gareth Baynam
- School of Earth and Planetary Sciences, Curtin University, Perth, Australia
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
- Western Australian Register of Developmental Anomalies and Genetic Services of WA, King Edward Memorial Hospital, Perth Australia
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20
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Taruscio D, Salvatore M, Lumaka A, Carta C, Cellai LL, Ferrari G, Sciascia S, Groft S, Alanay Y, Azam M, Baynam G, Cederroth H, Cutiongco-de la Paz EM, Dissanayake VHW, Giugliani R, Gonzaga-Jauregui C, Hettiarachchi D, Kvlividze O, Landoure G, Makay P, Melegh B, Ozbek U, Puri RD, Romero V, Scaria V, Jamuar SS, Shotelersuk V, Roccatello D, Gahl WA, Wiafe SA, Bodamer O, Posada M. Undiagnosed diseases: Needs and opportunities in 20 countries participating in the Undiagnosed Diseases Network International. Front Public Health 2023; 11:1079601. [PMID: 36935719 PMCID: PMC10017550 DOI: 10.3389/fpubh.2023.1079601] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Rare diseases (RD) are a health priority worldwide, overall affecting hundreds of millions of people globally. Early and accurate diagnosis is essential to support clinical care but remains challenging in many countries, especially the low- and medium-income ones. Hence, undiagnosed RD (URD) account for a significant portion of the overall RD burden. Methods In October 2020, the Developing Nations Working Group of the Undiagnosed Diseases Network International (DNWG-UDNI) launched a survey among its members, belonging to 20 countries across all continents, to map unmet needs and opportunities for patients with URD. The survey was based on questions with open answers and included eight different domains. Conflicting interpretations were resolved in contact with the partners involved. Results All members responded to the survey. The results indicated that the scientific and medical centers make substantial efforts to respond to the unmet needs of patients. In most countries, there is a high awareness of RD issues. Scarcity of resources was highlighted as a major problem, leading to reduced availability of diagnostic expertise and research. Serious equity in accessibility to services were highlighted both within and between participating countries. Regulatory problems, including securing informed consent, difficulties in sending DNA to foreign laboratories, protection of intellectual property, and conflicts of interest on the part of service providers, remain issues of concern. Finally, most respondents stressed the need to strengthen international cooperation in terms of data sharing, clinical research, and diagnostic expertise for URD patients in low and medium income countries. Discussion The survey highlighted that many countries experienced a discrepancy between the growing expertise and scientific value, the level of awareness and commitment on the part of relevant parties, and funding bodies. Country-tailored public health actions, including general syllabus of medical schools and of the education of other health professionals, are needed to reduce such gaps.
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Affiliation(s)
- Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Domenica Taruscio
| | - Marco Salvatore
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Aimè Lumaka
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Service de Génétique Humaine, University Hospitals of Liège, Liège, Belgium
| | - Claudio Carta
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Laura L. Cellai
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Gianluca Ferrari
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Savino Sciascia
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, University of Turin, Turin, Italy
| | - Stephen Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yasemin Alanay
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Turkey
| | - Maleeha Azam
- COMSATS University Islamabad, Islamabad, Pakistan
| | - Gareth Baynam
- Rare Care, Clinical Centre of Expertise for Rare and Undiagnosed Diseases, Perth Children's Hospital, Perth, WA, Australia
| | | | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Roberto Giugliani
- House of Rares, Medical Genetics Service, HCPA, Department Genetics UFRGS and DASA, Porto Alegre, Brazil
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Universidad Nacional Autonoma de Mexico, Juriquilla, Queretaro, Mexico
| | - Dineshani Hettiarachchi
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Oleg Kvlividze
- Georgian Foundation for Genetic and Rare Diseases (GeRaD), School of Medicine, New Vision University, Tbilisi, Georgia
| | - Guida Landoure
- Faculté de Médecine et d'Odontostomatologie, l'Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Prince Makay
- Reference Center for Rare and Undiagnosed Diseases, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Béla Melegh
- Department of Medical Genetics, School of Medicine, University of Pécs, Pécs, Hungary
| | - Ugur Ozbek
- ACURARE-Rare and Undiagnosed Diseases Center, Acibadem University, Istanbul, Turkey
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Vanessa Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saumya S. Jamuar
- Singhealth Duke-NUS Genomic Medicine Centre, KK Women's and Children's Hospital, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital and Chulalongkorn University, Bangkok, Thailand
| | - Dario Roccatello
- Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) With Nephrology and Dialysis Unit, San Giovanni Bosco Hub Hospital, University of Turin, Turin, Italy
| | - William A. Gahl
- National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, United States
| | | | - Olaf Bodamer
- Division of Genetics and Genomics, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Manuel Posada
- Rare Diseases Research Institute (IIER), SpainUDP, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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21
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Tumiene B, Peters H, Melegh B, Peterlin B, Utkus A, Fatkulina N, Pfliegler G, Graessner H, Hermanns S, Scarpa M, Blay JY, Ashton S, McKay L, Baynam G. Rare disease education in Europe and beyond: time to act. Orphanet J Rare Dis 2022; 17:441. [PMID: 36536417 PMCID: PMC9761619 DOI: 10.1186/s13023-022-02527-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 10/02/2022] [Indexed: 12/23/2022] Open
Abstract
People living with rare diseases (PLWRD) still face huge unmet needs, in part due to the fact that care systems are not sufficiently aligned with their needs and healthcare workforce (HWF) along their care pathways lacks competencies to efficiently tackle rare disease-specific challenges. Level of rare disease knowledge and awareness among the current and future HWF is insufficient. In recent years, many educational resources on rare diseases have been developed, however, awareness of these resources is still limited and rare disease education is still not sufficiently taken into account by some crucial stakeholders as academia and professional organizations. Therefore, there is a need to fundamentally rethink rare disease education and HWF development across the whole spectrum from students to generalists, specialists and experts, to engage and empower PLWRD, their families and advocates, and to work towards a common coherent and complementary strategy on rare disease education and training in Europe and beyond. Special consideration should be also given to the role of nurse coordinators in care coordination, interprofessional training for integrated multidisciplinary care, patient and family-centered education, opportunities given by digital learning and fostering of social accountability to enforce the focus on socially-vulnerable groups such as PLWRD. The strategy has to be developed and implemented by multiple rare disease education and training providers: universities, medical and nursing schools and their associations, professional organizations, European Reference Networks, patient organizations, other organizations and institutions dedicated to rare diseases and rare cancers, authorities and policy bodies.
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Affiliation(s)
- Birute Tumiene
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Harm Peters
- grid.6363.00000 0001 2218 4662Dieter Scheffner Center for Medical Education and Educational Research, Dean’s Office of Study Affairs, Charité - Universitätsmedizin, Berlin, Germany ,Association of Medical Schools in Europe e.V., Berlin, Germany
| | - Bela Melegh
- grid.9679.10000 0001 0663 9479Department of Medical Genetics, and Szentagothai Research Center, University of Pecs, School of Medicine, Pecs, Hungary
| | - Borut Peterlin
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Algirdas Utkus
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania ,Association of Medical Schools in Europe e.V., Berlin, Germany
| | - Natalja Fatkulina
- grid.6441.70000 0001 2243 2806Institute of Health Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - György Pfliegler
- grid.7122.60000 0001 1088 8582Centre for Rare Diseases, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Holm Graessner
- grid.10392.390000 0001 2190 1447Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Sanja Hermanns
- grid.10392.390000 0001 2190 1447Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Maurizio Scarpa
- grid.411492.bRegional Center for Rare Diseases, University Hospital of Udine, Udine, Italy
| | - Jean-Yves Blay
- grid.7849.20000 0001 2150 7757Centre Léon Berard, University Claude Bernard Lyon 1& Unicancer Lyon, Lyon, France
| | - Sharon Ashton
- grid.433753.5EURORDIS - Rare Diseases Europe, Paris, France
| | - Lucy McKay
- Medics4RareDiseases, High Wycombe, England, UK
| | - Gareth Baynam
- grid.1012.20000 0004 1936 7910Telethon Kids Institute and the Faculty of Health and Medical Sciences, Division of Paediatrics, He University of Western Australia, Nedlands, WA Australia ,grid.413880.60000 0004 0453 2856Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Perth, WA Australia ,Rare Care Centre, Child and Adolescent Health Service, Perth, WA Australia
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22
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Wilson YA, Smithers‐Sheedy H, Ostojic K, Waight E, Kruer MC, Fahey MC, Baynam G, Gécz J, Badawi N, McIntyre S. Common data elements to standardize genomics studies in cerebral palsy. Dev Med Child Neurol 2022; 64:1470-1476. [PMID: 35441707 PMCID: PMC9790418 DOI: 10.1111/dmcn.15245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 01/31/2023]
Abstract
AIM To define clinical common data elements (CDEs) and a mandatory minimum data set (MDS) for genomic studies of cerebral palsy (CP). METHOD Candidate data elements were collated following a review of the literature and existing CDEs. An online, three-round Delphi survey was used to rate each data element as either 'core', 'recommended', 'exploratory', or 'not required'. Members of the International Cerebral Palsy Genomics Consortium (ICPGC) rated the core CDEs as either mandatory or not, to form the MDS. For both the CDEs and the MDS, a data element was considered to have reached consensus if more than 75% of respondents agreed. RESULTS Forty-six individuals from around the world formed the Delphi panel: consumers (n=2), scientists/researchers (n=17), medical (n=19), and allied health professionals (n=8). The CDEs include 107 data elements across six categories: demographics, diagnostics, family history, antenatal and neonatal details, clinical traits, and CP-specific assessments. Of these, 10 are mandatory, 42 core, 41 recommended, and 14 are exploratory. INTERPRETATION The ICPGC CDEs provide a foundation for the standardization of phenotype data captured in CP genomic studies and will benefit international collaborations and pooling of data, particularly in rare conditions. WHAT THIS PAPER ADDS A set of 107 common data elements (CDEs) for genomics studies in cerebral palsy is provided. The CDEs include standard definitions and data values domains. The CDEs will facilitate international data sharing, collaboration, and improved clinical interpretation of findings.
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Affiliation(s)
- Yana A. Wilson
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Hayley Smithers‐Sheedy
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Katarina Ostojic
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Emma Waight
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Michael C. Kruer
- Pediatric Movement Disorders ProgramBarrow Neurological InstitutePhoenixArizonaUSA,Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in GeneticsUniversity of Arizona College of MedicinePhoenixArizonaUSA
| | | | | | - Gareth Baynam
- Western Australian Register of Developmental Anomalies King Edward Memorial HospitalPerthWAAustralia,Faculty of Health and Medical Sciences, Division of PaediatricsUniversity of Western AustraliaPerthWAAustralia,Institute for Immunology and Infectious DiseasesMurdoch UniversityPerthWAAustralia,Telethon Kids InstituteUniversity of Western AustraliaWAAustralia,Spatial Sciences, Department of Science and EngineeringCurtin UniversityWAAustralia
| | - Jozef Gécz
- Robinson Research InstituteThe University of AdelaideAdelaideSAAustralia,Adelaide Medical SchoolThe University of AdelaideSAAustralia,South Australian Health and Medical Research InstituteAdelaideSAAustralia
| | - Nadia Badawi
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Grace Centre for Newborn Intensive Care, The Children's Hospital at WestmeadWestmeadNSWAustralia
| | - Sarah McIntyre
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Cerebral Palsy Alliance Research Institute, Specialty of Child & Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia,Telethon Kids InstituteUniversity of Western AustraliaWAAustralia
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23
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Halliday BJ, Baynam G, Ewans L, Greenhalgh L, Leventer RJ, Pilz DT, Sachdev R, Scheffer IE, Markie DM, McGillivray G, Robertson SP, Mandelstam S. Distinctive Brain Malformations in Zhu-Tokita-Takenouchi-Kim Syndrome. AJNR Am J Neuroradiol 2022; 43:1660-1666. [PMID: 36229163 PMCID: PMC9731255 DOI: 10.3174/ajnr.a7663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND PURPOSE Zhu-Tokita-Takenouchi-Kim syndrome is a severe multisystem malformation disorder characterized by developmental delay and a diverse array of congenital abnormalities. However, these currently identified phenotypic components provide limited guidance in diagnostic situations, due to both the nonspecificity and variability of these features. Here we report a case series of 7 individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome, 5 ascertained by their presentation with the neuronal migration disorder, periventricular nodular heterotopia. MATERIALS AND METHODS Individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome were recruited from 2 sources, a high-throughput sequencing study of individuals with periventricular nodular heterotopia or from clinical diagnostic sequencing studies. We analyzed available brain MR images of recruited individuals to characterize periventricular nodular heterotopia distribution and to identify the presence of any additional brain abnormalities. RESULTS Pathogenic variants in SON, causative of Zhu-Tokita-Takenouchi-Kim syndrome, were identified in 7 individuals. Brain MR images from these individuals were re-analyzed. A characteristic set of imaging anomalies in addition to periventricular nodular heterotopia was identified, including the elongation of the pituitary stalk, cerebellar enlargement with an abnormally shaped posterior fossa, rounding of the caudate nuclei, hippocampal malformations, and cortical anomalies including polymicrogyria or dysgyria. CONCLUSIONS The recurrent neuroradiologic changes identified here represent an opportunity to guide diagnostic formulation of Zhu-Tokita-Takenouchi-Kim syndrome on the basis of brain MR imaging evaluation.
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Affiliation(s)
- B J Halliday
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - G Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia (G.B.), Undiagnosed Diseases Program, King Edward Memorial Hospital, Perth, Australia
| | - L Ewans
- Centre for Population Genomics (L.E.), Garvan Institute of Medical Research, Sydney, Australia
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - L Greenhalgh
- Liverpool Centre for Genomic Medicine (L.G.), Liverpool Women's Hospital, Liverpool, England
| | - R J Leventer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Departments of Neurology (R.J.L., I.E.S.)
| | - D T Pilz
- West of Scotland Genetics Service (D.T.P.), Queen Elizabeth University Hospital, Glasgow, UK
| | - R Sachdev
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - I E Scheffer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Austin Health (I.E.S.)
- Florey Institute (I.E.S.), University of Melbourne, Melbourne, Australia
- Departments of Neurology (R.J.L., I.E.S.)
| | - D M Markie
- Pathology (D.M.M.), OtagoMedical School, University of Otago, Dunedin, New Zealand
| | - G McGillivray
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Victorian Clinical Genetics Services (G.M.), Murdoch Children's Research Institute, Melbourne, Australia
| | - S P Robertson
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - S Mandelstam
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Radiology (S.M.), Royal Children's Hospital, Melbourne, Australia
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24
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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25
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Ta D, Downs J, Baynam G, Wilson A, Richmond P, Schmidt A, Decker A, Leonard H. Development of an International Database for a Rare Genetic Disorder: The MECP2 Duplication Database (MDBase). Children 2022; 9:children9081111. [PMID: 35892614 PMCID: PMC9332564 DOI: 10.3390/children9081111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
The natural history of MECP2 duplication syndrome (MDS), a rare X-linked neurodevelopmental disorder with an estimated birth prevalence of 1/150,000 live births, is poorly understood due to a lack of clinical data collected for research. Such information is critical to the understanding of disease progression, therapeutic endpoints and outcome measures for clinical trials, as well as the development of therapies and orphan products. This clinical information can be systematically collected from caregivers through data collation efforts—yet, no such database has existed for MDS before now. Here, in this methodological study, we document the development, launch and management of the international MECP2 Duplication Database (MDBase). The MDBase consists of an extensive family questionnaire that collects information on general medical history, system-specific health problems, medication and hospitalisation records, developmental milestones and function, and quality of life (for individuals with MDS, and their caregivers). Launched in 2020, in its first two years of operation the MDBase has collected clinical data from 154 individuals from 26 countries—the largest sample size to date. The success of this methodology for the establishment and operation of the MDBase may provide insight and aid in the development of databases for other rare neurodevelopmental disorders.
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Affiliation(s)
- Daniel Ta
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
| | - Jenny Downs
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
- Curtin School of Allied Health, Curtin University, Bentley, WA 6102, Australia
| | - Gareth Baynam
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
- Rare Care Centre, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA 6904, Australia
| | - Andrew Wilson
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
- Curtin School of Allied Health, Curtin University, Bentley, WA 6102, Australia
- North Entrance, Perth Children’s Hospital, 15 Hospital Ave, Nedlands, WA 6009, Australia
- Discipline of Paediatrics, School of Medicine, University of Western Australia, Perth, WA 6009, Australia
| | - Peter Richmond
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
- North Entrance, Perth Children’s Hospital, 15 Hospital Ave, Nedlands, WA 6009, Australia
- Discipline of Paediatrics, School of Medicine, University of Western Australia, Perth, WA 6009, Australia
| | - Aron Schmidt
- MECP2 Duplication Foundation, Tuscon, AZ 85724, USA; (A.S.); (A.D.)
| | - Amelia Decker
- MECP2 Duplication Foundation, Tuscon, AZ 85724, USA; (A.S.); (A.D.)
- Department of Paediatrics, University of Arizona College of Medicine, Tuscon, AZ 85724, USA
| | - Helen Leonard
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (D.T.); (J.D.); (G.B.); (A.W.); (P.R.)
- Correspondence:
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26
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Matthews H, Vanneste M, Katsura K, Aponte D, Patton M, Hammond P, Baynam G, Spritz R, Klein OD, Hallgrimsson B, Peeters H, Claes P. Refining nosology by modelling variation among facial phenotypes: the RASopathies. J Med Genet 2022; 60:jmedgenet-2021-108366. [PMID: 35858754 PMCID: PMC9852361 DOI: 10.1136/jmedgenet-2021-108366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/18/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND In clinical genetics, establishing an accurate nosology requires analysis of variations in both aetiology and the resulting phenotypes. At the phenotypic level, recognising typical facial gestalts has long supported clinical and molecular diagnosis; however, the objective analysis of facial phenotypic variation remains underdeveloped. In this work, we propose exploratory strategies for assessing facial phenotypic variation within and among clinical and molecular disease entities and deploy these techniques on cross-sectional samples of four RASopathies: Costello syndrome (CS), Noonan syndrome (NS), cardiofaciocutaneous syndrome (CFC) and neurofibromatosis type 1 (NF1). METHODS From three-dimensional dense surface scans, we model the typical phenotypes of the four RASopathies as average 'facial signatures' and assess individual variation in terms of direction (what parts of the face are affected and in what ways) and severity of the facial effects. We also derive a metric of phenotypic agreement between the syndromes and a metric of differences in severity along similar phenotypes. RESULTS CFC shows a relatively consistent facial phenotype in terms of both direction and severity that is similar to CS and NS, consistent with the known difficulty in discriminating CFC from NS based on the face. CS shows a consistent directional phenotype that varies in severity. Although NF1 is highly variable, on average, it shows a similar phenotype to CS. CONCLUSIONS We established an approach that can be used in the future to quantify variations in facial phenotypes between and within clinical and molecular diagnoses to objectively define and support clinical nosologies.
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Affiliation(s)
- Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Flemish Brabant, Belgium
- Facial Sciences Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Michiel Vanneste
- Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Flemish Brabant, Belgium
| | - Kaitlin Katsura
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - David Aponte
- Department of Cell Biology and Anatomy, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Michael Patton
- Medical Genetics Unit, St George's University of London, London, UK
| | - Peter Hammond
- Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Western Australia, Australia
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- School of Earth and Planetary Sciences, Faculty of Science and Engineering, Curtin University, Perth, Western Australia, Australia
- Faculty of Medicine, Notre Dame University, Fremantle, Western Australia, Australia
| | - Richard Spritz
- Department of Paediatrics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Flemish Brabant, Belgium
- Facial Sciences Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Electrical Engineering ESAT/PSI, KU Leuven, Leuven, Flemish Brabant, Belgium
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27
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Poulton C, Baynam G, Pugh K, Mason M, Kiraly-Borri C, Gration D, Dreyer L, Viti L, Agostino M, Heng JIT. Further evidence for distinct traits associated with RBM10 missense variants. Clin Genet 2022; 102:161-163. [PMID: 35645043 DOI: 10.1111/cge.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/28/2022]
Abstract
A case of a missense RBM10 variant in an adult with mild to moderate intellectual disability.
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Affiliation(s)
- Cathryn Poulton
- Western Australian Register of Developmental Anomalies, Perth, Australia.,Genetic Services of WA, Government of Western Australia, Perth, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, Perth, Australia.,Genetic Services of WA, Government of Western Australia, Perth, Australia.,Faculty of Health and Medicine, University of Western Australia, Perth, Australia.,Telethon Kids Institute, Perth, Australia.,Faculty of Medicine, University of Notre Dame, Fremantle, Australia.,Faculty of Science and Engineering, Curtin University, Perth, Australia
| | - Kye Pugh
- Curtin Medical School, Curtin University, Bentley, Australia
| | | | | | - Dylan Gration
- Genetic Services of WA, Government of Western Australia, Perth, Australia
| | - Lauren Dreyer
- Genetic Services of WA, Government of Western Australia, Perth, Australia
| | - Leon Viti
- Curtin Medical School, Curtin University, Bentley, Australia
| | - Mark Agostino
- Curtin Medical School, Curtin University, Bentley, Australia.,Curtin Institute for Computation, Bentley, Australia
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28
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Chediak L, Bedlington N, Gadson A, Kent A, Khalek AA, Rosen L, Rust M, Shaikh MF, Tan MY, Wiafe SA, Baynam G, Steward CA. Unlocking sociocultural and community factors for the global adoption of genomic medicine. Orphanet J Rare Dis 2022; 17:191. [PMID: 35549752 PMCID: PMC9097338 DOI: 10.1186/s13023-022-02328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
Advances in genomic sequencing and genetic testing are increasingly transforming the diagnosis and treatment of diseases-specifically, rare diseases. However, the application and benefit of such technologies remain inequitable globally. There is a clear and urgent need to provide genomic sequencing to people across the global population, including people living in under-resourced areas and/or underrepresented populations. Financial considerations are the most obvious barriers to the adoption of genomic medicine, yet there are many other factors that are not so obvious, such as geography, language, communication, and culture. Herein, we use the lens of rare diseases and focus on firstly, selected socio-cultural factors, and in particular stigma; and secondly, empowering community factors such as education, advocacy and connectivity amongst people living with rare diseases globally. These are critical areas of need and opportunity if genomic medicine is to achieve equitable and global adoption in the patient best-interest across low- middle- and high-income country health systems. Furthermore, we touch on specific child health aspects and how they can point towards opportunities to build on specific infrastructures.
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Affiliation(s)
- Lynsey Chediak
- Patient Advocacy and Engagement Advisory Board, Congenica Ltd, Wellcome Genome Campus, Hinxton, CB10 1DR, UK. .,Rarebase PBC, 1804 Embarcadero Road, Palo Alto, CA, 94303, USA.
| | - Nicola Bedlington
- Patient Advocacy and Engagement Advisory Board, Congenica Ltd, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
| | - Ayesha Gadson
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia
| | - Alastair Kent
- Patient Advocacy and Engagement Advisory Board, Congenica Ltd, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
| | - Aiedah Abdul Khalek
- Malaysia Immersion Hub, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Luke Rosen
- Patient Advocacy and Engagement Advisory Board, Congenica Ltd, Wellcome Genome Campus, Hinxton, CB10 1DR, UK.,KIF1A.ORG, 808 Columbus Avenue, New York, NY, 10025, USA
| | - Malisa Rust
- Patient Advocacy and Engagement Advisory Board, Congenica Ltd, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
| | - Mohd Farooq Shaikh
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Meng Yoe Tan
- School of Arts and Social Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | | | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia. .,Rare Care, Clinical Centre of Expertise for Rare and Undiagnosed Diseases, Perth Children's Hospital, Perth, WA, Australia.
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29
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Fear VS, Forbes CA, Anderson D, Rauschert S, Syn G, Shaw N, Jamieson S, Ward M, Baynam G, Lassmann T. CRISPR single base editing, neuronal disease modelling and functional genomics for genetic variant analysis: pipeline validation using Kleefstra syndrome EHMT1 haploinsufficiency. Stem Cell Res Ther 2022; 13:69. [PMID: 35139903 PMCID: PMC8827184 DOI: 10.1186/s13287-022-02740-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Background Over 400 million people worldwide are living with a rare disease. Next Generation Sequencing (NGS) identifies potential disease causative genetic variants. However, many are identified as variants of uncertain significance (VUS) and require functional laboratory validation to determine pathogenicity, and this creates major diagnostic delays. Methods In this study we test a rapid genetic variant assessment pipeline using CRISPR homology directed repair to introduce single nucleotide variants into inducible pluripotent stem cells (iPSCs), followed by neuronal disease modelling, and functional genomics on amplicon and RNA sequencing, to determine cellular changes to support patient diagnosis and identify disease mechanism. Results As proof-of-principle, we investigated an EHMT1 (Euchromatin histone methyltransferase 1; EHMT1 c.3430C > T; p.Gln1144*) genetic variant pathogenic for Kleefstra syndrome and determined changes in gene expression during neuronal progenitor cell differentiation. This pipeline rapidly identified Kleefstra syndrome in genetic variant cells compared to healthy cells, and revealed novel findings potentially implicating the key transcription factors REST and SP1 in disease pathogenesis. Conclusion The study pipeline is a rapid, robust method for genetic variant assessment that will support rare diseases patient diagnosis. The results also provide valuable information on genome wide perturbations key to disease mechanism that can be targeted for drug treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02740-3.
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Affiliation(s)
- Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
| | - Denise Anderson
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Sebastian Rauschert
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Genevieve Syn
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Nicole Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
| | - Sarra Jamieson
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia.,Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Timo Lassmann
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.,Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
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30
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Junaid M, Slack-Smith L, Wong K, Baynam G, Calache H, Hewitt T, Leonard H. Epidemiology of Hospital Admissions for Craniosynostosis in Australia: A Population-Based Study. Cleft Palate Craniofac J 2022. [PMID: 35130078 DOI: 10.1177/105566562210742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
To describe trends, age, and sex-specific patterns of population hospital admissions with a diagnosis of craniosynostosis (CS) in Australia. Population data for hospital separations (in-patient) from public and private hospitals (July 1996-June 2018) were obtained from the publicly available Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database. The outcome variables were hospital separation rates (HSR) (number of hospital separations divided by the estimated resident population [ERP] per year) and average length of stay (aLOS) (patient days divided by the number of hospital separations) with a diagnosis of CS. Trends in HSR and aLOS adjusted for age, sex, and type of CS were investigated by negative binomial regression presented as annual percent change (APC). In 8057 admissions identified, we observed no significant change in the annual trend for HSR for the 22-year period. However, a marginal annual decrease of 1.6% (95% CI: -0.7, -2.4) in the aLOS was identified for the same time period. HSR were higher for males, infants, and single suture synostosis. aLOS was 3.8 days (95% CI: 3.8, 3.9) per visit, longer for syndromic conditions. There was a minor reduction in the average length of hospital stay for CS over the 22-year period potentially indicative of improved care. Population-level information on hospitalisations for rare craniofacial conditions can inform research, clinical, and surgical practice.
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Affiliation(s)
- Mohammed Junaid
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Linda Slack-Smith
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Kingsley Wong
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Gareth Baynam
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Health, 569007Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Hanny Calache
- School of Health and Social Development, Faculty of Health, Deakin Health Economics, Institute of Health Transformation, 91844Deakin University, Geelong, Victoria, Australia.,Department of Dentistry and Oral Health, 56371La Trobe Rural Health School, La Trobe University, Bendigo, Victoria, Australia
| | - Timothy Hewitt
- Department of Plastic Surgery, 60081Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Helen Leonard
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia.,Faculty of Health and Medical Sciences, Centre of Child Health Research, University of Western Australia, Nedlands, Western Australia, Australia
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31
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Junaid M, Slack-Smith L, Wong K, Baynam G, Calache H, Hewitt T, Leonard H. Epidemiology of Hospital Admissions for Craniosynostosis in Australia: A Population-Based Study. Cleft Palate Craniofac J 2022; 60:569-576. [PMID: 35130078 DOI: 10.1177/10556656221074215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To describe trends, age, and sex-specific patterns of population hospital admissions with a diagnosis of craniosynostosis (CS) in Australia. Population data for hospital separations (in-patient) from public and private hospitals (July 1996-June 2018) were obtained from the publicly available Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database. The outcome variables were hospital separation rates (HSR) (number of hospital separations divided by the estimated resident population [ERP] per year) and average length of stay (aLOS) (patient days divided by the number of hospital separations) with a diagnosis of CS. Trends in HSR and aLOS adjusted for age, sex, and type of CS were investigated by negative binomial regression presented as annual percent change (APC). In 8057 admissions identified, we observed no significant change in the annual trend for HSR for the 22-year period. However, a marginal annual decrease of 1.6% (95% CI: -0.7, -2.4) in the aLOS was identified for the same time period. HSR were higher for males, infants, and single suture synostosis. aLOS was 3.8 days (95% CI: 3.8, 3.9) per visit, longer for syndromic conditions. There was a minor reduction in the average length of hospital stay for CS over the 22-year period potentially indicative of improved care. Population-level information on hospitalisations for rare craniofacial conditions can inform research, clinical, and surgical practice.
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Affiliation(s)
- Mohammed Junaid
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Linda Slack-Smith
- School of Population and Global Health, The University of Western Australia, Nedlands, Western Australia, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Kingsley Wong
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Gareth Baynam
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Health, 569007Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Hanny Calache
- School of Health and Social Development, Faculty of Health, Deakin Health Economics, Institute of Health Transformation, 91844Deakin University, Geelong, Victoria, Australia.,Department of Dentistry and Oral Health, 56371La Trobe Rural Health School, La Trobe University, Bendigo, Victoria, Australia
| | - Timothy Hewitt
- Department of Plastic Surgery, 60081Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Helen Leonard
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia, Australia.,Faculty of Health and Medical Sciences, Centre of Child Health Research, University of Western Australia, Nedlands, Western Australia, Australia
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32
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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33
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Khoshnood B, Baynam G, Loane M, Rissmann A, Botto L. Editorial: Congenital anomalies: State of the art and the new paradigms for a precision public health approach. Front Pediatr 2022; 10:968923. [PMID: 35923780 PMCID: PMC9340261 DOI: 10.3389/fped.2022.968923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Babak Khoshnood
- INSERM U1153 Centre de Recherche Épidémiologie et Statistique, Paris, France
| | - Gareth Baynam
- University of Western Australia, Perth, WA, Australia
| | - Maria Loane
- Faculty of Life and Health Sciences, Ulster University, Northern Ireland, United Kingdom
| | | | - Lorenzo Botto
- University of Utah Medical Center, Salt Lake City, UT, United States
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34
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Shah M, Selvanathan A, Baynam G, Berman Y, Boughtwood T, Freckmann M, Parasivam G, White SM, Grainger N, Kirk EP, Ma ASL, Sachdev R. Paediatric genomic testing: Navigating genomic reports for the general paediatrician. J Paediatr Child Health 2022; 58:8-15. [PMID: 34427008 PMCID: PMC9292248 DOI: 10.1111/jpc.15703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
Monogenic rare disorders contribute significantly to paediatric morbidity and mortality, and elucidation of the underlying genetic cause may have benefits for patients, families and clinicians. Advances in genomic technology have enabled diagnostic yields of up to 50% in some paediatric cohorts. This has led to an increase in the uptake of genetic testing across paediatric disciplines. This can place an increased burden on paediatricians, who may now be responsible for interpreting and explaining test results to patients. However, genomic results can be complex, and sometimes inconclusive for the ordering paediatrician. Results may also cause uncertainty and anxiety for patients and their families. The paediatrician's genetic literacy and knowledge of genetic principles are therefore critical to inform discussions with families and guide ongoing patient care. Here, we present four hypothetical case vignettes where genomic testing is undertaken, and discuss possible results and their implications for paediatricians and families. We also provide a list of key terms for paediatricians.
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Affiliation(s)
- Margit Shah
- Centre for Clinical GeneticsSydney Children's Hospital, Sydney Children's Hospitals NetworkSydneyNew South WalesAustralia,Department of Clinical GeneticsChildren's Hospital at Westmead, Sydney Children's Hospitals NetworkSydneyNew South WalesAustralia,Faculty of Health and Medical ScienceUniversity of SydneySydneyNew South WalesAustralia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders ServiceSydney Children's Hospitals NetworkSydneyNew South WalesAustralia
| | - Gareth Baynam
- Genetic Services of Western AustraliaKing Edward Memorial HospitalPerthWestern AustraliaAustralia,Western Australian Register of Developmental AnomaliesKing Edward Memorial HospitalPerthWestern AustraliaAustralia
| | - Yemima Berman
- Department of Clinical GeneticsRoyal North Shore HospitalSydneyNew South WalesAustralia,Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Tiffany Boughtwood
- Australian GenomicsMelbourneVictoriaAustralia,Murdoch Children’s Research InstituteMelbourneVictoriaAustralia
| | - Mary‐Louise Freckmann
- Department of Clinical GeneticsRoyal North Shore HospitalSydneyNew South WalesAustralia,ACT Genetics ServiceThe Canberra HospitalCanberraAustralian Capital TerritoryAustralia
| | - Gayathri Parasivam
- NSW Health Centre for Genetics EducationRoyal North Shore HospitalSydneyNew South WalesAustralia,Present address:
Women's and Children's HospitalAdelaideSouth AustraliaAustralia
| | - Susan M White
- Victorian Clinical Genetics ServicesMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Natalie Grainger
- NSW Health Centre for Genetics EducationRoyal North Shore HospitalSydneyNew South WalesAustralia
| | - Edwin P Kirk
- Centre for Clinical GeneticsSydney Children's Hospital, Sydney Children's Hospitals NetworkSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia,NSW Health Pathology Randwick Genomics LaboratorySydneyNew South WalesAustralia
| | - Alan SL Ma
- Department of Clinical GeneticsChildren's Hospital at Westmead, Sydney Children's Hospitals NetworkSydneyNew South WalesAustralia,Specialty of Genomic MedicineUniversity of SydneySydneyNew South WalesAustralia
| | - Rani Sachdev
- Centre for Clinical GeneticsSydney Children's Hospital, Sydney Children's Hospitals NetworkSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
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35
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Saggu H, Jones C, Lewis A, Baynam G. mEDUrare: Supporting Integrated Care for Rare Diseases by Better Connecting Health and Education Through Policy. Yale J Biol Med 2021; 94:693-702. [PMID: 34970108 PMCID: PMC8686785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Rare diseases affect an estimated 6-10% of the Australian population, a prevalence similar to that seen in other regions worldwide. These multi-system conditions are often severely debilitating and affect multiple domains of a person's life. A salient necessity for effective care provision thus, is holistic care, achieved by appropriate and continual multi-disciplinary and cross-sectoral collaboration. Synonymous with this priority for collaborative care, is the need for increased partnerships between the health and education sectors. This partnership has the potential to benefit people with rare disease of all educational ages, but in particular, school-aged children and young adults. More than 70% of rare diseases affect children, and this population often experiences difficulties with overall well-being and functioning, including impaired school performance and confounding mental and social comorbidities. Ensuring adequate schooling needs and experiences along with provision of adequate medical care, is crucial in ensuring overall well-being for this population. For this, effective partnerships between the health and education sectors are paramount. This article highlights fundamental elements of health and education priorities, ingrained in current strategic documents, to build a policy foundation that informs and supports increased inter-sectoral partnerships between health and education services. Shared priorities identified in both sectors' guidelines, co-developed with those with lived experience of rare diseases, build a strong policy base for future advocative initiatives to mold better integration between the sectors, a partnership which is vital to improving the overall quality of life, experiences and journeys of people living with rare disease.
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Affiliation(s)
- Harleen Saggu
- Faculty of Health & Medical Sciences, The
University of Western Australia, Perth, Australia,To whom all correspondence should be addressed:
Harleen Saggu, Faculty of Health & Medical Sciences, The University of
Western Australia, Perth, Australia;
| | - Caleb Jones
- Department of Education, School of Special Education
Needs, Government of Western Australia, Perth, Australia
| | - Amber Lewis
- Methodist Ladies College, Claremont, Western
Australia, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth,
Australia
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36
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Matthews L, Chin V, Taliangis M, Samanek A, Baynam G. Childhood rare diseases and the UN convention on the rights of the child. Orphanet J Rare Dis 2021; 16:523. [PMID: 34952617 PMCID: PMC8709987 DOI: 10.1186/s13023-021-02153-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
This letter discusses an initiative that considered the rights of a child living with a rare disease in the context of the United Nations Convention on the Rights of the Child (UNCRC). The aim was to inform laypeople on the intersection between the UNCRC and rare and undiagnosed diseases. The Project was initiated in Western Australia for a national audience, with a view that it might also provide a framework that is translatable to other jurisdictions internationally. This letter discusses some of the key themes raised by the Project and the potential for further work.
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Affiliation(s)
| | - Vaughan Chin
- University of Western Australia, Perth, Australia
| | | | | | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, Department of Health Western Australia, King Edward Memorial Hospital, Perth, Australia.
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37
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Liu P, Gong M, Li J, Baynam G, Zhu W, Zhu Y, Chen L, Gu W, Zhang S. Innovation in Informatics to Improve Clinical Care and Drug Accessibility for Rare Diseases in China. Front Pharmacol 2021; 12:719415. [PMID: 34721018 PMCID: PMC8553959 DOI: 10.3389/fphar.2021.719415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background: In China, there are severe unmet medical needs of people living with rare diseases. Relatedly, there is a dearth of data to inform rare diseases policy. This is historically partially due to the lack of informatics infrastructure, including standards and terminology, data sharing mechanisms and network; and concerns over patient privacy protection. Objective: This study aims to introduce the progress of China's rare disease informatics platform and knowledgebase, and to discuss critical enablers of rare disease informatics innovation, including: data standardization; knowledgebase construction; national policy support; and multi-stakeholder participation. Methods: A systemic national strategy, delivered through multi-stakeholder engagement, has been implemented to create and accelerate the informatics infrastructure to support rare diseases management. This includes a disease registry system, together with more than 80 hospitals, to perform comprehensive research information collection, including clinical, genomic and bio-sample data. And a case reporting system, with a network of 324 hospitals, covering all mainland Chinese provinces, to further support reporting of rare diseases data. International standards were incorporated, and privacy issues were addressed through HIPAA compliant rules. Results: The National Rare Diseases Registry System of China (NRDRS) now covers 166 rare diseases and more than 63,000 registered patients. The National Rare Diseases Case Reporting System of China (NRDCRS) was primarily founded on the National Network of Rare Diseases (NNRD) of 324 hospitals and focused on real-time rare diseases case reporting; more than 400,000 cases have been reported. Based on the data available in the two systems, the National Center for Health Technology Assessment (HTA) of Orphan Medicinal Products (OMP) has been established and the expert consensus on HTA of OMP was produced. The largest knowledgebase for rare disease in Chinese has also been developed. Conclusion: A national strategy and the coordinating mechanism is the key to success in the improvement of Chinese rare disease clinical care and drug accessibility. Application of innovative informatics solutions can help accelerate the process, improve quality and increase efficiency.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Mengchun Gong
- Institute of Health Management, Southern Medical University, Guangzhou, China
| | - Jie Li
- Digital Health China Technologies Co., LTD, Beijing, China
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, WA, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, WA, Australia
| | - Weiguo Zhu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yicheng Zhu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Limeng Chen
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Weihong Gu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Wilson YA, McIntyre S, Waight E, Thornton M, van Otterloo S, Marmont SR, Kruer M, Baynam G, Gecz J, Badawi N. People with Cerebral Palsy and Their Family's Preferences about Genomics Research. Public Health Genomics 2021; 25:1-10. [PMID: 34537775 DOI: 10.1159/000518942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The goal of this study was to understand individuals with cerebral palsy (CP) and their family's attitudes and preferences to genomic research, including international data sharing and biobanking. METHODS Individuals with CP and their family members were invited to participate in the web-based survey via email (NSW/ACT CP Register) or via posts on social media by Cerebral Palsy Alliance, CP Research Network, and CP Now. Survey responses included yes/no/unsure, multiple choices, and Likert scales. Fisher's exact and χ2 tests were used to assess if there were significant differences between subgroups. RESULTS Individuals with CP and their families (n = 145) were willing to participate in genomics research (68%), data sharing (82%), and biobanking efforts (75%). This willingness to participate was associated with completion of tertiary education, previous genetic testing experience, overall higher genomic awareness, and trust in international researchers. The survey respondents also expressed ongoing communication and diverse information needs regarding the use of their samples and data. Major concerns were associated with privacy and data security. DISCUSSION The success of genomic research and international data sharing efforts in CP are contingent upon broad support and recruitment. Ongoing consultation and engagement of individuals with CP and their families will facilitate trust and promote increased awareness of genomics in CP that may in turn maximize participant uptake and recruitment.
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Affiliation(s)
- Yana Alexandra Wilson
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Cerebral Palsy Alliance, Sydney, New South Wales, Australia
| | - Sarah McIntyre
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Cerebral Palsy Alliance, Sydney, New South Wales, Australia
| | - Emma Waight
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Cerebral Palsy Alliance, Sydney, New South Wales, Australia
| | - Marelle Thornton
- CP Quest, Cerebral Palsy Alliance, Sydney, New South Wales, Australia
| | | | | | - Michael Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Gareth Baynam
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, Washington, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, Washington, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Washington, Australia
- Telethon Kids Institute, University of Western Australia, Perth, Washington, Australia
- Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, Washington, Australia
| | - Jozef Gecz
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Sciences Institute, Adelaide, South Australia, Australia
| | - Nadia Badawi
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Cerebral Palsy Alliance, Sydney, New South Wales, Australia
- Grace Centre for Newborn Care, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
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Nunez C, Morris A, Jones CA, Badawi N, Baynam G, Hansen M, Elliott EJ. Microcephaly in Australian children, 2016-2018: national surveillance study. Arch Dis Child 2021; 106:849-854. [PMID: 33229416 DOI: 10.1136/archdischild-2020-320456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To describe infants aged <12 months reported with microcephaly to the Australian Paediatric Surveillance Unit (APSU) following emergence of Zika virus infection internationally. DESIGN, SETTING AND PATIENTS National, active, monthly surveillance for microcephaly using the APSU. Microcephaly was defined as occipitofrontal circumference (OFC) of more than 2 SDs below the mean for age, gender and gestation. MAIN OUTCOME MEASURES Clinical spectrum, aetiology and birth prevalence of microcephaly reported by paediatricians. RESULTS Between June 2016 and July 2018, 106 notifications were received, with clinical details provided for 96 (91%). After excluding ineligible notifications, 70 cases were confirmed, giving an annual birth prevalence of 1.12 (95% CI 0.88 to 1.42) per 10 000 live births. Of the total number of cases, 47 (67%) had primary microcephaly (at birth); and 25 (36%) had severe microcephaly (OFC >3 SDs). Birth defects were reported in 42 (60%). Of 49 infants with developmental assessment details available, 25 (51%) had failed to reach all milestones. Vision impairment was reported in 14 (26%). The cause of microcephaly was unknown in 60%: 13 (19%) had been diagnosed with genetic disorders; 22 (39%) had anomalies on neuroimaging. No congenital or probable Zika infection was identified. Severe microcephaly was more often associated with hearing impairment than microcephaly of >2 SDs but ≤3 SDs below the mean (p<0.007). Indigenous children and children with socioeconomic advantage were over-represented among children with microcephaly. CONCLUSION Novel national data on microcephaly highlight the high proportion of idiopathic cases. This has implications for prevention and management and suggests the need for a standardised diagnostic approach and ongoing surveillance mechanism in Australia.
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Affiliation(s)
- Carlos Nunez
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia .,The Australian Paediatric Surveillance Unit, Sydney, New South Wales, Australia
| | - Anne Morris
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,The Australian Paediatric Surveillance Unit, Sydney, New South Wales, Australia.,The Sydney Children's Hospitals Network (Westmead), Sydney, NSW, Australia
| | - Cheryl A Jones
- The Sydney Children's Hospitals Network (Westmead), Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Nadia Badawi
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,The Sydney Children's Hospitals Network (Westmead), Sydney, NSW, Australia.,Professor of Cerebral Plasy, Macquarie Group Foundation, The CP Research Institute, Sydney, NSW, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital Perth, Perth, Western Australia, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Michele Hansen
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Elizabeth J Elliott
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia.,The Australian Paediatric Surveillance Unit, Sydney, New South Wales, Australia.,The Sydney Children's Hospitals Network (Westmead), Sydney, NSW, Australia
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40
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Junaid M, Slack-Smith L, Wong K, Baynam G, Calache H, Hewitt T, Leonard H. Description of Total Population Hospital Admissions for Treacher Collins Syndrome in Australia. Cleft Palate Craniofac J 2021; 59:1167-1175. [PMID: 34410170 DOI: 10.1177/10556656211036618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe patterns and demographic characteristics of total-population hospital admissions with a diagnosis of Treacher Collins syndrome (TCS) in Australia. DATA SOURCE Population summary data for inpatient hospitals admissions (public and private) with a principal diagnosis of TCS (ICD10-AM-Q87.04) were obtained from the Australian Institute of Health and Welfare National Hospital Morbidity Database for a 11-year period (2002-2013). MAIN OUTCOME MEASURES The primary outcome was hospital separation rate (HSR), calculated by dividing the number of hospital separations by estimated resident population per year. Trends in HSR s adjusted for age and sex were investigated by negative binomial regression presented as annual percent change and the association of rates with age and sex was expressed as incidence rate ratio. RESULTS In 244 admissions identified, we observed an increase of 4.55% (95% confidence interval [CI] -1.78, 11.29) in HSR's over the 11-year period. Rates were higher during infancy (1.87 [95% CI 1.42, 2.42]), declining markedly with increasing age. The average length of hospital stay was 6.09 days (95% CI 5.78, 6.40) per episode, but longer for females and infants. CONCLUSIONS Findings indicate an increase in hospitalization rates, especially among infants and females which potentially relates to early airway intervention procedures possibly influenced by sex specific-disease severity and phenotypic variability of TCS. Awareness of the TCS phenotype and improved access to genetic testing may support more personalized and efficient care. Total-population administrative data offers a potential to better understand the health burden of rare craniofacial diseases.
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Affiliation(s)
- Mohammed Junaid
- School of Population and Global Health, The University of Western Australia, Nedlands, WA, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Linda Slack-Smith
- School of Population and Global Health, The University of Western Australia, Nedlands, WA, Australia.,117610Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Kingsley Wong
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Gareth Baynam
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia.,569007Genetic Services of Western Australia, Perth, WA, Australia
| | - Hanny Calache
- Institute of Health Transformation, School of Health and Social Development, 91844Deakin University, Geelong, VIC, Australia.,56371La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | | | - Helen Leonard
- 117610Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
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Singh R, Cohen ASA, Poulton C, Hjortshøj TD, Akahira-Azuma M, Mendiratta G, Khan WA, Azmanov DN, Woodward KJ, Kirchhoff M, Shi L, Edelmann L, Baynam G, Scott SA, Jabs EW. Deletion of ERF and CIC causes abnormal skull morphology and global developmental delay. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005991. [PMID: 34117072 PMCID: PMC8208047 DOI: 10.1101/mcs.a005991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
The ETS2 repressor factor (ERF) is a transcription factor in the RAS-MEK-ERK signal transduction cascade that regulates cell proliferation and differentiation, and pathogenic sequence variants in the ERF gene cause variable craniosynostosis inherited in an autosomal dominant pattern. The reported ERF variants are largely loss-of-function, implying haploinsufficiency as a primary disease mechanism; however, ERF gene deletions have not been reported previously. Here we describe three probands with macrocephaly, craniofacial dysmorphology, and global developmental delay. Clinical genetic testing for fragile X and other relevant sequencing panels were negative; however, chromosomal microarray identified heterozygous deletions (63.7–583.2 kb) on Chromosome 19q13.2 in each proband that together included five genes associated with Mendelian diseases (ATP1A3, ERF, CIC, MEGF8, and LIPE). Parental testing indicated that the aberrations were apparently de novo in two of the probands and were inherited in the one proband with the smallest deletion. Deletion of ERF is consistent with the reported loss-of-function ERF variants, prompting clinical copy-number-variant classifications of likely pathogenic. Moreover, the recent characterization of heterozygous loss-of-function CIC sequence variants as a cause of intellectual disability and neurodevelopmental disorders inherited in an autosomal dominant pattern is also consistent with the developmental delays and intellectual disabilities identified among the two probands with CIC deletions. Taken together, this case series adds to the previously reported patients with ERF and/or CIC sequence variants and supports haploinsufficiency of both genes as a mechanism for a variable syndromic cranial phenotype with developmental delays and intellectual disability inherited in an autosomal dominant pattern.
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Affiliation(s)
- Ram Singh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ana S A Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Cathryn Poulton
- Genetic Service of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Moe Akahira-Azuma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Wahab A Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Dimitar N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Karen J Woodward
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia.,Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia 6008, Australia.,Faculty of Medicine, University of Notre Dame, Australia, Perth, Western Australia 6160, Australia
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Koromina M, Fanaras V, Baynam G, Mitropoulou C, Patrinos GP. Ethics and equity in rare disease research and healthcare. Per Med 2021; 18:407-416. [PMID: 34085867 DOI: 10.2217/pme-2020-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid advances in next-generation sequencing technology, particularly whole exome sequencing and whole genome sequencing, have greatly affected our understanding of genetic variation underlying rare genetic diseases. Herein, we describe ethical principles of guiding consent and sharing of genomics research data. We also discuss ethical dilemmas in rare diseases research and patient recruitment policies and address bioethical and societal aspects influencing the ethical framework for genetic testing. Moreover, we focus on addressing ethical issues surrounding research in low- and middle-income countries. Overall, this perspective aims to address key aspects and issues for building proper ethical frameworks, when conducting research involving genomics data with a particular emphasis on rare diseases and genetics testing.
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Affiliation(s)
- Maria Koromina
- Department of Pharmacy, Laboratory of Pharmacogenomics & Individualized Therapy, School of Health Sciences, University of Patras, Patras, Greece
| | - Vasileios Fanaras
- The Golden Helix Foundation, London, UK.,School of Theology, Faculty of Social Theology & the Study of Religion, National & Kapodistrian University of Athens, Athens, Greece
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Western Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia.,Telethon Kids Institute & Division of Pediatrics, School of Health & Medical Sciences, University of Western Australia, Perth, Australia.,Faculty of Medicine, Notre Dame University, Australia
| | | | - George P Patrinos
- Department of Pharmacy, Laboratory of Pharmacogenomics & Individualized Therapy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE
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Mannucci I, Dang NDP, Huber H, Murry JB, Abramson J, Althoff T, Banka S, Baynam G, Bearden D, Beleza-Meireles A, Benke PJ, Berland S, Bierhals T, Bilan F, Bindoff LA, Braathen GJ, Busk ØL, Chenbhanich J, Denecke J, Escobar LF, Estes C, Fleischer J, Groepper D, Haaxma CA, Hempel M, Holler-Managan Y, Houge G, Jackson A, Kellogg L, Keren B, Kiraly-Borri C, Kraus C, Kubisch C, Le Guyader G, Ljungblad UW, Brenman LM, Martinez-Agosto JA, Might M, Miller DT, Minks KQ, Moghaddam B, Nava C, Nelson SF, Parant JM, Prescott T, Rajabi F, Randrianaivo H, Reiter SF, Schuurs-Hoeijmakers J, Shieh PB, Slavotinek A, Smithson S, Stegmann APA, Tomczak K, Tveten K, Wang J, Whitlock JH, Zweier C, McWalter K, Juusola J, Quintero-Rivera F, Fischer U, Yeo NC, Kreienkamp HJ, Lessel D. Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders. Genome Med 2021; 13:90. [PMID: 34020708 PMCID: PMC8140440 DOI: 10.1186/s13073-021-00900-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00900-3.
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Affiliation(s)
- Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Nghi D P Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Hannes Huber
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Jaclyn B Murry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thorsten Althoff
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gareth Baynam
- Faculty of Medicine and Health Sciences, University of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - David Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Ana Beleza-Meireles
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Luis F Escobar
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Caroline Estes
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yolanda Holler-Managan
- Division of Neurology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Ulf W Ljungblad
- Department of Pediatrics, Vestfold Hospital, 3116, Tønsberg, Norway
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kelly Q Minks
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | | | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA.,Center for Duchenne Muscular Dystrophy, University of California Los Angeles, Los Angeles, CA, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanitra Randrianaivo
- UF de Génétique Médicale, GHSR, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Simone F Reiter
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | | | - Perry B Shieh
- Department of Neurology at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Smithson
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kinga Tomczak
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Jordan H Whitlock
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | | | | | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA.
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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McKenzie F, Mina K, Callewaert B, Beyens A, Dickinson JE, Jevon G, Papadimitriou J, Diness BR, Steensberg JN, Ek J, Baynam G. Severe congenital cutis laxa: Identification of novel homozygous LOX gene variants in two families. Clin Genet 2021; 100:168-175. [PMID: 33866545 DOI: 10.1111/cge.13969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022]
Abstract
We report three babies from two families with a severe lethal form of congenital cutis laxa. All three had redundant and doughy-textured skin and two siblings from one family had facial dysmorphism. Echocardiograms showed thickened and poorly contractile hearts, arterial dilatation and tortuosity. Post-mortem examination in two of the babies further revealed widespread ectasia and tortuosity of medium and large sized arteries, myocardial hypertrophy, rib and skull fractures. The presence of fractures initially suggested a diagnosis of osteogenesis imperfecta. Under light microscopy bony matrices were abnormal and arterial wall architecture was grossly abnormal showing fragmented elastic fibres. Molecular analysis of known cutis laxa genes did not yield any pathogenic defects. Whole exome sequencing of DNA following informed consent identified two separate homozygous variants in the LOX (Lysyl Oxidase) gene. LOX belongs to the 5-lysyl oxidase gene family involved in initiation of cross-linking of elastin and collagen. A mouse model of a different variant in this gene recapitulates the phenotype seen in the three babies. Our findings suggest that the LOX gene is a novel cause of severe congenital cutis laxa with arterial tortuosity, bone fragility and respiratory failure.
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Affiliation(s)
- Fiona McKenzie
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Kym Mina
- Department of Diagnostic Genomics, PathWest, Perth, Western Australia, Australia
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Aude Beyens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jan E Dickinson
- Maternal Fetal Medicine Service, King Edward Memorial Hospital, Perth, Western Australia, Australia.,Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia
| | - Gareth Jevon
- Department of Paediatric Pathology, PathWest, Perth Children's Hospital, Perth, Western Australia, Australia
| | - John Papadimitriou
- Centre for Orthopaedic Translational Research, Medical School, University of Western Australia, Nedlands, Western Australia, Australia.,Pathwest Laboratories, Perth, Western Australia, Australia
| | - Birgitte Rode Diness
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
| | | | - Jakob Ek
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gareth Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia.,The Western Australia Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.,School of Medicine, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
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Dalach P, Savarirayan R, Baynam G, McGaughran J, Kowal E, Massey L, Jenkins M, Paradies Y, Kelaher M. "This is my boy's health! Talk straight to me!" perspectives on accessible and culturally safe care among Aboriginal and Torres Strait Islander patients of clinical genetics services. Int J Equity Health 2021; 20:103. [PMID: 33865398 PMCID: PMC8052687 DOI: 10.1186/s12939-021-01443-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Aboriginal and Torres Strait Islander people do not enjoy equal access to specialist health services that adequately meet their needs. Clinical genetics services are at the vanguard of realising the health benefits of genomic medicine. As the field continues to expand in clinical utility and implementation, it is critical that Aboriginal and Torres Strait Islander people are able to participate and benefit equally to avoid further widening of the existing health gap. This is the first study to explore barriers to accessing clinical genetics services among Aboriginal and Torres Strait Islander people, which has been acknowledged as a key strategic priority in Australian genomic health policy. METHODS A participatory design process engaged a majority-Aboriginal Project Reference Group and Aboriginal End-User Group. 63 semi-structured interviews were conducted with Aboriginal and/or Torres Strait Islander people who had accessed the government-funded clinical genetics service in Western Australia, Queensland or the Northern Territory between 2014 and 2018. The sample included patients, parents and carers. Participants were asked to recount their 'patient journey', from referral through to post-appointment and reflect on their perceptions of genetics and its implications for the health of themselves and their families. Analysis tracked chronological service engagement, followed by an inductive thematic approach. RESULTS Barriers to access and engagement were present at each stage of the patient journey. These included challenges in obtaining a referral, long waiting periods, limited genetic literacy, absence of Aboriginal support services, communication challenges and lack of adequate psychosocial support and follow-up after attendance. Participants' overall experiences of attending a genetic health service were varied, with positive perceptions tied closely to a diagnosis being achieved. The experience of (and expectation for) recognition of cultural identity and provision of culturally safe care was low among participants. Unaddressed concerns continued to cause significant distress in some people years after their appointment took place. CONCLUSIONS There is significant scope for improving the care provided to Aboriginal and Torres Strait Islander people at clinical genetics services. Immediate attention to minimising logistical barriers, developing relationships with Aboriginal Community Controlled Health Services and providing practical and specific cultural safety training for practitioners is required at the service-level. Our findings strongly support the development of guidelines or policies recognising the collective cultural needs of Aboriginal and Torres Strait Islander people in relation to genomic health care.
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Affiliation(s)
- Philippa Dalach
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia.
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Gareth Baynam
- Western Australian Department of Health, Genetic Services of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Australia
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Emma Kowal
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Libby Massey
- Machado Joseph Disease Foundation, Alyangula, Northern Territory, Australia
- James Cook University, Townsville, Queensland, Australia
| | - Misty Jenkins
- Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Yin Paradies
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Margaret Kelaher
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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Bell JC, Baynam G, Bergman JEH, Bermejo-Sánchez E, Botto LD, Canfield MA, Dastgiri S, Gatt M, Groisman B, Hurtado-Villa P, Kallen K, Khoshnood B, Konrad V, Landau D, Lopez-Camelo JS, Martinez L, Morgan M, Mutchinick OM, Nance AE, Nembhard W, Pierini A, Rissmann A, Shan X, Sipek A, Szabova E, Tagliabue G, Yevtushok LS, Zarante I, Nassar N. Survival of infants born with esophageal atresia among 24 international birth defects surveillance programs. Birth Defects Res 2021; 113:945-957. [PMID: 33734618 DOI: 10.1002/bdr2.1891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Esophageal atresia (EA) affects around 2.3-2.6 per 10,000 births world-wide. Infants born with this condition require surgical correction soon after birth. Most survival studies of infants with EA are locally or regionally based. We aimed to describe survival across multiple world regions. METHODS We included infants diagnosed with EA between 1980 and 2015 from 24 birth defects surveillance programs that are members of the International Clearinghouse for Birth Defects Surveillance and Research. We calculated survival as the proportion of liveborn infants alive at 1 month, 1- and 5-years, among all infants with EA, those with isolated EA, those with EA and additional anomalies or EA and a chromosomal anomaly or genetic syndrome. We also investigated trends in survival over the decades, 1980s-2010s. RESULTS We included 6,466 liveborn infants with EA. Survival was 89.4% (95% CI 88.1-90.5) at 1-month, 84.5% (95% CI 83.0-85.9) at 1-year and 82.7% (95% CI 81.2-84.2) at 5-years. One-month survival for infants with isolated EA (97.1%) was higher than for infants with additional anomalies (89.7%) or infants with chromosomal or genetic syndrome diagnoses (57.3%) with little change at 1- and 5-years. Survival at 1 month improved from the 1980s to the 2010s, by 6.5% for infants with isolated EA and by 21.5% for infants with EA and additional anomalies. CONCLUSIONS Almost all infants with isolated EA survived to 5 years. Mortality was higher for infants with EA and an additional anomaly, including chromosomal or genetic syndromes. Survival improved from the 1980s, particularly for those with additional anomalies.
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Affiliation(s)
- Jane C Bell
- Child Population and Translational Health Research, Children's Hospital at Westmead Clinical School, University of Sydney, Sydney, Australia
| | - Gareth Baynam
- The Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Subiaco, Australia.,School of Medicine, Division of Pediatrics; and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Jorieke E H Bergman
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eva Bermejo-Sánchez
- ECEMC, Research Unit on Congenital Anomalies, Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorenzo D Botto
- International Center on Birth Defects (ICBD) of the International Clearinghouse for Birth Defects Surveillance and Research (ICBDSR), Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mark A Canfield
- Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, Texas, USA
| | - Saeed Dastgiri
- Tabriz Health Services Management Research Center, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miriam Gatt
- Malta Congenital Anomalies Registry, Directorate for Health Information and Research, Guardamangia, Malta
| | - Boris Groisman
- National Network of Congenital Anomalies of Argentina (RENAC), National Center of Medical Genetics, National Administration of Laboratories and Health Institutes (ANLIS), National Ministry of Health, Buenos Aires, Argentina
| | - Paula Hurtado-Villa
- Pontificia Universidad Javeriana Cali, Centro Médico Imbanaco, Cali, Colombia
| | - Karin Kallen
- Swedish National Board of Health and Welfare and Institution of Clinical Sciences, Lund, University of Lund, Stockholm, Sweden
| | - Babak Khoshnood
- Université de Paris, Center of Research in Epidemiology and Statistics/CRESS/Obstetrical Perinatal and Pediatric Epidemiology Research Team (EPOPé), INSERM, INRA, Paris, France
| | - Victoria Konrad
- National Center on Birth Defects and Developmental Disabilities, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,National Center on Birth Defects and Developmental Disabilities, Carter Consulting, Incorporated, Atlanta, Georgia, USA
| | - Danielle Landau
- Department of Obstetrics and Gynecology, Soroka University Medical Center, Beersheva, Israel
| | - Jorge S Lopez-Camelo
- ECLAMC, Latin American Collaborative Study of Congenital Malformations, Buenos Aires, Argentina
| | - Laura Martinez
- Registro DAN (Registro de Defectos al Nacimiento), Departamento de Genética, Hospital Universitario Dr. José E. González. Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Margery Morgan
- CARIS (Congenital Anomaly Register & Information Services), Public Health Wales, Singleton Hospital, Swansea, UK
| | - Osvaldo M Mutchinick
- RYVMCE, Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Amy E Nance
- Utah Department of Health, Bureau of Children with Special Health Care Needs, Utah Birth Defect Network, Salt Lake City, Utah, USA
| | - Wendy Nembhard
- Department of Epidemiology and the Arkansas Reproductive Health Monitoring System, University of Arkansas for Medical Sciences, Fay W Boozman College of Medicine, Little Rock, Arkansas, USA
| | - Anna Pierini
- Institute of Clinical Physiology, National Research Council/Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Anke Rissmann
- Malformation Monitoring Centre Saxony-Anhalt, Medical Faculty Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Xiaoyi Shan
- Arkansas Children's Hospital, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Antonin Sipek
- Department of Medical Genetics, Thomayer Hospital, Prague, Czech Republic
| | - Elena Szabova
- Slovak Medical University in Bratislava, Faculty of Public Health, Bratislava, Slovak Republic
| | - Giovanna Tagliabue
- Cancer Registry Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Lombardy, Italy
| | - Lyubov S Yevtushok
- OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine.,Rivne Regional Medical Diagnostic Center, Rivne, Ukraine
| | - Ignacio Zarante
- Instituto de Genética Humana, Pontificia Universidad Javeriana Bogotá, Bogota, Colombia
| | - Natasha Nassar
- Child Population and Translational Health Research, Children's Hospital at Westmead Clinical School, University of Sydney, Sydney, Australia
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Ferdinand A, Massey L, Cullen J, Temple J, Meiselbach K, Paradies Y, Baynam G, Savarirayan R, Kelaher M. Culturally competent communication in Indigenous disability assessment: a qualitative study. Int J Equity Health 2021; 20:68. [PMID: 33648504 PMCID: PMC7923453 DOI: 10.1186/s12939-021-01402-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Indigenous people tend to exhibit a higher burden of disability than their non-Indigenous counterparts, and are often underserved by disability services. Engaging appropriately with Indigenous communities, families and individuals in the initial stages of disability assessment and planning is crucial in order to build trust and understanding of disability service models and ensure that Indigenous people receive support that is tailored to their needs and cultural realities. This article aims to identify key elements of culturally competent communication in Indigenous disability assessment and planning, and provide recommendations for strengthening capacity in this area. METHODS This qualitative research was designed to involve Aboriginal and Torres Strait Islander people at all stages and to reflect the views of Aboriginal and Torres Strait Islander researchers, people and families affected by disability and the community-controlled health sector. Semi-structured individual interviews were undertaken with staff implementing the National Disability Insurance Scheme (NDIS) (n = 4), NDIS participants (n = 24), disability support providers and organisational partners (n = 19) and Community Connectors (n = 8) in Queensland and the Northern Territory of Australia. Key themes derived from thematic analysis included appropriate and adequate engagement of individuals with disability and their families, the role of trusted relationships, and culturally safe and appropriate communication during planning meetings. RESULTS Overall, the research findings highlight that a low level of cultural competence in the initial stages of the disability assessment and planning process exacerbated participant confusion and distrust towards assessment staff and the NDIS. Given difficulties in communication, participant understanding of the NDIS was generally limited. The necessity of culturally safe and appropriate use of interpreters was stressed, as was the role of trusted individuals, including existing service providers, Community Connectors and family members in providing a solid base for participant understanding of the NDIS. CONCLUSIONS Cultural competence in disability assessment and planning can be strengthened through multi-level engagement with the Aboriginal community-controlled sector and community leaders. Implementing mechanisms to enable the involvement of families, trusted service providers and Community Connectors can support a more meaningful understanding of individuals' needs within their cultural context and in relation to their cultural roles.
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Affiliation(s)
- Angeline Ferdinand
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, VIC, 3011, Australia.
| | - Libby Massey
- MJD Foundation, Nightcliff, NT, 0814, Australia
- James Cook University, Cairns,, QLD, 4870, Australia
| | - Jennifer Cullen
- Synapse, Level 1/262 Montague Road, West End, QLD, 4101, Australia
| | - Jeromey Temple
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, VIC, 3011, Australia
| | - Kristy Meiselbach
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, VIC, 3011, Australia
| | - Yin Paradies
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, 374 Bagot Rd, Subiaco, WA, 6008, Australia
- Telethon Kids Institute and the Faculty of Health and Medical Science, Division of Paediatrics, University of Western Australia, Monash Avenue, Nedlands, WA, 6009, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
- University of Melbourne, Parkville, VIC, 3052, Australia
| | - Margaret Kelaher
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, VIC, 3011, Australia
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48
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Di Zanni E, Palagano E, Lagostena L, Strina D, Rehman A, Abinun M, De Somer L, Martire B, Brown J, Kariminejad A, Balasubramaniam S, Baynam G, Gurrieri F, Pisanti MA, De Maggio I, Abboud MR, Chiesa R, Burren CP, Villa A, Sobacchi C, Picollo A. Pathobiologic Mechanisms of Neurodegeneration in Osteopetrosis Derived From Structural and Functional Analysis of 14 ClC-7 Mutants. J Bone Miner Res 2021; 36:531-545. [PMID: 33125761 DOI: 10.1002/jbmr.4200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/18/2022]
Abstract
ClC-7 is a chloride-proton antiporter of the CLC protein family. In complex with its accessory protein Ostm-1, ClC-7 localizes to lysosomes and to the osteoclasts' ruffled border, where it plays a critical role in acidifying the resorption lacuna during bone resorption. Gene inactivation in mice causes severe osteopetrosis, neurodegeneration, and lysosomal storage disease. Mutations in the human CLCN7 gene are associated with diverse forms of osteopetrosis. The functional evaluation of ClC-7 variants might be informative with respect to their pathogenicity, but the cellular localization of the protein hampers this analysis. Here we investigated the functional effects of 13 CLCN7 mutations identified in 13 new patients with severe or mild osteopetrosis and a known ADO2 mutation. We mapped the mutated amino acid residues in the homology model of ClC-7 protein, assessed the lysosomal colocalization of ClC-7 mutants and Ostm1 through confocal microscopy, and performed patch-clamp recordings on plasma-membrane-targeted mutant ClC-7. Finally, we analyzed these results together with the patients' clinical features and suggested a correlation between the lack of ClC-7/Ostm1 in lysosomes and severe neurodegeneration. © 2020 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Eleonora Di Zanni
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica (CNR-IBF), Dulbecco Telethon Laboratory, Genoa, Italy
| | - Eleonora Palagano
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Laura Lagostena
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica (CNR-IBF), Dulbecco Telethon Laboratory, Genoa, Italy
| | - Dario Strina
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Asma Rehman
- UMB Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA
| | - Mario Abinun
- Department of Pediatric Immunology, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lien De Somer
- Department of Pediatric Rheumatology, University Hospital Leuven, Leuven, Belgium
| | | | - Justin Brown
- Department of Pediatrics, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia.,Department of Pediatric Endocrinology and Diabetes, Monash Children's Hospital, Monash Health, Clayton, Australia
| | | | - Shanti Balasubramaniam
- Department of Metabolic Medicine and Rheumatology, Perth Children's Hospital, Perth, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute and Division of Pediatrics, School of Health and Medical Sciences, University of Western Australia, Perth, Australia.,Faculty of Medicine, Notre Dame University, Fremantle, Australia
| | | | - Maria A Pisanti
- Medical Genetics Unit, "Antonio Cardarelli" Hospital, Naples, Italy
| | - Ilaria De Maggio
- Medical Genetics Unit, "Antonio Cardarelli" Hospital, Naples, Italy
| | - Miguel R Abboud
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Robert Chiesa
- Bone Marrow Transplantation Department, Great Ormond Street Hospital for Children, London, UK
| | - Christine P Burren
- Department of Pediatric Endocrinology and Diabetes, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK.,Bristol Medical School, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anna Villa
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan, Italy.,San Raffaele Telethon Institute for Gene Therapy SR-Tiget, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Sobacchi
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Alessandra Picollo
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica (CNR-IBF), Dulbecco Telethon Laboratory, Genoa, Italy
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Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett M, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres M, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg A, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res 2021; 49:D1207-D1217. [PMID: 33264411 PMCID: PMC7778952 DOI: 10.1093/nar/gkaa1043] [Citation(s) in RCA: 476] [Impact Index Per Article: 158.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/11/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022] Open
Abstract
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.
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Affiliation(s)
| | - Michael Gargano
- Monarch Initiative
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nicolas Matentzoglu
- Monarch Initiative
- Semanticly Ltd, London, UK
- European Bioinformatics Institute (EMBL-EBI)
| | - Leigh C Carmody
- Monarch Initiative
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Clinical Neurosciences, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicole A Vasilevsky
- Monarch Initiative
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University
| | | | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS ‘G. Gaslini’ Institute, Genoa, Italy
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward memorial Hospital, Perth, Australia
- Telethon Kids Institute and the Division of Paediatrics, Faculty of Helath and Medical Sciences, University of Western Australia, Perth, Australia
| | - Amy M Brower
- American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA
| | - Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Colorado, USA
| | | | - Johanna L Est
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Peter D Galer
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Marc Hanauer
- INSERM, US14––Orphanet, Plateforme Maladies Rares, Paris, France
| | - Nomi L Harris
- Monarch Initiative
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Michael J Hartnett
- American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA
| | - Maximilian Hastreiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
| | - Yongqun He
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tim Jeske
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hugh Kearney
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Ireland
| | - Gerhard Kindle
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI). Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Centre for Biobanking FREEZE, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - David Lagorce
- INSERM, US14––Orphanet, Plateforme Maladies Rares, Paris, France
| | - Julie A McMurry
- Monarch Initiative
- Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA
| | - Jillian A Miller
- American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA
| | - Monica C Munoz-Torres
- Monarch Initiative
- Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA
| | - Rebecca L Peters
- American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA
| | - Christina K Rapp
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany
| | - Ana M Rath
- INSERM, US14––Orphanet, Plateforme Maladies Rares, Paris, France
| | - Shahmir A Rind
- WA Register of Developmental Anomalies
- Curtin University, Western Australia, Australia
| | - Avi Z Rosenberg
- Division of Kidney-Urologic Pathology, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Markus G Seidel
- Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Damian Smedley
- The William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Tomer Talmy
- Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel
- Faculty of Medicine, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yarlalu Thomas
- West Australian Register of Developmental Anomalies, East Perth, WA, Australia
| | | | - Julie Xian
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, PA, USA
| | - Zafer Yüksel
- Human Genetics, Bioscientia GmbH, Ingelheim, Germany
| | - Ingo Helbig
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher J Mungall
- Monarch Initiative
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Melissa A Haendel
- Monarch Initiative
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University
- Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA
| | - Peter N Robinson
- Monarch Initiative
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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50
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D'Angelo CS, Hermes A, McMaster CR, Prichep E, Richer É, van der Westhuizen FH, Repetto GM, Mengchun G, Malherbe H, Reichardt JKV, Arbour L, Hudson M, du Plessis K, Haendel M, Wilcox P, Lynch SA, Rind S, Easteal S, Estivill X, Thomas Y, Baynam G. Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations. Front Pediatr 2020; 8:579924. [PMID: 33381478 PMCID: PMC7767925 DOI: 10.3389/fped.2020.579924] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
Advances in omics and specifically genomic technologies are increasingly transforming rare disease diagnosis. However, the benefits of these advances are disproportionately experienced within and between populations, with Indigenous populations frequently experiencing diagnostic and therapeutic inequities. The International Rare Disease Research Consortium (IRDiRC) multi-stakeholder partnership has been advancing toward the vision of all people living with a rare disease receiving an accurate diagnosis, care, and available therapy within 1 year of coming to medical attention. In order to further progress toward this vision, IRDiRC has created a taskforce to explore the access barriers to diagnosis of rare genetic diseases faced by Indigenous peoples, with a view of developing recommendations to overcome them. Herein, we provide an overview of the state of play of current barriers and considerations identified by the taskforce, to further stimulate awareness of these issues and the passage toward solutions. We focus on analyzing barriers to accessing genetic services, participating in genomic research, and other aspects such as concerns about data sharing, the handling of biospecimens, and the importance of capacity building.
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Affiliation(s)
- Carla S. D'Angelo
- IRDiRC Scientific Secretariat, National Institute for Health and Medical Research, Paris, France
| | - Azure Hermes
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
| | | | - Elissa Prichep
- Precision Medicine, Platform on Shaping the Future of Health and Healthcare, World Economic Forum, San Francisco, CA, United States
| | - Étienne Richer
- Institute of Genetics, Canadian Institutes of Health Research, Government of Canada, Ottawa, ON, Canada
| | | | - Gabriela M. Repetto
- Facultad de Medicina, Center for Genetics and Genomics, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gong Mengchun
- Institute of Health Management, Southern Medical University, Guangdong, China
| | - Helen Malherbe
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
- Rare Diseases South Africa, Johannesburg, South Africa
| | - Juergen K. V. Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, Australia
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Victoria, BC, Canada
| | - Maui Hudson
- Faculty of Maori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Melissa Haendel
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, United States
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Sally Ann Lynch
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Ireland
- Academic Centre on Rare Diseases, University College Dublin, Dublin, Ireland
| | - Shamir Rind
- Western Australian Register of Developmental Anomalies, Perth, WA, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qgenomics), Esplugues de Llobregat, Barcelona, Spain
| | - Yarlalu Thomas
- Western Australian Register of Developmental Anomalies, Perth, WA, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medicine, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Faculty of Medicine, University of Notre Dame, Fremantle, WA, Australia
- Faculty of Science and Engineering, Spatial Sciences, Curtin University, Perth, WA, Australia
- Faculty of Medicine, Notre Dame University, Perth, WA, Australia
- School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
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