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Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, Çalıcı SZ, Cedillo LR, Berardelli S, Özden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, Özkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafmüller A, Barrón LTJ, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT. Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594558. [PMID: 38798479 PMCID: PMC11118473 DOI: 10.1101/2024.05.16.594558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods to accurately determine the clinical impact of variants of unknown significance (VUS). Towards this goal, the ARSA Critical Assessment of Genome Interpretation (CAGI) challenge was designed to characterize progress by utilizing 219 experimentally assayed missense VUS in the Arylsulfatase A (ARSA) gene to assess the performance of community-submitted predictions of variant functional effects. The challenge involved 15 teams, and evaluated additional predictions from established and recently released models. Notably, a model developed by participants of a genetics and coding bootcamp, trained with standard machine-learning tools in Python, demonstrated superior performance among submissions. Furthermore, the study observed that state-of-the-art deep learning methods provided small but statistically significant improvement in predictive performance compared to less elaborate techniques. These findings underscore the utility of variant effect prediction, and the potential for models trained with modest resources to accurately classify VUS in genetic and clinical research.
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Affiliation(s)
- Shantanu Jain
- The Institute for Experiential AI, Northeastern University, Boston, MA, USA
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Thanh Binh Nguyen
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | | | | | - Fang Ge
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing, China
| | | | | | | | - Boqi Wang
- Department of Bioinformatics and System Biology, University of California, San Diego, La Jolla, CA, USA
| | - Kobra Rahimi
- Department of Computational Biology, School of Life Sciences, Ochanomizu University, Tokyo, Japan
| | - Sümeyra Zeynep Çalıcı
- Department of Genomics, Faculty of Aquatic Science, Istanbul University, Istanbul, Türkiye
| | | | - Silvia Berardelli
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
- enGenome srl, Pavia, Italy
| | - Buse Özden
- Program of Molecular Biotechnology and Genetics, Institute of Science, Istanbul University, Istanbul, Türkiye
| | - Ken Chen
- University of California, Berkeley, Berkeley, CA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | - Eshel Faraggi
- Research and Information Systems LLC, Indianapolis, IN, USA
- Physics Department, Indiana University-Purdue University, Indianapolis, IN, USA
| | - Robert Jernigan
- Roy J. Carver Department of Biochemistry, Iowa State University, Ames, IA, USA
| | - Andrzej Kloczkowski
- Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jierui Xu
- University of California, Berkeley, Berkeley, CA, USA
| | | | - Selen Özkan
- Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Natàlia Padilla
- Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- Universitat Autonoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | | | | | | | | | - Giulia Babbi
- Biocomputing Group, University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Yuanfei Sun
- Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Shaowen Zhu
- Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yang Shen
- Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Gabriel Cia
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium
| | | | - Pauline Hermans
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Sofia Kwee
- University of California, Berkeley, Berkeley, CA, USA
| | - Ella Chen
- University of California, Berkeley, Berkeley, CA, USA
| | | | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rashika Ramola
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Michelle Velyunskiy
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Reet Mishra
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, San Francisco, CA, USA
| | | | - Jennifer L Goldstein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jose Lugo-Martinez
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Sindy Li
- University of California, Berkeley, Berkeley, CA, USA
| | - Kinsey Long
- University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
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Faye F, Crocione C, Anido de Peña R, Bellagambi S, Escati Peñaloza L, Hunter A, Jensen L, Oosterwijk C, Schoeters E, de Vicente D, Faivre L, Wilbur M, Le Cam Y, Dubief J. Time to diagnosis and determinants of diagnostic delays of people living with a rare disease: results of a Rare Barometer retrospective patient survey. Eur J Hum Genet 2024:10.1038/s41431-024-01604-z. [PMID: 38755315 DOI: 10.1038/s41431-024-01604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 05/18/2024] Open
Abstract
Timely diagnosis is one of the most serious challenges faced by people living with a rare disease (PLWRD), and this study estimates that in Europe, the average total diagnosis time (TDT) is close to 5 years. We investigated the duration of the TDT for PLWRD in Europe, the difficulties associated with their diagnosis odyssey and the main determinants of diagnosis delays for all rare diseases (RD). We conducted a survey of PLWRD and their families using Rare Barometer, the survey initiative of EURORDIS-Rare Diseases Europe. In geographical Europe, we surveyed 6507 people living with 1675 RD in 41 countries. We then performed a descriptive analysis and ordinal logistic regressions to identify the main determinants of diagnosis delays. Average TDT is 4.7 years. 56% of respondents were diagnosed more than 6 months after a first medical contact. The main determinants of diagnosis delays are symptom onset before 30 years of age, especially during childhood (OR = 3.11; 95% CI: 2.4-4.0) and adolescence (OR = 4.79; 95% CI: 3.7-6.2), being a woman (OR = 1.22; 95% CI:1.1-1.4), living in Northern Europe (OR = 2.15; 95% CI:1.8-2.6) or Western Europe (OR = 1.96; 95% CI:1.6-2.3), the number of healthcare professionals consulted (OR = 5.15; 95% CI:4.1-6.4), misdiagnosis (OR = 2.48; 95% CI:2.1-2.9), referral to a centre of expertise (OR = 1.17; 95% CI:1.0-1.3), unmet needs for psychological support (OR = 1.34; 95% CI:1.2-1.5) and financial support (OR = 1.16; 95% CI:1.0-1.3), having a genetic disease (OR = 1.33; 95% CI:1.1-1.5) and a family history of an RD (OR = 1.36; 95% CI:1.1-1.6). These determinants can inform policies and actions to improve access to diagnosis for all PLWRD.
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Affiliation(s)
| | | | | | | | | | | | - Lene Jensen
- Sjaeldne Diagnoser - Rare Diseases Denmark, Taastrup, Denmark
| | - Cor Oosterwijk
- VSOP - Vereniging Samenwerkende Ouder En Patiëntenorganisaties, Soest, Netherlands
| | - Eva Schoeters
- RaDiOrg - Rare Diseases Belgium asbl/vzw, Brussels, Belgium
| | | | - Laurence Faivre
- Centre Hospitalier Universitaire Dijon-Bourgogne, Dijon, France
| | | | - Yann Le Cam
- EURORDIS-Rare Diseases Europe, Paris, France
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Heath O, Hammerl E, Spitzinger A, Wortmann SB. Ending an Odyssey? The Psychosocial Experiences of Parents after the Genetic Diagnosis of a Mitochondrial Disease in Children. J Pers Med 2024; 14:523. [PMID: 38793105 PMCID: PMC11122152 DOI: 10.3390/jpm14050523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Obtaining a genetic diagnosis of a primary mitochondrial disease (PMD) is often framed as a diagnostic odyssey. Yet, even after receiving a diagnosis, parents of affected children experience ongoing therapeutic and prognostic uncertainty and considerable psychosocial challenges. Semi-structured interviews (N = 24) were conducted with parents of 13 children (aged 2-19 years) with a genetically confirmed PMD. Paternal (N = 11) and maternal (N = 13) perspectives were obtained, and thematic analysis was performed on all interviews. A genetic diagnosis was valuable and empowering for parents, despite eliciting varied emotional responses. While the diagnosis helped focus management decisions, families often felt overwhelmed and unsupported in navigating the healthcare system. Most parents reported a serious impact on their romantic relationship. The sources of social support varied, with a preference for established friendship and family support networks over disease-specific community support groups. Most parents favored prenatal genetic testing in the event of a future pregnancy. This study provides insight into the lived experiences of parents after a genetic diagnosis of PMD in their children. The findings draw awareness to supportive care needs and highlight important gaps that should be addressed to ensure that parents feel supported within a holistic framework of management for PMDs.
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Affiliation(s)
- Oliver Heath
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
| | - Emma Hammerl
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
| | - Anna Spitzinger
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
- Institut für Klinische Psychologie der UK für Psychiatrie, Psychotherapie und Psychosomatik der PMU, 5020 Salzburg, Austria
| | - Saskia B. Wortmann
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
- Nijmegen Centre for Mitochondrial Disorders (NCMD), Amalia Children’s Hospital, Radboudumc, 6525 Nijmegen, The Netherlands
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Wu D, Yang J, Liu C, Hsieh TC, Marchi E, Blair J, Krawitz P, Weng C, Chung W, Lyon GJ, Krantz ID, Kalish JM, Wang K. GestaltMML: Enhancing Rare Genetic Disease Diagnosis through Multimodal Machine Learning Combining Facial Images and Clinical Texts. ARXIV 2024:arXiv:2312.15320v2. [PMID: 38711434 PMCID: PMC11071539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Individuals with suspected rare genetic disorders often undergo multiple clinical evaluations, imaging studies, laboratory tests and genetic tests, to find a possible answer over a prolonged period of time. Addressing this "diagnostic odyssey" thus has substantial clinical, psychosocial, and economic benefits. Many rare genetic diseases have distinctive facial features, which can be used by artificial intelligence algorithms to facilitate clinical diagnosis, in prioritizing candidate diseases to be further examined by lab tests or genetic assays, or in helping the phenotype-driven reinterpretation of genome/exome sequencing data. Existing methods using frontal facial photos were built on conventional Convolutional Neural Networks (CNNs), rely exclusively on facial images, and cannot capture non-facial phenotypic traits and demographic information essential for guiding accurate diagnoses. Here we introduce GestaltMML, a multimodal machine learning (MML) approach solely based on the Transformer architecture. It integrates facial images, demographic information (age, sex, ethnicity), and clinical notes (optionally, a list of Human Phenotype Ontology terms) to improve prediction accuracy. Furthermore, we also evaluated GestaltMML on a diverse range of datasets, including 528 diseases from the GestaltMatcher Database, several in-house datasets of Beckwith-Wiedemann syndrome (BWS, over-growth syndrome with distinct facial features), Sotos syndrome (overgrowth syndrome with overlapping features with BWS), NAA10-related neurodevelopmental syndrome, Cornelia de Lange syndrome (multiple malformation syndrome), and KBG syndrome (multiple malformation syndrome). Our results suggest that GestaltMML effectively incorporates multiple modalities of data, greatly narrowing candidate genetic diagnoses of rare diseases and may facilitate the reinterpretation of genome/exome sequencing data.
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Affiliation(s)
- Da Wu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jingye Yang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Justin Blair
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gholson J. Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
| | - Ian D. Krantz
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer M. Kalish
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Aiyegbusi OL, Fenton A. The impact of rare kidney diseases on kidney failure. Lancet 2024; 403:1211-1213. [PMID: 38492577 DOI: 10.1016/s0140-6736(24)00198-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Affiliation(s)
- Olalekan Lee Aiyegbusi
- Centre for Patient Reported Outcomes Research, Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK; NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK; NIHR Applied Research Collaboration West Midlands, Birmingham, UK.
| | - Anthony Fenton
- Department of Renal Medicine, Royal Stoke University Hospital, Stoke-on-Trent, UK
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Noyek S, Jessa JS, Faulkner V, Boerner KE, Dewan T, Doyle D, Genik L, Grainger-Schatz S, McMorris C, McMurtry CM, Nania CG, Oberlander T, Lorenzetti D, Turner K, Birnie KA. A systematic review of self and observer assessment of pain and related functioning in youth with brain-based developmental disabilities. Pain 2024; 165:523-536. [PMID: 37870234 PMCID: PMC10859851 DOI: 10.1097/j.pain.0000000000003066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 10/24/2023]
Abstract
ABSTRACT Pain experiences of youth with brain-based developmental disabilities are often overlooked and/or misinterpreted, increasing the risk for poor or inadequate pain assessment and management. Ample measures exist to assess acute and chronic pain, yet their utility and frequency of use in youth with brain-based developmental disabilities is unclear and available measures do not have strong measurement properties for this diverse group. This systematic review identified the scope of self-reported and observer-reported pain assessment in studies of youth (aged 3-24 years) with brain-based developmental disabilities (phase 1) and summarized other measures of pain-related functioning for acute and chronic pain (ie, physical, emotional, social, sleep, and quality of life, within the subset of quantitative studies focused primarily on pain, phase 2). A comprehensive search for English-language studies was conducted in August 2022 in Web of Science, CINAHL, MEDLINE, Cochrane CENTRAL, EMBASE, and APA PsychINFO (PROSPERO registration: CRD42021237444). A total of 17,029 unique records were screened. Of the 707 articles included in phase 1, most assessed chronic pain (n = 314; 62.0%) and primarily used observer-report (n = 155; 31%) over self-report (n = 67; 13%). Of the 137 articles included in phase 2, other outcomes assessed alongside pain intensity included motor ability (16.8%), adaptive functioning (11%), quality of life (8%), pain interference (6.6%), mental health (5.8%), and communication ability (2.9%). Cerebral palsy was the most common population in both phase 1 (n = 343; 48.5%) and phase 2 (n = 83; 59.7%). This review provides a foundational understanding of pain assessment in brain-based developmental disabilities and highlights continued inequities in holistic pain assessment for this population.
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Affiliation(s)
- Samantha Noyek
- Department of Psychology, University of Calgary, Calgary, AB, Canada
| | - Jenna S. Jessa
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Violeta Faulkner
- Department of Anesthesiology, University of Calgary, Calgary, AB, Canada
| | | | - Tammie Dewan
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Dacey Doyle
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Anesthesiology, University of Calgary, Calgary, AB, Canada
- Department of Psychology, University of British Columbia, BC, Canada
- Department of Psychology, University of Guelph, ON, Canada
- Werklund School of Education, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of British Columbia, BC, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, AB, Canada
| | - Lara Genik
- Department of Psychology, University of Guelph, ON, Canada
| | - Stacy Grainger-Schatz
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Anesthesiology, University of Calgary, Calgary, AB, Canada
- Department of Psychology, University of British Columbia, BC, Canada
- Department of Psychology, University of Guelph, ON, Canada
- Werklund School of Education, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of British Columbia, BC, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, AB, Canada
| | - Carly McMorris
- Werklund School of Education, University of Calgary, Calgary, AB, Canada
| | | | - Cara G. Nania
- Werklund School of Education, University of Calgary, Calgary, AB, Canada
| | - Tim Oberlander
- Department of Pediatrics, University of British Columbia, BC, Canada
| | - Diane Lorenzetti
- Department of Psychology, University of Calgary, Calgary, AB, Canada
| | - Kailyn Turner
- Werklund School of Education, University of Calgary, Calgary, AB, Canada
| | - Kathryn A. Birnie
- Department of Anesthesiology, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, AB, Canada
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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] [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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Paudel N, Daly A, Waters F, Stratieva P. Genetic Testing Experiences of People Living with Inherited Retinal Degenerations: Results of a Global Survey. Ophthalmic Res 2024; 67:201-210. [PMID: 38368861 DOI: 10.1159/000537818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Obtaining a genetic diagnosis via genetic testing (GT) is a fundamental step in determining the eligibility of a patient to be enrolled in emerging clinical trials and research studies. Besides, the knowledge of genetic outcome allows patients to plan for significant life choices. However, critical barriers exist to an equitable access to genetic services globally. The objective of this study was to explore patient experiences while seeking genomic services for inherited retinal degenerations (IRDs). METHODS An online survey was designed based on a focus group conducted by Retina International and including people affected by IRDs and their families living in different regions around the world. The survey was then circulated to 43 Retina International member organisations globally via email newsletters and social networks. The survey involved questions in relation to the accessibility, affordability, and timeliness of genomic services for IRDs as well as patient perceived awareness of genomic services for IRDs among healthcare professionals. RESULTS A total of 410 respondents (IRD patients and caregivers) from over 30 countries across all continents responded to the survey. A considerable number of the patients had to go through a long and arduous journey to access GT and counselling services, wherein 40% had to visit more than 5 physicians, 27% had to visit more than 5 clinics, and 57% had to wait for more than 3 years before obtaining a genetic diagnosis. Furthermore, 46% of respondents reported not receiving genetic counselling prior to undergoing GT, and 39% reported not receiving genetic counselling after undergoing GT. Over 3/4th of the participants reported that they did not have to pay for their genomic services for IRDs. Thirty-seven percent of the respondents reported that their eye care professionals (ECPs) were either not aware of GT, remained neutral, or did not encourage them to undergo GT. CONCLUSION Patients with IRDs do not have equitable access to best practice GT and counselling services. Greater awareness and training regarding IRDs and the benefits of GT and genetic counselling for patients and families are needed among ECPs. A best practice model on access to genomic services for IRDs is required.
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Kobayashi Takahashi Y, Hayakawa I, Abe Y. Diagnostic odyssey of Guillain-Barré syndrome in children. Brain Dev 2024; 46:108-113. [PMID: 37914621 DOI: 10.1016/j.braindev.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/04/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND AND OBJECTIVES A gap exists between difficulty in diagnosis and importance of early recognition and intervention in pediatric Guillain-Barré syndrome (GBS). Therefore, this study aimed to establish a diagnostic odyssey plot that allows "at-a-glance" overview of the diagnostic odyssey of GBS in children, including overall diagnostic delay, physician-related and patient-related diagnostic delays, and length and frequency of diagnostic errors. METHODS In this single-center retrospective cohort study, standardized data were obtained from children with GBS from 2003 to 2020. Overall diagnostic delay (time between symptom onset and diagnosis), physician-related diagnostic delay (time between the first medical visit and diagnosis), and patient-related diagnostic delay (time between symptom onset and the first medical visit) were analyzed. RESULTS The study examined a total of 21 patients (11 men, median age 4.5 years). Overall, there were 40 misdiagnoses among 17 patients, while four were diagnosed correctly at the first visit. The overall diagnostic delay was 9 days [interquartile range (IQR), 6-17 days]. Physician-related diagnostic delay, but not patient-related diagnostic delay, was correlated with the overall diagnostic delay. Patients in the late-diagnosed group were more frequently misdiagnosed during their diagnostic odyssey than patients in the other groups. Risk factors associated with diagnostic delay included delayed onset of weakness and sensory deficits, absence of swallowing problems, and misdiagnosis as orthopedic disorders or viral infections. DISCUSSION A unique diagnostic odyssey exists in pedaitric GBS. Several clinical risk factors were associated with the diagnostic delay.
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Affiliation(s)
- Yoko Kobayashi Takahashi
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan; Department of Child Neurology, National Center for Neurology and Psychiatry, Tokyo, Japan
| | - Itaru Hayakawa
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, University of Tokyo, Tokyo, Japan.
| | - Yuichi Abe
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
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10
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Bordini BJ, Walsh RD, Basel D, Deshmukh T. Attaining Diagnostic Excellence: How the Structure and Function of a Rare Disease Service Contribute to Ending the Diagnostic Odyssey. Med Clin North Am 2024; 108:1-14. [PMID: 37951644 DOI: 10.1016/j.mcna.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Patients with rare or otherwise undiagnosed disorders frequently find themselves on a diagnostic odyssey, the often-prolonged journey toward diagnosis that can be characterized by significant physical, emotional, and financial hardship, as well as by diagnostic errors and delays. The wider availability of clinical exome sequencing has helped end many diagnostic odysseys, though diagnostic success rates of around 35% for exome sequencing leave many patients undiagnosed. Diagnostic yields can be improved via the implementation of advanced genetic testing modalities, though both these modalities and exome sequencing perform significantly better when paired with high-quality phenotypic data. Diagnostic centers of excellence can improve outcomes for patients on a diagnostic odyssey by providing a process and environment that address shortfalls in diagnostic access while providing high-quality phenotyping. Features of successful undiagnosed and rare disease evaluation teams are discussed and an illustrative case is provided.
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Affiliation(s)
- Brett J Bordini
- Department of Pediatrics, Division of Hospital Medicine, Nelson Service for Undiagnosed and Rare Diseases, Medical College of Wisconsin.
| | - Ryan D Walsh
- Department of Neurology, Medical College of Wisconsin; Eye Institute - Froedtert Hospital, 925 North 87th Street, Milwaukee, WI 53226, USA
| | - Donald Basel
- Department of Pediatrics, Section Chief, Division of Medical Genetics, Medical College of Wisconsin, 9000 West Wisconsin Avenue MC716, Milwaukee, WI 53226, USA
| | - Tejaswini Deshmukh
- Department of Radiology, Division of Pediatric Radiology, Medical College of Wisconsin; Department of Pediatric Imaging, 9000 West Wisconsin Avenue, Milwaukee, WI 53226, USA
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11
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Domaradzki J, Walkowiak D. Ultra-rare ultra-care: Assessing the impact of caring for children with ultra rare diseases. Eur J Paediatr Neurol 2024; 48:78-84. [PMID: 38071849 DOI: 10.1016/j.ejpn.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 03/23/2024]
Abstract
BACKGROUND We sought to assesses the impact of caring for children with ultra rare diseases (URDs) on family carers and to analyse the way these experiences differ among the caregivers of children diagnosed through prenatal or newborn screening, and those with symptom-based diagnosis. METHODS A total of 200 caregivers of 219 URDs children completed an on-line survey regarding the challenges and experiences of caregivers of URDs children. RESULTS The majority of URD caregivers felt burdened by their children's health problems, emotional and behavioural changes. 46.5% reported feelings of care overload, 43% coped poorly with the stress, and many experienced a variety of feelings of distress towards the role of caregiver. While most caregivers struggled with the diagnostic odyssey and were dissatisfied with the healthcare services for URD children, caregivers of children diagnosed through prenatal or newborn screening were significantly less burdened than the parents of children with symptom-based diagnoses. CONCLUSION Although caregivers of URDs children experience physical and emotional strain, they are often neglected by the healthcare system. A bio-psychosocial approach to URDs should therefore also include family caregivers' physical and psychosocial needs. Apart from financial and emotional support, enhancing access to genetic testing and newborn screening should be prioritised.
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Affiliation(s)
- Jan Domaradzki
- Department of Social Sciences and Humanities, Poznan University of Medical Sciences, Poznań, Poland.
| | - Dariusz Walkowiak
- Department of Organization and Management in Health Care, Poznan University of Medical Sciences, Pozna&nacute, Poland
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12
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Garnier N, Berghout J, Zygmunt A, Singh D, Huang KA, Kantz W, Blankart CR, Gillner S, Zhao J, Roettger R, Saier C, Kirschner J, Schenk J, Atkins L, Ryan N, Zarakowska K, Zschüntzsch J, Zuccolo M, Müllenborn M, Man YS, Goodman L, Trad M, Chalandon AS, Sansen S, Martinez-Fresno M, Badger S, Walther van Olden R, Rothmann R, Lehner P, Tschohl C, Baillon L, Gumus G, Gross E, Stefanov R, Iskrov G, Raycheva R, Kostadinov K, Mitova E, Einhorn M, Einhorn Y, Schepers J, Hübner M, Alves F, Iskandar R, Mayer R, Renieri A, Piperkova A, Gut I, Beltran S, Matthiesen ME, Poetz M, Hansson M, Trollmann R, Agolini E, Ottombrino S, Novelli A, Bertini E, Selvatici R, Farnè M, Fortunato F, Ferlini A. Genetic newborn screening and digital technologies: A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe. PLoS One 2023; 18:e0293503. [PMID: 37992053 PMCID: PMC10664952 DOI: 10.1371/journal.pone.0293503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 11/24/2023] Open
Abstract
Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research project, which resulted of a joint effort between the European Union Commission and the European Federation of Pharmaceutical Industries and Associations. It focuses on genetic newborn screening and artificial intelligence-based tools which will be applied to a large European population of about 25.000 infants. The neonatal screening strategy will be based on targeted sequencing, while whole genome sequencing will be offered to all enrolled infants who may show early symptoms but have resulted negative at the targeted sequencing-based newborn screening. We will leverage artificial intelligence-based algorithms to identify patients using Electronic Health Records (EHR) and to build a repository "symptom checkers" for patients and healthcare providers. S4C will design an equitable, ethical, and sustainable framework for genetic newborn screening and new digital tools, corroborated by a large workout where legal, ethical, and social complexities will be addressed with the intent of making the framework highly and flexibly translatable into the diverse European health systems.
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Affiliation(s)
- Nicolas Garnier
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Joanne Berghout
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Aldona Zygmunt
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Deependra Singh
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Kui A. Huang
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Waltraud Kantz
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Carl Rudolf Blankart
- KPM Center for Public Management and Swiss Institute for Translational and Entrepreneurial Medicine, University of Bern, Bern, Switzerland
| | - Sandra Gillner
- KPM Center for Public Management and Swiss Institute for Translational and Entrepreneurial Medicine, University of Bern, Bern, Switzerland
| | - Jiawei Zhao
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Richard Roettger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Christina Saier
- Department of Neuropediatric and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Kirschner
- Department of Neuropediatric and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joern Schenk
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Leon Atkins
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Nuala Ryan
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Kaja Zarakowska
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Jana Zschüntzsch
- Department of Neurology, University Medical Center Goettingen, Göttingen, Germany
| | | | | | - Yuen-Sum Man
- Novo Nordisk Health Care AG, Switzerland &Novo Nordisk A/S, Kloten, Denmark
| | - Liz Goodman
- University College Dublin, National University of Ireland, Dublin, Ireland
| | | | | | | | | | | | | | - Robert Rothmann
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | - Patrick Lehner
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | - Christof Tschohl
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | | | | | | | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Iskrov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Ralitsa Raycheva
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Kostadin Kostadinov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Elena Mitova
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | | | | | - Josef Schepers
- Berlin Institute of Health (at) Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam Hübner
- Berlin Institute of Health (at) Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frauke Alves
- Translational Molecular Imaging, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany
| | - Rowan Iskandar
- Swiss Institute for Translational and Entrepreneurial Medicine (sitem-insel), Bern, Switzerland
| | | | | | - Aneta Piperkova
- Bulgarian Association for Personalized Medicine, Sofia, Bulgaria
| | - Ivo Gut
- Centro Nacional de Analisis Genomico, CNAG, Barcelona, Spain
| | - Sergi Beltran
- Centro Nacional de Analisis Genomico, CNAG, Barcelona, Spain
| | | | - Marion Poetz
- Department of Strategy and Innovation, Copenhagen Business School, Copenhagen, Denmark
| | | | | | | | | | | | | | - Rita Selvatici
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marianna Farnè
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Fortunato
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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13
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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14
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Backeljauw PF, Andrews M, Bang P, Dalle Molle L, Deal CL, Harvey J, Langham S, Petriczko E, Polak M, Storr HL, Dattani MT. Challenges in the care of individuals with severe primary insulin-like growth factor-I deficiency (SPIGFD): an international, multi-stakeholder perspective. Orphanet J Rare Dis 2023; 18:312. [PMID: 37805563 PMCID: PMC10559630 DOI: 10.1186/s13023-023-02928-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/24/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Severe primary insulin-like growth factor-I (IGF-I) deficiency (SPIGFD) is a rare growth disorder characterized by short stature (standard deviation score [SDS] ≤ 3.0), low circulating concentrations of IGF-I (SDS ≤ 3.0), and normal or elevated concentrations of growth hormone (GH). Laron syndrome is the best characterized form of SPIGFD, caused by a defect in the GH receptor (GHR) gene. However, awareness of SPIGFD remains low, and individuals living with SPIGFD continue to face challenges associated with diagnosis, treatment and care. OBJECTIVE To gather perspectives on the key challenges for individuals and families living with SPIGFD through a multi-stakeholder approach. By highlighting critical gaps in the awareness, diagnosis, and management of SPIGFD, this report aims to provide recommendations to improve care for people affected by SPIGFD globally. METHODS An international group of clinical experts, researchers, and patient and caregiver representatives from the SPIGFD community participated in a virtual, half-day meeting to discuss key unmet needs and opportunities to improve the care of people living with SPIGFD. RESULTS As a rare disorder, limited awareness and understanding of SPIGFD amongst healthcare professionals (HCPs) poses significant challenges in the diagnosis and treatment of those affected. Patients often face difficulties associated with receiving a formal diagnosis, delayed treatment initiation and limited access to appropriate therapy. This has a considerable impact on the physical health and quality of life for patients, highlighting a need for more education and clearer guidance for HCPs. Support from patient advocacy groups is valuable in helping patients and their families to find appropriate care. However, there remains a need to better understand the burden that SPIGFD has on individuals beyond height, including the impact on physical, emotional, and social wellbeing. CONCLUSIONS To address the challenges faced by individuals and families affected by SPIGFD, greater awareness of SPIGFD is needed within the healthcare community, and a consensus on best practice in the care of individuals affected by this condition. Continued efforts are also needed at a global level to challenge existing perceptions around SPIGFD, and identify solutions that promote equitable access to appropriate care. Medical writing support was industry-sponsored.
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Affiliation(s)
- Philippe F Backeljauw
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Mary Andrews
- The Major Aspects of Growth in Children (MAGIC) Foundation, Warrenville, IL, USA
- The MAGIC Foundation International Coalition for Organizations Supporting Endocrine Patients (MAGIC-ICOSEP), Atlanta, GA, USA
| | - Peter Bang
- Division of Children's and Women's Health, Department of Biomedical and Clinical Sciences (BKV), Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | | | - Cheri L Deal
- Université de Montréal, Montréal, QC, Canada
- Centre Hospitalier Universitaire (CHU) Sainte-Justine, Montréal, QC, Canada
| | - Jamie Harvey
- The Major Aspects of Growth in Children (MAGIC) Foundation, Warrenville, IL, USA
- The MAGIC Foundation International Coalition for Organizations Supporting Endocrine Patients (MAGIC-ICOSEP), Atlanta, GA, USA
| | - Shirley Langham
- Paediatric Endocrinology, Great Ormond Street Hospital UCL Hospitals, London, UK
| | - Elżbieta Petriczko
- Department of Paediatrics, Endocrinology, Diabetology, Metabolic Disorders, and Cardiology of Developmental Age, Pomeranian Medical University, Szczecin, Poland
| | - Michel Polak
- Department of Pediatric Endocrinology, Gynecology and Diabetology, Hôpital Universitaire Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mehul T Dattani
- Paediatric Endocrinology, Great Ormond Street Hospital UCL Hospitals, London, UK.
- UCL Great Ormond Street Institute of Child Health, London, UK.
- Adolescent Endocrinology, UCL Hospitals, London, UK.
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15
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McBride DJ, Fielding C, Newington T, Vatsiou A, Fischl H, Bajracharya M, Thomson VS, Fraser LJ, Fujita PA, Becq J, Kingsbury Z, Ross MT, Moat SJ, Morgan S. Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen. Int J Neonatal Screen 2023; 9:52. [PMID: 37754778 PMCID: PMC10532340 DOI: 10.3390/ijns9030052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
The collection of dried blood spots (DBS) facilitates newborn screening for a variety of rare, but very serious conditions in healthcare systems around the world. Sub-punches of varying sizes (1.5-6 mm) can be taken from DBS specimens to use as inputs for a range of biochemical assays. Advances in DNA sequencing workflows allow whole-genome sequencing (WGS) libraries to be generated directly from inputs such as peripheral blood, saliva, and DBS. We compared WGS metrics obtained from libraries generated directly from DBS to those generated from DNA extracted from peripheral blood, the standard input for this type of assay. We explored the flexibility of DBS as an input for WGS by altering the punch number and size as inputs to the assay. We showed that WGS libraries can be successfully generated from a variety of DBS inputs, including a single 3 mm or 6 mm diameter punch, with equivalent data quality observed across a number of key metrics of importance in the detection of gene variants. We observed no difference in the performance of DBS and peripheral-blood-extracted DNA in the detection of likely pathogenic gene variants in samples taken from individuals with cystic fibrosis or phenylketonuria. WGS can be performed directly from DBS and is a powerful method for the rapid discovery of clinically relevant, disease-causing gene variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Stuart J. Moat
- Wales Newborn Screening Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
- School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
| | - Sian Morgan
- All Wales Genetics Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
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16
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Zappas MP, Devereaux A, Pesch MH. The Psychosocial Impact of Congenital Cytomegalovirus on Caregivers and Families: Lived Experiences and Review of the Literature. Int J Neonatal Screen 2023; 9:30. [PMID: 37367211 DOI: 10.3390/ijns9020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Caring for a child with congenital cytomegalovirus (cCMV) can be costly for families, not only in terms of out-of-pocket expenses, but also in terms of caregiver time, relationships, career trajectories, and mental health. These additional burdens are sometimes referred to as "spillover effects". As parents of children with cCMV, we, the authors of this article, discuss the impact that cCMV has had on our families. While multiple studies have reported on the epidemiology, prevention, screening, diagnosis, and management of cCMV, there has been minimal research regarding the possible impact on the family unit. In this narrative review, we discuss the various areas of the lives of families and caregivers that may be impacted by raising a child with cCMV. Whether children are minimally or severely affected by the sequelae of cCMV, they and their families merit the progression of awareness of the virus and governmental policies to help end cCMV. As the existing cCMV-specific literature is limited, we correlate studies of other childhood disabilities and find the mutuality experienced by families affected by cCMV.
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Affiliation(s)
- Michelle P Zappas
- Department of Nursing, Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA 90015, USA
| | | | - Megan H Pesch
- National CMV Foundation, Tampa, FL 33606, USA
- Division of Developmental and Behavioral Pediatrics, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Smith HS, Bonkowski ES, Hickingbotham MR, Deloge RB, Pereira S. Framing the Family: A Qualitative Exploration of Factors That Shape Family-Level Experience of Pediatric Genomic Sequencing. CHILDREN (BASEL, SWITZERLAND) 2023; 10:774. [PMID: 37238322 PMCID: PMC10217651 DOI: 10.3390/children10050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023]
Abstract
Families of children with rare and undiagnosed conditions face many psychosocial and logistical challenges that may affect their approach to decisions about their child's care and their family's well-being. As genomic sequencing (GS) is increasingly incorporated into pediatric diagnostic workups, assessing the family-level characteristics that shape the experience of pediatric GS is crucial to understanding how families approach decision-making about the test and how they incorporate the results into their family life. We conducted semi-structured interviews with parents and other primary caregivers of pediatric patients who were evaluated for a suspected genetic condition and who were recommended to have GS (n = 20) or who had recently completed GS (n = 21). We analyzed qualitative data using multiple rounds of thematic analysis. We organized our thematic findings into three domains of factors that influence the family-level experience of GS: (1) family structure and dynamics; (2) parental identity, relationships, and philosophies; and (3) social and cultural differences. Participants conceptualized their child's family in various ways, ranging from nuclear biological family to support networks made up of friends and communities. Our findings can inform the design and interpretation of preference research to advance family-level value assessment of GS as well as genetic counseling for families.
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Affiliation(s)
- Hadley Stevens Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily S. Bonkowski
- Institute for Public Health Genetics, University of Washington School of Public Health, Seattle, WA 98195, USA
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Madison R. Hickingbotham
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Raymond Belanger Deloge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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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] [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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Sánchez-Bellver L, Férriz-Gordillo A, Carrillo-Pz M, Rabanal L, Garcia-Gonzalo FR, Marfany G. The Deubiquitinating Enzyme USP48 Interacts with the Retinal Degeneration-Associated Proteins UNC119a and ARL3. Int J Mol Sci 2022; 23:ijms232012527. [PMID: 36293380 PMCID: PMC9603860 DOI: 10.3390/ijms232012527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins related to the ubiquitin-proteasome system play an important role during the differentiation and ciliogenesis of photoreceptor cells. Mutations in several genes involved in ubiquitination and proteostasis have been identified as causative of inherited retinal dystrophies (IRDs) and ciliopathies. USP48 is a deubiquitinating enzyme whose role in the retina is still unexplored although previous studies indicate its relevance for neurosensory organs. In this work, we describe that a pool of endogenous USP48 localises to the basal body in retinal cells and provide data that supports the function of USP48 in the photoreceptor cilium. We also demonstrate that USP48 interacts with the IRD-associated proteins ARL3 and UNC119a, and stabilise their protein levels using different mechanisms. Our results suggest that USP48 may act in the regulation/stabilisation of key ciliary proteins for photoreceptor function, in the modulation of intracellular protein transport, and in ciliary trafficking to the photoreceptor outer segment.
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Affiliation(s)
- Laura Sánchez-Bellver
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Férriz-Gordillo
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Marc Carrillo-Pz
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Laura Rabanal
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Francesc R. Garcia-Gonzalo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, 28029 Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC), 28029 Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina-Institut de Recerca Sant Joan de Déu (IBUB-IRSJD), Universitat de Barcelona, 08028 Barcelona, Spain
- DBGen Ocular Genomics, 08028 Barcelona, Spain
- Correspondence:
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20
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Martinez-Delgado B, Barrero MJ. Epigenomic Approaches for the Diagnosis of Rare Diseases. EPIGENOMES 2022; 6:epigenomes6030021. [PMID: 35997367 PMCID: PMC9397041 DOI: 10.3390/epigenomes6030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the disease. Patients with negative results for these tests frequently undergo whole exome or genome sequencing, leading to the identification of the molecular cause of the disease in 50% of patients at best. Therefore, a significant proportion of patients remain undiagnosed after sequencing their genome. Recently, approaches based on functional aspects of the genome, including transcriptomics and epigenomics, are beginning to emerge. Here, we will review these approaches, including studies that have successfully provided diagnoses for complex undiagnosed cases.
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Affiliation(s)
- Beatriz Martinez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER U758, 28029 Madrid, Spain
| | - Maria J. Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), 28220 Madrid, Spain
- Correspondence:
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