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Yin R, Gutierrez A, Kobren SN, Avillach P. VarPPUD: Variant post prioritization developed for undiagnosed genetic disorders. medRxiv 2024:2024.04.15.24305876. [PMID: 38699371 PMCID: PMC11065012 DOI: 10.1101/2024.04.15.24305876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Rare and ultra-rare genetic conditions are estimated to impact nearly 1 in 17 people worldwide, yet accurately pinpointing the diagnostic variants underlying each of these conditions remains a formidable challenge. Because comprehensive, in vivo functional assessment of all possible genetic variants is infeasible, clinicians instead consider in silico variant pathogenicity predictions to distinguish plausibly disease-causing from benign variants across the genome. However, in the most difficult undiagnosed cases, such as those accepted to the Undiagnosed Diseases Network (UDN), existing pathogenicity predictions cannot reliably discern true etiological variant(s) from other deleterious candidate variants that were prioritized through N-of-1 efforts. Pinpointing the disease-causing variant from a pool of plausible candidates remains a largely manual effort requiring extensive clinical workups, functional and experimental assays, and eventual identification of genotype- and phenotype-matched individuals. Here, we introduce VarPPUD, a tool trained on prioritized variants from UDN cases, that leverages gene-, amino acid-, and nucleotide-level features to discern pathogenic variants from other deleterious variants that are unlikely to be confirmed as disease relevant. VarPPUD achieves a cross-validated accuracy of 79.3% and precision of 77.5% on a held-out subset of uniquely challenging UDN cases, respectively representing an average 18.6% and 23.4% improvement over nine traditional pathogenicity prediction approaches on this task. We validate VarPPUD's ability to discriminate likely from unlikely pathogenic variants on synthetic, GAN-generated candidate variants as well. Finally, we show how VarPPUD can be probed to evaluate each input feature's importance and contribution toward prediction-an essential step toward understanding the distinct characteristics of newly-uncovered disease-causing variants. Significance Statement Patients with chronic, undiagnosed and underdiagnosed genetic conditions often endure expensive and excruciating years-long diagnostic odysseys without clear results. In many instances, clinical genome sequencing of patients and their family members fails to reveal known disease-causing variants, although compelling variants of uncertain significance are frequently encountered. Existing computational tools struggle to reliably differentiate truly disease-causing variants from other plausible candidate variants within these prioritized sets. Consequently, the confirmation of disease-causing variants often necessitates extensive experimental follow-up, including studies in model organisms and identification of other similarly presenting genotype-matched individuals, a process that can extend for several years. Here, we present VarPPUD, a tool trained specifically to distinguish likely from unlikely to be confirmed pathogenic variants that were prioritized across cases in the Undiagnosed Diseases Network. By evaluating the importance and impact of different input feature values on prediction, we gain deeper insights into the distinctive attributes of difficult-to-identify diagnostic variants. For patients who remain undiagnosed following comprehensive whole genome sequencing, our new method VarPPUD may reveal pathogenic variants amid a pool of candidate variants, thereby advancing diagnostic efforts where progress has otherwise stalled.
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Affiliation(s)
- William A Gahl
- Senior Investigator, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20, ,892
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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [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] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Witt S, Schuett K, Wiegand-Grefe S, Boettcher J, Quitmann J. Living with a rare disease - experiences and needs in pediatric patients and their parents. Orphanet J Rare Dis 2023; 18:242. [PMID: 37568186 PMCID: PMC10422846 DOI: 10.1186/s13023-023-02837-9] [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: 06/09/2022] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND A rare disease (RD) diagnosis and therapy can affect the family's quality of life and mental health. A lack of information and missing care options lead to helplessness and psychological stress within families. This work aims to identify patients' and parents' experiences in daily life and with the health care system as well as their needs and current pathways to psychosocial care to develop implementation strategies adapted to the families' needs. METHODS The present analysis is part of the national multicenter study "Children Affected by Rare Disease and Their Families-Network (CARE-FAM-NET)." We conducted semi-structured telephone interviews with children, adolescents, and young adults with RD (aged 12 to 21 years) and parents of children with RD (aged 0 to 17 years). We analyzed the transcribed and anonymized interviews using the method of focused interview analyses to identify previous experiences with medical and psychosocial care and possible needs for improvement and support. RESULTS Seventy-four parents of children with RD and 15 children, adolescents, and young adults with RD participated. Five main themes emerged. Daily life with an RD: RD affects the everyday and social life of the respondents, negatively impacting mental well-being. Experiences with the health care system: The long diagnostic path is stressful for families. Professionals' lack of information/education leads to inadequate care for those affected. Psychosocial support: Families do not know about psychosocial care services. In some cases, the families take advantage of psychosocial support services (such as support groups or advocacy groups), which are predominantly very helpful. Difficulties and barriers: Time, socio-legal and organizational problems burden families and lead to advantages in using psychosocial services. Improvements for patient-oriented support: Those affected wished for timely, preventive support (especially in administrative and socio-legal matters) and education regarding psychosocial care services. CONCLUSION RD represent a great challenge for all family members - patients, parents, and siblings. The patients' and parents' previous experiences in daily life, medical and psychosocial care show a need for target-group specific support, including training of health care professionals and low-threshold access care services and practical help for all family members.
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Affiliation(s)
- Stefanie Witt
- Department of Medical Psychology, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52 W 26, Hamburg, 20246, Germany.
| | - Katharina Schuett
- Department of Medical Psychology, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52 W 26, Hamburg, 20246, Germany
| | - Silke Wiegand-Grefe
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Boettcher
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Quitmann
- Department of Medical Psychology, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52 W 26, Hamburg, 20246, Germany
- Faculty of Business and Social Sciences, University of Applied Sciences Hamburg, Hamburg, Germany
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Halley MC, Olson NW. Blurred Boundaries: Toward an Expanded Ethics of Research and Clinical Care. Am J Bioeth 2023; 23:5-9. [PMID: 38410998 DOI: 10.1080/15265161.2023.2224148] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
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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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Gahl WA, Perry M. Desperately seeking solutions. Genet Med 2022; 24:2419-2421. [PMID: 36112139 DOI: 10.1016/j.gim.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 10/14/2022] Open
Affiliation(s)
- William A Gahl
- NIH Undiagnosed Diseases Program, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD.
| | - Mary Perry
- Office of Strategic Coordination, Office of the Director, National Institutes of Health, Bethesda, MD
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Montano C, Cassini T, Ziegler SG, Boehm M, Nicoli ER, Mindell JA, Soldatos AG, Manoli I, Wolfe L, Macnamara EF, Malicdan MCV, Adams DR, Tifft CJ, Toro C, Gahl WA. Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program. J Inherit Metab Dis 2022; 45:907-918. [PMID: 35490291 DOI: 10.1002/jimd.12506] [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: 02/16/2022] [Revised: 04/14/2022] [Accepted: 04/27/2022] [Indexed: 11/11/2022]
Abstract
Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.
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Affiliation(s)
- Carolina Montano
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Thomas Cassini
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Shira G Ziegler
- Departments of Pediatrics and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Elena-Raluca Nicoli
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Joseph A Mindell
- Membrane Transport Biophysics Section, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Ariane G Soldatos
- Office of the Clinical Director, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Irini Manoli
- Organic Acid Research Section, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Lynne Wolfe
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | | | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Cynthia J Tifft
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
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Abstract
Many large research initiatives have cumulatively enrolled thousands of patients with a range of complex medical issues but no clear genetic etiology. However, it is unclear how researchers, institutions, and funders should manage the data and relationships with those participants who remain undiagnosed when these studies end. In this comment, we outline the current literature relevant to post-study obligations in clinical genomics research and discuss the application of current guidelines to research with undiagnosed participants.
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Harnish JM, Li L, Rogic S, Poirier-Morency G, Kim SY, Boycott KM, Wangler MF, Bellen HJ, Hieter P, Pavlidis P, Liu Z, Yamamoto S. ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. Hum Mutat 2022; 43:743-759. [PMID: 35224820 PMCID: PMC9133126 DOI: 10.1002/humu.24364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/30/2021] [Revised: 02/12/2022] [Accepted: 02/23/2022] [Indexed: 11/08/2022]
Abstract
Next-generation sequencing is a prevalent diagnostic tool for undiagnosed diseases and has played a significant role in rare disease gene discovery. Although this technology resolves some cases, others are given a list of possibly damaging genetic variants necessitating functional studies. Productive collaborations between scientists, clinicians, and patients (affected individuals) can help resolve such medical mysteries and provide insights into in vivo function of human genes. Furthermore, facilitating interactions between scientists and research funders, including nonprofit organizations or commercial entities, can dramatically reduce the time to translate discoveries from bench to bedside. Several systems designed to connect clinicians and researchers with a shared gene of interest have been successful. However, these platforms exclude some stakeholders based on their role or geography. Here we describe ModelMatcher, a global online matchmaking tool designed to facilitate cross-disciplinary collaborations, especially between scientists and other stakeholders of rare and undiagnosed disease research. ModelMatcher is integrated into the Rare Diseases Models and Mechanisms Network and Matchmaker Exchange, allowing users to identify potential collaborators in other registries. This living database decreases the time from when a scientist or clinician is making discoveries regarding their genes of interest, to when they identify collaborators and sponsors to facilitate translational and therapeutic research.
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Affiliation(s)
- J. Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
| | - Lucian Li
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | | | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Graduate Program, BCM, Houston, TX, 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
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12
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van der Velde KJ, Singh G, Kaliyaperumal R, Liao X, de Ridder S, Rebers S, Kerstens HHD, de Andrade F, van Reeuwijk J, De Gruyter FE, Hiltemann S, Ligtvoet M, Weiss MM, van Deutekom HWM, Jansen AML, Stubbs AP, Vissers LELM, Laros JFJ, van Enckevort E, Stemkens D, 't Hoen PAC, Beliën JAM, van Gijn ME, Swertz MA. FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Sci Data 2022; 9:169. [PMID: 35418585 PMCID: PMC9008059 DOI: 10.1038/s41597-022-01265-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/20/2021] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org .
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Affiliation(s)
- K Joeri van der Velde
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gurnoor Singh
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Rajaram Kaliyaperumal
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - XiaoFeng Liao
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Sander de Ridder
- Amsterdam University Medical Center, University of Amsterdam, Department of Pathology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Susanne Rebers
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hindrik H D Kerstens
- Prinses Máxima Center for Pediatric Oncology, Kemmeren group, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Fernanda de Andrade
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jeroen van Reeuwijk
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Fini E De Gruyter
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Saskia Hiltemann
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Maarten Ligtvoet
- Nictiz - Dutch competence centre for electronic exchange of health and care information, Oude Middenweg 55, 2491 AC, The Hague, The Netherlands
| | - Marjan M Weiss
- Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hanneke W M van Deutekom
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Anne M L Jansen
- University Medical Center Utrecht, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Andrew P Stubbs
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisenka E L M Vissers
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen F J Laros
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Leiden University Medical Center, Department of Clinical Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Esther van Enckevort
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Daphne Stemkens
- VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands, Koninginnelaan 23, 3762 DA, Soest, The Netherlands
| | - Peter A C 't Hoen
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen A M Beliën
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Mariëlle E van Gijn
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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13
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Yamamoto Y, Kanayama N, Nakayama Y, Matsushima N. Current Status, Issues and Future Prospects of Personalized Medicine for Each Disease. J Pers Med 2022; 12:444. [PMID: 35330444 PMCID: PMC8949099 DOI: 10.3390/jpm12030444] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, with the advancement of next-generation sequencing (NGS) technology, gene panel tests have been approved in the field of cancer diseases, and approaches to prescribe optimal molecular target drugs to patients are being developed. In the field of rare diseases, whole-genome and whole-exome analysis has been used to identify the causative genes of undiagnosed diseases and to diagnose patients’ diseases, and further progress in personalized medicine is expected. In order to promote personalized medicine in the future, we investigated the current status and progress of personalized medicine in disease areas other than cancer and rare diseases, where personalized medicine is most advanced. We selected rheumatoid arthritis and psoriasis as the inflammatory disease, in addition to Alzheimer’s disease. These diseases have high unmet needs for personalized medicine from the viewpoints of disease mechanisms, diagnostic biomarkers, therapeutic drugs with diagnostic markers and treatment satisfaction. In rheumatoid arthritis and psoriasis, there are many therapeutic options; however, diagnostic methods have not been developed to select the best treatment for each patient. In addition, there are few effective therapeutic agents in Alzheimer’s disease, although clinical trials of many candidate drugs have been conducted. In rheumatoid arthritis and psoriasis, further elucidation of the disease mechanism is desired to enable the selection of appropriate therapeutic agents according to the patient profile. In the case of Alzheimer’s disease, progress in preventive medicine is desired through the establishment of an early diagnosis method as well as the research and development of innovative therapeutic agents. To this end, we hope for further research and development of diagnostic markers and new drugs through progress in comprehensive data analysis such as comprehensive genomic and transcriptomic information. Furthermore, new types of markers such as miRNAs and the gut microbiome are desired to be utilized in clinical diagnostics.
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Puri RD, Dalal A, Moirangthem A. Indian Undiagnosed Diseases Program (I-UDP) — The Unmet Need. Indian Pediatr 2022. [DOI: 10.1007/s13312-022-2464-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Groft SC, Posada M, Taruscio D. Progress, challenges and global approaches to rare diseases. Acta Paediatr 2021; 110:2711-2716. [PMID: 34105798 DOI: 10.1111/apa.15974] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 03/20/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022]
Abstract
Rare diseases occur globally at every stage of life. Patients, families and caregivers have many unmet medical and social needs leading to extraordinary psychosocial and economic burdens. Efforts to improve diagnostic capabilities and to develop therapies for an estimated 7000 rare diseases have met with considerable success. In the United States, a rare disease or condition is one affecting fewer than 200,000 people. In the European Union (EU), a rare disease is any disease affecting fewer than 5 people in 10,000 (less than 1 in 2000 people). However, there are no effective treatments for 90 per cent of rare diseases. There is a need to expand awareness, advocacy and outreach to everyone including those with low incomes, poor literacy, minority ethnic status and living in underserved and marginalised populations in urban and rural areas as well as in developing nations throughout the world. The acceptance of patients as research partners complements the increased research emphasis and major regulatory initiatives leading to expedited review and approval programmes for products for serious or life-threatening conditions. The pipeline of new therapies provides hope to untreated patients. Advances in medical bioinformatics, artificial intelligence and machine learning with access to big data continue to identify novel therapeutics for screening and evaluation. Advanced analytics can identify the patterns of disease occurrence, predict disease progression, identify patient response to treatments, establish optimal care guidelines and generate research hypotheses with the narrowly identified research patient populations.
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Affiliation(s)
- Stephen C. Groft
- National Center for Advancing Translational Sciences National Institutes of Health Bethesda MD USA
| | - Manuel Posada
- Institute of Rare Diseases Research (IIER) Instituto de Salud Carlos III Madrid Spain
| | - Domenica Taruscio
- National Centre for Rare Diseases Istituto Superiore di Sanità Rome Italy
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16
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Fox G, Fergusson DA, Daham Z, Youssef M, Foster M, Poole E, Sharif A, Richards DP, Hendrick K, Mendelson AA, Macala KF, Monfaredi Z, Montroy J, Fiest KM, Presseau J, Lalu MM. Patient engagement in preclinical laboratory research: A scoping review. EBioMedicine 2021; 70:103484. [PMID: 34280783 DOI: 10.1016/j.ebiom.2021.103484] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND 'Patient engagement' involves meaningful collaboration between researchers and 'patient partners' to co-create research. It helps ensure that research being conducted is relevant to its ultimate end-users. Although patient engagement within clinical research has been well documented, the prevalence and effects of patient engagement in translational preclinical laboratory research remain unclear. The aim of this scoping review is to present current patient engagement activities reported in preclinical laboratory research. METHODS MEDLINE, Embase, and grey literature were systematically searched from inception to April 2021. Studies that described or investigated patient engagement in preclinical laboratory research were included. Patient engagement activities where patients (i.e. patients, family members, caregivers or community members) provided input, or consultation on at least one element of the research process were eligible for inclusion. Study characteristics and outcomes were extracted and organized thematically. FINDINGS 32 reports were included (30 primary studies, 1 narrative review, and 1 researcher guide). Most studies engaged patients at the education or priority setting stages (n=26). The most frequently reported benefit of patient engagement was 'providing a mutual learning opportunity'. Reported barriers to patient engagement reflected concerns around 'differences in knowledge and research experience' and how this may challenge communication and limit meaningful collaboration. INTERPRETATION Patient engagement is feasible and beneficial for preclinical laboratory research. Future work should focus on assessing the impacts of patient engagement in this area of research.
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17
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Taruscio D, Mantovani A. Multifactorial Rare Diseases: Can Uncertainty Analysis Bring Added Value to the Search for Risk Factors and Etiopathogenesis? ACTA ACUST UNITED AC 2021; 57:medicina57020119. [PMID: 33525390 PMCID: PMC7911455 DOI: 10.3390/medicina57020119] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022]
Abstract
Uncertainty analysis is the process of identifying limitations in knowledge and evaluating their implications for scientific conclusions. Uncertainty analysis is a stable component of risk assessment and is increasingly used in decision making on complex health issues. Uncertainties should be identified in a structured way and prioritized according to their likely impact on the outcome of scientific conclusions. Uncertainty is inherent to the rare diseases (RD) area, where research and healthcare have to cope with knowledge gaps due to the rarity of the conditions; yet a systematic approach toward uncertainties is not usually undertaken. The uncertainty issue is particularly relevant to multifactorial RD, whose etiopathogenesis involves environmental factors and genetic predisposition. Three case studies are presented: the newly recognized acute multisystem inflammatory syndrome in children and adolescents associated with SARS-CoV-2 infection; the assessment of risk factors for neural tube defects; and the genotype-phenotype correlation in familial Mediterranean fever. Each case study proposes the initial identification of the main epistemic and sampling uncertainties and their impacts. Uncertainty analysis in RD may present aspects similar to those encountered when conducting risk assessment in data-poor scenarios; therefore, approaches such as expert knowledge elicitation may be considered. The RD community has a main strength in managing uncertainty, as it proactively develops stakeholder involvement, data sharing and open science. The open science approaches can be profitably integrated by structured uncertainty analysis, especially when dealing with multifactorial RD involving environmental and genetic risk factors.
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Affiliation(s)
- Domenica Taruscio
- National Center for Rare Diseases, Italian National Institute of Health (ISS), 00161 Roma, Italy
- Correspondence:
| | - Alberto Mantovani
- Department on Food Safety, Nutrition and Veterinary Public Health, Italian National Institute of Health (ISS), 00161 Roma, Italy;
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18
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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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19
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Salvatore M, Polizzi A, De Stefano MC, Floridia G, Baldovino S, Roccatello D, Sciascia S, Menegatti E, Remuzzi G, Daina E, Iatropoulos P, Bembi B, Da Riol RM, Ferlini A, Neri M, Novelli G, Sangiuolo F, Brancati F, Taruscio D. Improving diagnosis for rare diseases: the experience of the Italian undiagnosed Rare diseases network. Ital J Pediatr 2020; 46:130. [PMID: 32928283 PMCID: PMC7488856 DOI: 10.1186/s13052-020-00883-8] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background For a number of persons with rare diseases (RDs) a definite diagnosis remains undiscovered with relevant physical, psychological and social consequences. Undiagnosed RDs (URDs) require other than specialised clinical centres, outstanding molecular investigations, common protocols and dedicated actions at national and international levels; thus, many “Undiagnosed RDs programs” have been gradually developed on the grounds of a well-structured multidisciplinary approach. Methods The Italian Undiagnosed Rare Diseases Network (IURDN) was established in 2016 to improve the level of diagnosis of persons with URD living in Italy. Six Italian Centres of Expertise represented the network. The National Centre for Rare Diseases at the Istituto Superiore di Sanità coordinates the whole project. The software PhenoTips was used to collect the information of the clinical cases. Results One hundred and ten cases were analysed between March 2016 and June 2019. The age of onset of the diseases ranged from prenatal age to 51 years. Conditions were predominantly sporadic; almost all patients had multiple organs involvements. A total of 13/71 family cases were characterized by WES; in some families more than one individual was affected, so leading to 20/71 individuals investigated. Disease causing variants were identified in two cases and were associated to previously undescribed phenotypes. In 5 cases, new candidate genes were identified, although confirmatory tests are pending. In three families, investigations were not completed due to the scarce compliance of members and molecular investigations were temporary suspended. Finally, three cases (one familial) remain still unsolved. Twelve undiagnosed clinical cases were then selected to be shared at International level through PhenomeCentral in accordance to the UDNI statement. Conclusions Our results showed a molecular diagnostic yield of 53,8%; this value is comparable to the diagnostic rates reported in other international studies. Cases collected were also pooled with those collected by UDNI International Network. This represents a unique example of global initiative aimed at sharing and validating knowledge and experience in this field. IURDN is a multidisciplinary and useful initiative linking National and International efforts aimed at making timely and appropriate diagnoses in RD patients who still do not have a confirmed diagnosis even after a long time.
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Affiliation(s)
- Marco Salvatore
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy.
| | - Agata Polizzi
- Department of Educational Science, University of Catania, Catania, Italy
| | | | | | - Simone Baldovino
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Dario Roccatello
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Savino Sciascia
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Elisa Menegatti
- Department of Clinical and Biological Sciences, University of Turin and S. Giovanni Bosco Hospital, Centre of Research of Immunopathology and Rare Diseases - Regional Coordinating Centre of the National Network for Rare Diseases, Turin, Italy
| | - Giuseppe Remuzzi
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Erica Daina
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Paraskevas Iatropoulos
- IRCCS Mario Negri Pharmacological Research Institute, Regional Coordinating Centre of the National Network for Rare Diseases, Clinical Research Centre for Rare Diseases "Aldo e Cele Daccò", Ranica, Bergamo, Italy
| | - Bruno Bembi
- S.O.C. Regional Coordinating Centre of the National Network for Rare Diseases, S. Maria della Misericordia Hospital, Udine, Italy
| | - Rosalia Maria Da Riol
- S.O.C. Regional Coordinating Centre of the National Network for Rare Diseases, S. Maria della Misericordia Hospital, Udine, Italy
| | - Alessandra Ferlini
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Marcella Neri
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Tor Vergata and University Hospital Tor Vergata, Unit of Medical Genetics Rome & IRCCS Neuromed, Pozzilli, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Tor Vergata and University Hospital Tor Vergata, Unit of Medical Genetics, Rome, Italy
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, Unit of Medical Genetics University of L'Aquila, L'Aquila, Italy
| | - Domenica Taruscio
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
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20
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Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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