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Westerheim I, Cormier-Daire V, Gilbert S, O'Malley S, Keen R. Osteogenesis Imperfecta: A study of the patient journey in 13 European countries. Orphanet J Rare Dis 2024; 19:331. [PMID: 39252130 PMCID: PMC11386111 DOI: 10.1186/s13023-024-03345-0] [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: 04/02/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
INTRODUCTION Osteogenesis imperfecta (OI) is a heritable skeletal disorder and comprises various subtypes that differ in clinical presentation, with Type I considered the least severe and Types III/IV the most severe forms. The study aim was to understand the OI patient diagnostic and treatment journey across Europe. METHODS We conducted a qualitative, descriptive study to understand the OI patient journey. A selection of people with OI/their caregivers and clinicians involved in OI-patient care from across Europe were interviewed using a specially developed questionnaire. RESULTS Between May 2022 and July 2022, 22 people with OI/caregivers and 22 clinicians (endocrinologists, orthopaedic surgeons, geneticists and metabolic specialists) from across Europe were interviewed. Our study showed various areas of concerns for the OI community. Timely diagnosis of OI is essential; misdiagnoses and a delay to treatment initiation are all too common. There are a lack of consensus guidelines regarding optimal treatments (including when bisphosphonate therapy should be initiated and the route of administration) and patient management throughout the duration of the patient's life. Adult OI patients do not have a medical home and are often managed by endocrinologists and rheumatologists. Adult care is often reactive based on the development of new symptoms. The psychosocial burden of OI impacts on the patient's quality of life. CONCLUSIONS There is an urgent need for increased awareness about OI and its wide range of symptoms. In particular, there is a need for consensus guidelines outlining the optimum care throughout the duration of the OI patient's life.
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Affiliation(s)
- Ingunn Westerheim
- Osteogenesis Imperfecta Federation Europe (OIFE), Schotelveldstraat 17, Heffen, 2801, Belgium.
| | - Valerie Cormier-Daire
- Reference Center for Skeletal Dysplasia, Paris Cité University, INSERM UMR 1163, Imagine Institute, Hôpital Necker-Enfants Malades, 149 rue de Sévres, Paris, 75015, France
| | - Scott Gilbert
- , Putnam Associates, 22-24 Torrington Place Fitzrovia, London, WC1E 7HJ, UK
| | - Sean O'Malley
- , Putnam Associates, 22-24 Torrington Place Fitzrovia, London, WC1E 7HJ, UK
| | - Richard Keen
- Royal National Orthopaedic Hospital NHS Trust, Brockley Hill, Stanmore, Middlesex, HA7 4LP, UK
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Kany S, Jurgens SJ, Rämö JT, Christophersen IE, Rienstra M, Chung MK, Olesen MS, Ackerman MJ, McNally EM, Semsarian C, Schnabel RB, Wilde AAM, Benjamin EJ, Rehm HL, Kirchhof P, Bezzina CR, Roden DM, Shoemaker MB, Ellinor PT. Genetic testing in early-onset atrial fibrillation. Eur Heart J 2024; 45:3111-3123. [PMID: 39028637 PMCID: PMC11379493 DOI: 10.1093/eurheartj/ehae298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/18/2024] [Accepted: 04/30/2024] [Indexed: 07/21/2024] Open
Abstract
Atrial fibrillation (AF) is a globally prevalent cardiac arrhythmia with significant genetic underpinnings, as highlighted by recent large-scale genetic studies. A prominent clinical and genetic overlap exists between AF, heritable ventricular cardiomyopathies, and arrhythmia syndromes, underlining the potential of AF as an early indicator of severe ventricular disease in younger individuals. Indeed, several recent studies have demonstrated meaningful yields of rare pathogenic variants among early-onset AF patients (∼4%-11%), most notably for cardiomyopathy genes in which rare variants are considered clinically actionable. Genetic testing thus presents a promising opportunity to identify monogenetic defects linked to AF and inherited cardiac conditions, such as cardiomyopathy, and may contribute to prognosis and management in early-onset AF patients. A first step towards recognizing this monogenic contribution was taken with the Class IIb recommendation for genetic testing in AF patients aged 45 years or younger by the 2023 American College of Cardiology/American Heart Association guidelines for AF. By identifying pathogenic genetic variants known to underlie inherited cardiomyopathies and arrhythmia syndromes, a personalized care pathway can be developed, encompassing more tailored screening, cascade testing, and potentially genotype-informed prognosis and preventive measures. However, this can only be ensured by frameworks that are developed and supported by all stakeholders. Ambiguity in test results such as variants of uncertain significance remain a major challenge and as many as ∼60% of people with early-onset AF might carry such variants. Patient education (including pretest counselling), training of genetic teams, selection of high-confidence genes, and careful reporting are strategies to mitigate this. Further challenges to implementation include financial barriers, insurability issues, workforce limitations, and the need for standardized definitions in a fast-moving field. Moreover, the prevailing genetic evidence largely rests on European descent populations, underscoring the need for diverse research cohorts and international collaboration. Embracing these challenges and the potential of genetic testing may improve AF care. However, further research-mechanistic, translational, and clinical-is urgently needed.
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Affiliation(s)
- Shinwan Kany
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, 02412, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital,185 Cambridge St, 02114, Boston, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, 02412, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital,185 Cambridge St, 02114, Boston, MA, USA
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, Netherlands
- Department of Experimental Cardiology, Heart Center, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Joel T Rämö
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, 02412, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital,185 Cambridge St, 02114, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ingrid E Christophersen
- Department of Medical Research, Baerum Hospital, Vestre Viken Hospital Trust, Rud, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mina K Chung
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Cleveland Clinic, Heart, Vascular & Thoracic Institute, Cleveland, OH, USA
| | - Morten S Olesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Ackerman
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smight Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
- Division of Pediatric Cardiology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Renate B Schnabel
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Arthur A M Wilde
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, Netherlands
- Department of Experimental Cardiology, Heart Center, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
- Department of Cardiology, Heart Center, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, theNetherlands
- European Reference Network for RARE, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart
| | - Emelia J Benjamin
- Department of Medicine, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, 25 Shattuck St, 02115, Boston, MA, USA
| | - Paulus Kirchhof
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Connie R Bezzina
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, Netherlands
- Department of Experimental Cardiology, Heart Center, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Benjamin Shoemaker
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, 02412, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital,185 Cambridge St, 02114, Boston, MA, USA
- Harvard Medical School, 25 Shattuck St, 02115, Boston, MA, USA
- Cardiology Division, Massachusetts General Hospital, 55 Fruit St, 02114, Boston, MA, USA
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Tikhonova TB, Sharkov AA, Zhorov BS, Vassilevski AA. Diverse biophysical mechanisms in voltage-gated sodium channel Na v1.4 variants associated with myotonia. FASEB J 2024; 38:e23883. [PMID: 39150825 DOI: 10.1096/fj.202400867r] [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: 04/16/2024] [Revised: 07/14/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024]
Abstract
Mutations in SCN4A gene encoding Nav1.4 channel α-subunit, are known to cause neuromuscular disorders such as myotonia or paralysis. Here, we study the effect of two amino acid replacements, K1302Q and G1306E, in the DIII-IV loop of the channel, corresponding to mutations found in patients with myotonia. We combine clinical, electrophysiological, and molecular modeling data to provide a holistic picture of the molecular mechanisms operating in mutant channels and eventually leading to pathology. We analyze the existing clinical data for patients with the K1302Q substitution, which was reported for adults with or without myotonia phenotypes, and report two new unrelated patients with the G1306E substitution, who presented with severe neonatal episodic laryngospasm and childhood-onset myotonia. We provide a functional analysis of the mutant channels by expressing Nav1.4 α-subunit in Xenopus oocytes in combination with β1 subunit and recording sodium currents using two-electrode voltage clamp. The K1302Q variant exhibits abnormal voltage dependence of steady-state fast inactivation, being the likely cause of pathology. K1302Q does not lead to decelerated fast inactivation, unlike several other myotonic mutations such as G1306E. For both mutants, we observe increased window currents corresponding to a larger population of channels available for activation. To elaborate the structural rationale for our experimental data, we explore the contacts involving K/Q1302 and E1306 in the AlphaFold2 model of wild-type Nav1.4 and Monte Carlo-minimized models of mutant channels. Our data provide the missing evidence to support the classification of K1302Q variant as likely pathogenic and may be used by clinicians.
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Affiliation(s)
- Tatiana B Tikhonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Artem A Sharkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University, Moscow, Russia
- Genomed Ltd., Moscow, Russia
| | - Boris S Zhorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Sechenov Institute of Evolutionary Physiology & Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Dolgoprudny, Russia
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Vavassori S, Russell S, Scotti C, Benvenuti S. Unlocking the full potential of rare disease drug development: exploring the not-for-profit sector's contributions to drug development and access. Front Pharmacol 2024; 15:1441807. [PMID: 39188954 PMCID: PMC11345155 DOI: 10.3389/fphar.2024.1441807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/29/2024] [Indexed: 08/28/2024] Open
Abstract
This commentary provides a comprehensive overview of the challenges and opportunities in the field of drug development for rare diseases and especially of gene therapy products for ultra-rare diseases. It discusses the limited market size, reimbursement and scientific complexities that deter pharmaceutical investment in this field. Highlighting the pivotal role of charitable organizations like Fondazione Telethon, it showcases their efforts in funding research and ensuring access to innovative therapies. This commentary also addresses the challenges in therapy distribution, particularly regarding sustainability and global access. It outlines Fondazione Telethon's operational model to try to address these challenges. Finally, it appeals to governments and regulatory bodies to implement policies and incentives aimed at further fostering innovation and accessibility in rare disease drug development and access.
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Magielski J, McSalley I, Parthasarathy S, McKee J, Ganesan S, Helbig I. Advances in big data and omics: Paving the way for discovery in childhood epilepsies. Curr Probl Pediatr Adolesc Health Care 2024; 54:101634. [PMID: 38825428 DOI: 10.1016/j.cppeds.2024.101634] [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] [Indexed: 06/04/2024]
Abstract
The insights gained from big data and omics approaches have transformed the field of childhood genetic epilepsy. With an increasing number of individuals receiving genetic testing for seizures, we are provided with an opportunity to identify clinically relevant subgroups and extract meaningful observations from this large-scale clinical data. However, the volume of data from electronic medical records and omics (e.g., genomics, transcriptomics) is so vast that standardized methods, such as the Human Phenotype Ontology, are necessary for reliable and comprehensive characterization. Here, we explore the integration of clinical and omics data, highlighting how these approaches pave the way for discovery in childhood epilepsies.
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Affiliation(s)
- Jan Magielski
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Ian McSalley
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Shridhar Parthasarathy
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jillian McKee
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19014, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Weymann D, Buckell J, Fahr P, Loewen R, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, Elliott AM, Wordsworth S, Buchanan J, Regier DA. Health Care Costs After Genome-Wide Sequencing for Children With Rare Diseases in England and Canada. JAMA Netw Open 2024; 7:e2420842. [PMID: 38985473 PMCID: PMC11238031 DOI: 10.1001/jamanetworkopen.2024.20842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 07/11/2024] Open
Abstract
Importance Etiologic diagnoses for rare diseases can involve a diagnostic odyssey, with repeated health care interactions and inconclusive diagnostics. Prior studies reported cost savings associated with genome-wide sequencing (GWS) compared with cytogenetic or molecular testing through rapid genetic diagnosis, but there is limited evidence on whether diagnosis from GWS is associated with reduced health care costs. Objective To measure changes in health care costs after diagnosis from GWS for Canadian and English children with suspected rare diseases. Design, Setting, and Participants This cohort study was a quasiexperimental retrospective analysis across 3 distinct English and Canadian cohorts, completed in 2023. Mixed-effects generalized linear regression was used to estimate associations between GWS and costs in the 2 years before and after GWS. Difference-in-differences regression was used to estimate associations of genetic diagnosis and costs. Costs are in 2019 US dollars. GWS was conducted in a research setting (Genomics England 100 000 Genomes Project [100KGP] and Clinical Assessment of the Utility of Sequencing and Evaluation as a Service [CAUSES] Research Clinic) or clinical outpatient setting (publicly reimbursed GWS in British Columbia [BC], Canada). Participants were children with developmental disorders, seizure disorders, or both undergoing GWS between 2014 and 2019. Data were analyzed from April 2021 to September 2023. Exposures GWS and genetic diagnosis. Main Outcomes and Measures Annual health care costs and diagnostic costs per child. Results Study cohorts included 7775 patients in 100KGP, among whom 788 children had epilepsy (mean [SD] age at GWS, 11.6 [11.1] years; 400 female [50.8%]) and 6987 children had an intellectual disability (mean [SD] age at GWS, 8.2 [8.4] years; 2750 female [39.4%]); 77 patients in CAUSES (mean [SD] age at GWS, 8.5 [4.4] years; 33 female [42.9%]); and 118 publicly reimbursed GWS recipients from BC (mean [SD] age at GWS, 5.5 [5.2] years; 58 female [49.2%]). GWS diagnostic yield was 143 children (18.1%) for those with epilepsy and 1323 children (18.9%) for those with an intellectual disability in 100KGP, 47 children (39.8%) in the BC publicly reimbursed setting, and 42 children (54.5%) in CAUSES. Mean annual per-patient spending over the study period was $5283 (95% CI, $5121-$5427) for epilepsy and $3373 (95% CI, $3322-$3424) for intellectual disability in the 100KGP, $724 (95% CI, $563-$886) in CAUSES, and $1573 (95% CI, $1372-$1773) in the BC reimbursed setting. Receiving a genetic diagnosis from GWS was not associated with changed costs in any cohort. Conclusions and Relevance In this study, receiving a genetic diagnosis was not associated with cost savings. This finding suggests that patient benefit and cost-effectiveness should instead drive GWS implementation.
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Affiliation(s)
- Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Buckell
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Primary Health Care Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Biochemical Genetics, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Alison M. Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Dean A. Regier
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Brock DC, Wang M, Hussain HMJ, Rauch DE, Marra M, Pennesi ME, Yang P, Everett L, Ajlan RS, Colbert J, Porto FBO, Matynia A, Gorin MB, Koenekoop RK, Lopez I, Sui R, Zou G, Li Y, Chen R. Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. Hum Mol Genet 2024; 33:945-957. [PMID: 38453143 PMCID: PMC11102593 DOI: 10.1093/hmg/ddae028] [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: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.
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Affiliation(s)
- Daniel C Brock
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Hafiz Muhammad Jafar Hussain
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - David E Rauch
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Lesley Everett
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Radwan S Ajlan
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Jason Colbert
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Rua dos Otoni, 735/507 - Santa Efigênia, Belo Horizonte, MG 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Av. Francisco Sales, 1111 - Santa Efigênia, Belo Horizonte, MG 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, R. Santa Catarina, 941 - Lourdes, Belo Horizonte, MG 30180070, Brazil
| | - Anna Matynia
- College of Optometry, University of Houston, 4401 Martin Luther King Boulevard, Houston, TX 77004, United States
| | - Michael B Gorin
- Jules Stein Eye Institute, University of California Los Angeles, 100 Stein Plaza, Los Angeles, CA 90095, United States
- Department of Ophthalmology, University of California Los Angeles David Geffen School of Medicine, 10833 Le Conte Ave, Los Angeles, CA 90095, United States
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, WC67+HW Dongcheng, Beijing 100005, China
| | - Gang Zou
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, F4RJ+43 Xixia District, Yinchuan, Ningxia, China
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
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8
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Duarte DM, da Silva Lima MB, Sepodes B. Trends from two decades of orphan designations in paediatric rare neuromuscular diseases. J Neurol Sci 2024; 460:122989. [PMID: 38581740 DOI: 10.1016/j.jns.2024.122989] [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: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Rare diseases are characterized by substantial unmet need mostly because the majority have limited, or no treatment options and a large number also affect children. Since the inception of EU orphan regulation in 2000 the European Medicines Agency Committee for Orphan Medicinal Products has received several applications for paediatric rare neuromuscular diseases (PERAN) however treatment options remain limited. Here we discuss the results form an observational, retrospective, cross-sectional study to characterize the currently authorised orphan medicinal products (OMP) and orphan designations (OD) given to products for PERAN in the last two decades. In the EU about half of PERAN diseases have at least one active OD approved since 2000, and about half of these are for Duchenne muscular dystrophy (DMD). The large majority of PERAN diseases do not have an authorised medicine with only 6 OMP currently authorised for Spinal muscular atrophy (3); DMD (1) and Myasthenia gravis (2). One in five products have inactive or discontinued regulatory development but clinical trials are ongoing for the vast majority of PERAN diseases, and more than half are in the final stage of clinical research with significantly more products with medical plausibility based in clinical data reaching advanced stages in clinical development.
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Affiliation(s)
- Dinah M Duarte
- INFARMED, National Authority of Medicines and Health Products, I.P.Lisboa, Portugal.
| | | | - Bruno Sepodes
- Universidade de Lisboa, Faculdade de Farmácia, Lisbon, Portugal
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9
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Stevens CS, Carmichael J, Watkinson R, Kowdle S, Reis RA, Hamane K, Jang J, Park A, Pernet O, Khamaikawin W, Hong P, Thibault P, Gowlikar A, An DS, Lee B. A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592383. [PMID: 38746439 PMCID: PMC11092779 DOI: 10.1101/2024.05.03.592383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhigh stem cell enriched subpopulation. The frequency of CCR5 editing exceeded 90% and bi-allelic CCR5 editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.
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Affiliation(s)
- Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jillian Carmichael
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ruth Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebecca A Reis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kory Hamane
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Jason Jang
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Arnold Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivier Pernet
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Wannisa Khamaikawin
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Patrick Hong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aditya Gowlikar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Dong Sung An
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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10
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Mao D, Liu C, Wang L, Ai-Ouran R, Deisseroth C, Pasupuleti S, Kim SY, Li L, Rosenfeld JA, Meng L, Burrage LC, Wangler MF, Yamamoto S, Santana M, Perez V, Shukla P, Eng CM, Lee B, Yuan B, Xia F, Bellen HJ, Liu P, Liu Z. AI-MARRVEL - A Knowledge-Driven AI System for Diagnosing Mendelian Disorders. NEJM AI 2024; 1:10.1056/aioa2300009. [PMID: 38962029 PMCID: PMC11221788 DOI: 10.1056/aioa2300009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
BACKGROUND Diagnosing genetic disorders requires extensive manual curation and interpretation of candidate variants, a labor-intensive task even for trained geneticists. Although artificial intelligence (AI) shows promise in aiding these diagnoses, existing AI tools have only achieved moderate success for primary diagnosis. METHODS AI-MARRVEL (AIM) uses a random-forest machine-learning classifier trained on over 3.5 million variants from thousands of diagnosed cases. AIM additionally incorporates expert-engineered features into training to recapitulate the intricate decision-making processes in molecular diagnosis. The online version of AIM is available at https://ai.marrvel.org. To evaluate AIM, we benchmarked it with diagnosed patients from three independent cohorts. RESULTS AIM improved the rate of accurate genetic diagnosis, doubling the number of solved cases as compared with benchmarked methods, across three distinct real-world cohorts. To better identify diagnosable cases from the unsolved pools accumulated over time, we designed a confidence metric on which AIM achieved a precision rate of 98% and identified 57% of diagnosable cases out of a collection of 871 cases. Furthermore, AIM's performance improved after being fine-tuned for targeted settings including recessive disorders and trio analysis. Finally, AIM demonstrated potential for novel disease gene discovery by correctly predicting two newly reported disease genes from the Undiagnosed Diseases Network. CONCLUSIONS AIM achieved superior accuracy compared with existing methods for genetic diagnosis. We anticipate that this tool may aid in primary diagnosis, reanalysis of unsolved cases, and the discovery of novel disease genes. (Funded by the NIH Common Fund and others.).
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Affiliation(s)
- Dongxue Mao
- Department of Pediatrics, Baylor College of Medicine, Houston
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Chaozhong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston
| | - Linhua Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston
| | - Rami Ai-Ouran
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Department of Data Science and AI, Al Hussein Technical University, Amman, Jordan
| | - Cole Deisseroth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Sasidhar Pasupuleti
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Seon Young Kim
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Lucian Li
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | | | | | | | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Human Genome Sequencing Center, Baylor College of Medicine, Houston
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Department of Neuroscience, Baylor College of Medicine, Houston
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
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11
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Marshall DA, Hua N, Buchanan J, Christensen KD, Frederix GWJ, Goranitis I, Ijzerman M, Jansen JP, Lavelle TA, Regier DA, Smith HS, Ungar WJ, Weymann D, Wordsworth S, Phillips KA. Paving the path for implementation of clinical genomic sequencing globally: Are we ready? HEALTH AFFAIRS SCHOLAR 2024; 2:qxae053. [PMID: 38783891 PMCID: PMC11115369 DOI: 10.1093/haschl/qxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicolle Hua
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - James Buchanan
- Health Economics and Policy Research Unit, Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London E1 2AB, United Kingdom
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Geert W J Frederix
- Epidemiology and Health Economics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Australian Genomics, Parkville, Victoria 3052, Australia
| | - Maarten Ijzerman
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria 3000, Australia
- Erasmus School of Health Policy & Management, Eramus University Rotterdam, 3062 PA Rotterdam, The Netherlands
| | - Jeroen P Jansen
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, United States
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hadley S Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario M5T 3M6, Canada
| | - Deirdre Weymann
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health and NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Kathryn A Phillips
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
- Health Affairs Scholar Emerging & Global Health Policy, Health Affairs, Washington, DC 20036, United States
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12
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Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. Their phenotypic impacts and evolutionary pattern over time, however, remain elusive in humans due to the technical and ethical complexities in functional studies. By combining human gene age dating and Mendelian disease phenotyping, our research reveals a gradual increase in disease gene proportions with gene age. Logistic regression modeling indicates that this increase could be related to longer protein lengths and higher burdens of deleterious de novo germline variants (DNVs) for older genes. We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials of phenotypic innovation for young genes than for older genes, a process subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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13
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Johnson D, Del Fiol G, Kawamoto K, Romagnoli KM, Sanders N, Isaacson G, Jenkins E, Williams MS. Genetically guided precision medicine clinical decision support tools: a systematic review. J Am Med Inform Assoc 2024; 31:1183-1194. [PMID: 38558013 PMCID: PMC11031215 DOI: 10.1093/jamia/ocae033] [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: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
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Affiliation(s)
- Darren Johnson
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Katrina M Romagnoli
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Nathan Sanders
- School of Medicine, Geisinger Health Systems, Danville, PA 17822, United States
| | - Grace Isaacson
- Family Medicine, Penn Highlands Healthcare, DuBois, PA 16830, United States
| | - Elden Jenkins
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
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14
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Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [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: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
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Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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15
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Piga D, Rimoldi M, Magri F, Zanotti S, Napoli L, Ripolone M, Pagliarani S, Ciscato P, Velardo D, D’Amico A, Bertini E, Comi GP, Ronchi D, Corti S. Case report: A novel ACTA1 variant in a patient with nemaline rods and increased glycogen deposition. Front Neurol 2024; 15:1340693. [PMID: 38500810 PMCID: PMC10944937 DOI: 10.3389/fneur.2024.1340693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Background Congenital myopathies are a group of heterogeneous inherited disorders, mainly characterized by early-onset hypotonia and muscle weakness. The spectrum of clinical phenotype can be highly variable, going from very mild to severe presentations. The course also varies broadly resulting in a fatal outcome in the most severe cases but can either be benign or lead to an amelioration even in severe presentations. Muscle biopsy analysis is crucial for the identification of pathognomonic morphological features, such as core areas, nemaline bodies or rods, nuclear centralizations and congenital type 1 fibers disproportion. However, multiple abnormalities in the same muscle can be observed, making more complex the myopathological scenario. Case presentation Here, we describe an Italian newborn presenting with severe hypotonia, respiratory insufficiency, inability to suck and swallow, requiring mechanical ventilation and gastrostomy feeding. Muscle biopsy analyzed by light microscopy showed the presence of vacuoles filled with glycogen, suggesting a metabolic myopathy, but also fuchsinophilic inclusions. Ultrastructural studies confirmed the presence of normally structured glycogen, and the presence of minirods, directing the diagnostic hypothesis toward a nemaline myopathy. An expanded Next Generation Sequencing analysis targeting congenital myopathies genes revealed the presence of a novel heterozygous c.965 T > A p. (Leu322Gln) variant in the ACTA1 gene, which encodes the skeletal muscle alpha-actin. Conclusion Our case expands the repertoire of molecular and pathological features observed in actinopathies. We highlight the value of ultrastructural examination to investigate the abnormalities detected at the histological level. We also emphasized the use of expanded gene panels in the molecular analysis of neuromuscular patients, especially for those ones presenting multiple bioptic alterations.
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Affiliation(s)
- Daniela Piga
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Martina Rimoldi
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Francesca Magri
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Simona Zanotti
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Laura Napoli
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Michela Ripolone
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Serena Pagliarani
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Patrizia Ciscato
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Daniele Velardo
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Adele D’Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu’ Children’s Research Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu’ Children’s Research Hospital, IRCCS, Rome, Italy
| | - Giacomo Pietro Comi
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Dario Ronchi
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Stefania Corti
- IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
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16
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Lee JY, Oh SH, Keum C, Lee BL, Chung WY. Clinical application of prospective whole-exome sequencing in the diagnosis of genetic disease: Experience of a regional disease center in South Korea. Ann Hum Genet 2024; 88:101-112. [PMID: 37795942 DOI: 10.1111/ahg.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
INTRODUCTION Next-generation sequencing helps clinicians diagnose patients with suspected genetic disorders. The current study aimed to investigate the diagnostic yield and clinical utility of prospective whole-exome sequencing (WES) in rare diseases. METHODS WES was performed in 92 patients who presented with clinical symptoms suggestive of genetic disorders. The WES data were analyzed using an in-house developed software. The patients' phenotypic characteristics were classified according to the human phenotype ontology. RESULTS WES detected 64 variants, 13 were classified as pathogenic, 26 as likely pathogenic, and 25 as variants of uncertain significance. In 57 patients with these variants, 30 were identified as causal variants. The diagnostic yield was higher in patients with abnormalities in joint mobility and skin morphology than in those with cerebellar hypoplasia/atrophy, epilepsy, global developmental delay, dysmorphic features/facial dysmorphisms, and chronic kidney disease/abnormal renal morphology. CONCLUSION In this study, a WES-based variant interpretation system was employed to provide a definitive diagnosis for 28.3% of the patients suspected of having genetic disorders. WES is particularly useful for diagnosing rare diseases with symptoms that affect more than one system, when targeted genetic panels are difficult to employ.
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Affiliation(s)
- Ja Young Lee
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, South Korea
| | - Seung-Hwan Oh
- Department of Laboratory Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | | | - Bo Lyun Lee
- Department of Pediatrics, Inje University College of Medicine, Busan, South Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Inje University College of Medicine, Busan, South Korea
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17
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Wu C, Chu X, Tang K, Cheng D, Ren L. Caregiving experiences of caregivers of children with rare diseases: A qualitative meta-synthesis. J Pediatr Nurs 2024; 75:31-40. [PMID: 38101309 DOI: 10.1016/j.pedn.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: 07/06/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
PROBLEM Most rare diseases occur in childhood and are difficult to diagnose and treat. The caregivers are faced with the challenge of providing care to the children afflicted with these rare diseases, resulting in a significant burden of care and an altered family dynamic. ELIGIBILITY CRITERIA A meta-synthesis review was conducted to explore the caregivers' experience of children with rare diseases using eight electronic databases PubMed, Web of Science, the Cochrane Library, EMBASE, VIP database, Wan Fang, Chinese BioMedical Literature Database, and China National Knowledge Infrastructure from each database's inception to October 5, 2023. SAMPLE 4207 records were identified and 20 eligible studies were included. RESULTS Three themes emerged: (1) Life is changed by "rare"; (2) many unmet needs; (3) Strive to adapt and grow. CONCLUSIONS Caregivers of children with rare diseases are full of stress and challenges in the process of caring for them, and their lives have changed greatly due to "rare". Appropriate measures need to be taken to reduce the burden on caregivers. IMPLICATIONS According to the findings, both the medical and health systems, as well as society, should pay attention to the care load and unmet requirements of carers of children with rare diseases, and offer them with practical supportive services. Finally, it can improve the quality of life for caregivers and families of children with rare diseases, as well as stimulate the development of rare diseases.
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Affiliation(s)
- Chenxi Wu
- College of Nursing, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Chu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Kexin Tang
- College of Nursing, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei Cheng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liangjuan Ren
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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18
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Guan J, Wu X, Zhang J, Li J, Wang H, Wang Q. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet 2024; 38:9-18. [PMID: 38647210 DOI: 10.1080/01677063.2024.2335171] [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: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
As the contribution of de novo mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
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Affiliation(s)
- Jing Guan
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Xiaonan Wu
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jiao Zhang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jin Li
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Hongyang Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Qiuju Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
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19
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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20
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Núñez-Carpintero I, Rigau M, Bosio M, O'Connor E, Spendiff S, Azuma Y, Topf A, Thompson R, 't Hoen PAC, Chamova T, Tournev I, Guergueltcheva V, Laurie S, Beltran S, Capella-Gutiérrez S, Cirillo D, Lochmüller H, Valencia A. Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes. Nat Commun 2024; 15:1227. [PMID: 38418480 PMCID: PMC10902324 DOI: 10.1038/s41467-024-45099-0] [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: 12/21/2022] [Accepted: 01/15/2024] [Indexed: 03/01/2024] Open
Abstract
Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network community detection analysis of complementary biomedical information provided by relevant data sources, namely protein-protein interactions, pathways and metabolomics. Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.
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Affiliation(s)
- Iker Núñez-Carpintero
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
| | - Maria Rigau
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Mattia Bosio
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sally Spendiff
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Rachel Thompson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Teodora Chamova
- Department of Neurology, Expert Centre for Hereditary Neurologic and Metabolic Disorders, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - Ivailo Tournev
- Department of Neurology, Expert Centre for Hereditary Neurologic and Metabolic Disorders, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
- Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, 1618, Bulgaria
| | - Velina Guergueltcheva
- Clinic of Neurology, University Hospital Sofiamed, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Steven Laurie
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
| | - Davide Cirillo
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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21
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Rahit KMTH, Avramovic V, Chong JX, Tarailo-Graovac M. GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM. BMC Bioinformatics 2024; 25:84. [PMID: 38413851 PMCID: PMC10898068 DOI: 10.1186/s12859-024-05693-x] [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: 08/15/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database. However, most of the information in OMIM is textual, and heterogeneous (e.g. summarized by different experts), which complicates automated reading and understanding of the data. Here, we used Natural Language Processing (NLP) to make a tool (Gene-Phenotype Association Discovery (GPAD)) that could syntactically process OMIM text and extract the data of interest. RESULTS GPAD applies a series of language-based techniques to the text obtained from OMIM API to extract GDA discovery-related information. GPAD can inform when a particular gene was associated with a specific phenotype, as well as the type of validation-whether through model organisms or cohort-based patient-matching approaches-for such an association. GPAD extracted data was validated with published reports and was compared with large language model. Utilizing GPAD's extracted data, we analysed trends in GDA discoveries, noting a significant increase in their rate after the introduction of exome sequencing, rising from an average of about 150-250 discoveries each year. Contrary to hopes of resolving most GDAs for Mendelian disorders by now, our data indicate a substantial decline in discovery rates over the past five years (2017-2022). This decline appears to be linked to the increasing necessity for larger cohorts to substantiate GDAs. The rising use of zebrafish and Drosophila as model organisms in providing evidential support for GDAs is also observed. CONCLUSIONS GPAD's real-time analyzing capacity offers an up-to-date view of GDA discovery and could help in planning and managing the research strategies. In future, this solution can be extended or modified to capture other information in OMIM and scientific literature.
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Affiliation(s)
- K M Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Avramovic
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
- Brotman-Baty Institute, Seattle, WA, 98195, USA
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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22
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Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
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Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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23
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Siebold D, Denton J, Hurst ACE, Moss I, Korf B. A qualitative evaluation of patient and parent experiences with an undiagnosed diseases program. Am J Med Genet A 2024; 194:131-140. [PMID: 37750194 DOI: 10.1002/ajmg.a.63417] [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: 03/27/2023] [Revised: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Previous studies have explored patient experiences before being seen or at the beginning of their evaluation by undiagnosed diseases programs. This study provides additional insight into experiences after participation through in-depth, qualitative evaluation, allowing for reflection of current practice and patient/parent needs. Semi-structured interviews were conducted with patients and parents of patients seen at the University of Alabama at Birmingham (UAB)'s unique, clinically focused Undiagnosed Diseases Program (UDP). Analysis of the interviews was guided by a thematic approach. Participants had undergone a diagnostic odyssey before being evaluated by the UDP and remained hopeful for a diagnosis. They appreciated the opportunity to be seen by the UDP. However, perception of experiences differed based on whether evaluation by the UDP led to a diagnosis. Additionally, while participants were pleased with initial communication, they indicated that there were unmet needs regarding follow-up. Patients and parents of patients believe that participation in an undiagnosed diseases program is the best option for diagnosis. The findings of this study provide a general overview of patient experiences and highlight strengths of the UAB UDP while also emphasizing areas to focus the improvement to optimize the benefit to patients and families with undiagnosed and rare diseases, which could be used helpful in the development of similar clinics.
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Affiliation(s)
- Dorothea Siebold
- University of Alabama (UAB), School of Health Professions, Birmingham, Alabama, USA
| | - Jessica Denton
- University of Alabama (UAB), School of Health Professions, Birmingham, Alabama, USA
| | | | - Irene Moss
- UAB Department of Genetics, Birmingham, Alabama, USA
| | - Bruce Korf
- UAB Department of Genetics, Birmingham, Alabama, USA
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24
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Wang T, Ren W, Fu F, Wang H, Li Y, Duan J. Digenic CHD7 and SMCHD1 inheritance Unveils phenotypic variability in a family mainly presenting with hypogonadotropic hypogonadism. Heliyon 2024; 10:e23272. [PMID: 38148819 PMCID: PMC10750161 DOI: 10.1016/j.heliyon.2023.e23272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Objectives CHARGE syndrome is a congenital hereditary condition involving multiple systems. Patients are easily misdiagnosed with idiopathic hypogonadotropic hypogonadism (IHH) due to the overlap of clinical manifestations. An accurate clinical diagnosis remains challenging when the predominant clinical manifestation resembles hypogonadotropic hypogonadism. Methods This original research is conducted based on the genetic finding and analysis of clinical cases. Whole-exome sequencing (WES) and in-silico analyse were performed on two sisters to investigate the pathogenesis in this family. Homology modelling was conducted to evaluate structural changes in the variants. Results WES and Sanger sequencing revealed two siblings carrying a nonsense mutation (NM_017780.4: c.115C > T) in exon 2 of CHD7 inherited from a mildly affected mother and a missense mutation (NM_015295.3: c.2582T > C) in exon 20 of SMCHD1 inherited from an asymptomatic father. The nonsense mutation in CHD7 was predicted to generate nonsense-mediated decay, whereas the missense mutation in SMCHD1 decreased protein stability. Conclusions We identified digenic CHD7 and SMCHD1 mutations in IHH-associated diseases for the first time and verified the synergistic role of oligogenic inheritance. It was also determined that WES is an effective tool for distinguishing diseases with overlapping features and establishing a molecular diagnosis for cases with digenic or oligogenic hereditary disorders, which is beneficial for timely treatment, and family genetic counseling.
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Affiliation(s)
- Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wu Ren
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fangfang Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hairong Wang
- Wuhan KDWS Biological Technology Co.,Ltd, Wuhan, 430000, China
| | - Yan Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jie Duan
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
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25
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Alghanmi BM, Alghanmi MM, Alhayli MR, Taffour RM, Alghubayshi SM. A Case of a Newborn With Nemaline Myopathy From Al-Qunfudhah City, Saudi Arabia. Cureus 2024; 16:e52523. [PMID: 38239845 PMCID: PMC10796190 DOI: 10.7759/cureus.52523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 01/22/2024] Open
Abstract
Nemaline myopathy is a primary skeletal muscle disorder and one of the congenital myopathies. It can be caused by mutations in at least 12 genes, with the nebulin (NEB) gene being the most common. Here, we present the first case of a neonate with nemaline myopathy from Al-Qunfudhah, Saudi Arabia. A full-term baby boy was delivered via cesarean section due to decreased fetal movement. The baby was covered with a thick meconium stain. He was born with severe distress and underwent an endotracheal tube placement. The baby presented generalized muscle weakness, hypotonia, and areflexia. Examination revealed arthrogryposis, bilateral small chin, undescended testicle, joint deformity, hip dislocation, and clubfoot. Chest examination revealed conducting sound and bilateral equal air entry. Moreover, he experienced bilateral chest wheeze and conducting sound. All laboratory tests were normal, and whole-exome sequencing revealed pathogenic homozygous splice acceptor variant NEB gene c.8889+1G˃A. The patient was first suspected to have spinal muscular atrophy as there was no previous nemaline myopathy case reported from Al-Qunfudhah. However, the typical symptoms and genetic sequencing confirmed his condition. As the society in Al-Qunfudhah is known for consanguinity, as in our case, clinicians should identify other types of myopathy as it is expected to occur in further cases.
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Affiliation(s)
- Bushra M Alghanmi
- General Practice, South Al-Qunfudah General Hospital, Al-Qunfudah, SAU
| | - Manal M Alghanmi
- General Practice, South Al-Qunfudah General Hospital, Al-Qunfudah, SAU
| | - Mohammed R Alhayli
- Pediatrics and Neonatal Intensive Care Unit, South Al-Qunfudah General Hospital, Al-Qunfudah, SAU
| | - Randa M Taffour
- Pediatric Intensive Care Unit, South Al-Qunfudah General Hospital, Al-Qunfudah, SAU
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26
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Chen J. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. RESEARCH SQUARE 2023:rs.3.rs-3632644. [PMID: 38045389 PMCID: PMC10690325 DOI: 10.21203/rs.3.rs-3632644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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27
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Raimondi D, Chizari H, Verplaetse N, Löscher BS, Franke A, Moreau Y. Genome interpretation in a federated learning context allows the multi-center exome-based risk prediction of Crohn's disease patients. Sci Rep 2023; 13:19449. [PMID: 37945674 PMCID: PMC10636050 DOI: 10.1038/s41598-023-46887-2] [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: 06/12/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
High-throughput sequencing allowed the discovery of many disease variants, but nowadays it is becoming clear that the abundance of genomics data mostly just moved the bottleneck in Genetics and Precision Medicine from a data availability issue to a data interpretation issue. To solve this empasse it would be beneficial to apply the latest Deep Learning (DL) methods to the Genome Interpretation (GI) problem, similarly to what AlphaFold did for Structural Biology. Unfortunately DL requires large datasets to be viable, and aggregating genomics datasets poses several legal, ethical and infrastructural complications. Federated Learning (FL) is a Machine Learning (ML) paradigm designed to tackle these issues. It allows ML methods to be collaboratively trained and tested on collections of physically separate datasets, without requiring the actual centralization of sensitive data. FL could thus be key to enable DL applications to GI on sufficiently large genomics data. We propose FedCrohn, a FL GI Neural Network model for the exome-based Crohn's Disease risk prediction, providing a proof-of-concept that FL is a viable paradigm to build novel ML GI approaches. We benchmark it in several realistic scenarios, showing that FL can indeed provide performances similar to conventional ML on centralized data, and that collaborating in FL initiatives is likely beneficial for most of the medical centers participating in them.
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Affiliation(s)
| | | | | | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, 3001, Leuven, Belgium
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28
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Bai JP, Wang J, Zhang Y, Wang L, Jiang X. Quantitative Systems Pharmacology for Rare Disease Drug Development. J Pharm Sci 2023; 112:2313-2320. [PMID: 37422281 DOI: 10.1016/j.xphs.2023.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
Though hundreds of drugs have been approved by the US Food and Drug Administration (FDA) for treating various rare diseases, most rare diseases still lack FDA-approved therapeutics. To identify the opportunities for developing therapies for these diseases, the challenges of demonstrating the efficacy and safety of a drug for treating a rare disease are highlighted herein. Quantitative systems pharmacology (QSP) has increasingly been used to inform drug development; our analysis of QSP submissions received by FDA showed that there were 121 submissions as of 2022, for informing rare disease drug development across development phases and therapeutic areas. Examples of published models for inborn errors of metabolism, non-malignant hematological disorders, and hematological malignancies were briefly reviewed to shed light on use of QSP in drug discovery and development for rare diseases. Advances in biomedical research and computational technologies can potentially enable QSP simulation of the natural history of a rare disease in the context of its clinical presentation and genetic heterogeneity. With this function, QSP may be used to conduct in-silico trials to overcome some of the challenges in rare disease drug development. QSP may play an increasingly important role in facilitating development of safe and effective drugs for treating rare diseases with unmet medical needs.
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Affiliation(s)
- Jane Pf Bai
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
| | - Jie Wang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
| | - Yifei Zhang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
| | - Lingshan Wang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
| | - Xiling Jiang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
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29
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Fermaglich LJ, Miller KL. A comprehensive study of the rare diseases and conditions targeted by orphan drug designations and approvals over the forty years of the Orphan Drug Act. Orphanet J Rare Dis 2023; 18:163. [PMID: 37353796 DOI: 10.1186/s13023-023-02790-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/18/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND Rare diseases affect more than 30 million Americans. The passage of the Orphan Drug Act (ODA) in the United States in 1983 represented a launching point for a rare disease drug development revolution for these patients. Financial incentives provided by the ODA through its Orphan Drug Designation Program, in addition to remarkable scientific advances over the past 40 years, have led to hundreds of drug approvals for rare diseases. Our research examines the rare diseases that have been targeted by orphan drug designations and subsequent approvals since the law was enacted. METHODS Using an internal FDA database, we classified and analyzed all orphan drug designations and approvals from 1983 to 2022 by disease and therapeutic area. RESULTS Over the 40 years of the ODA, 6,340 orphan drug designations were granted, representing drug development for 1,079 rare diseases. Additionally, 882 of those designations resulted in at least one FDA approval for use in 392 rare diseases. Much of this development has been concentrated in oncology as seven of the top ten most designated and approved diseases were rare cancers. CONCLUSIONS Researchers have estimated that there may be 7000-10,000 rare diseases that have been identified and described. Based on our study, we can conclude that around 5% of rare diseases have an FDA-approved drug and up to 15% of rare diseases have at least one drug that has been developed and shown promise in their treatment, diagnosis or prevention. Funding of basic and translational science for rare disease drug development should continue in order to bring therapies to the millions of affected patients who remain without treatment options.
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Affiliation(s)
- Lewis J Fermaglich
- Office of Orphan Products Development, Office of the Commissioner, US Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
| | - Kathleen L Miller
- Office of Orphan Products Development, Office of the Commissioner, US Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
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30
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Banerjee J, Taroni JN, Allaway RJ, Prasad DV, Guinney J, Greene C. Machine learning in rare disease. Nat Methods 2023:10.1038/s41592-023-01886-z. [PMID: 37248386 DOI: 10.1038/s41592-023-01886-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/22/2023] [Indexed: 05/31/2023]
Abstract
High-throughput profiling methods (such as genomics or imaging) have accelerated basic research and made deep molecular characterization of patient samples routine. These approaches provide a rich portrait of genes, molecular pathways and cell types involved in disease phenotypes. Machine learning (ML) can be a useful tool for extracting disease-relevant patterns from high-dimensional datasets. However, depending upon the complexity of the biological question, machine learning often requires many samples to identify recurrent and biologically meaningful patterns. Rare diseases are inherently limited in clinical cases, leading to few samples to study. In this Perspective, we outline the challenges and emerging solutions for using ML for small sample sets, specifically in rare diseases. Advances in ML methods for rare diseases are likely to be informative for applications beyond rare diseases for which few samples exist with high-dimensional data. We propose that the method community prioritize the development of ML techniques for rare disease research.
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Affiliation(s)
| | - Jaclyn N Taroni
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA
| | | | | | | | - Casey Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
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31
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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32
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Al-Kurbi AA, Aliyev E, AlSa’afin S, Aamer W, Palaniswamy S, Al-Maraghi A, Kilani H, Akil AAS, Stotland MA, Fakhro KA. A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes. Genes (Basel) 2023; 14:genes14040849. [PMID: 37107607 PMCID: PMC10137688 DOI: 10.3390/genes14040849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Clefts of the lip and/or palate (CL/P) are considered the most common form of congenital anomalies occurring either in isolation or in association with other clinical features. Van der woude syndrome (VWS) is associated with about 2% of all CL/P cases and is further characterized by having lower lip pits. Popliteal pterygium syndrome (PPS) is a more severe form of VWS, normally characterized by orofacial clefts, lower lip pits, skin webbing, skeletal anomalies and syndactyly of toes and fingers. Both syndromes are inherited in an autosomal dominant manner, usually caused by heterozygous mutations in the Interferon Regulatory Factor 6 (IRF6) gene. Here we report the case of a two-generation family where the index presented with popliteal pterygium syndrome while both the father and sister had clinical features of van der woude syndrome, but without any point mutations detected by re-sequencing of known gene panels or microarray testing. Using whole genome sequencing (WGS) followed by local de novo assembly, we discover and validate a copy-neutral, 429 kb complex intra-chromosomal rearrangement in the long arm of chromosome 1, disrupting the IRF6 gene. This variant is copy-neutral, novel against publicly available databases, and segregates in the family in an autosomal dominant pattern. This finding suggests that missing heritability in rare diseases may be due to complex genomic rearrangements that can be resolved by WGS and de novo assembly, helping deliver answers to patients where no genetic etiology was identified by other means.
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Affiliation(s)
- Alya A. Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sana AlSa’afin
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | | | | | - Houda Kilani
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
| | | | - Mitchell A. Stotland
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
- Department of Surgery, Weill Cornell Medical College, Doha 24144, Qatar
| | - Khalid A. Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha 24144, Qatar
- Correspondence:
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33
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Hwang SE, Kim M, Hong Y, Lee D, Kim T, Park J, Bae J, Lee JH. Effect of the copayment reduction system on accessibility to orphan drugs in South Korea. Expert Rev Pharmacoecon Outcomes Res 2023; 23:519-525. [PMID: 36922505 DOI: 10.1080/14737167.2023.2192481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
OBJECTIVE This study aims to analyze the effect of the copayment reduction system on accessibility to orphan drugs (ODs) in South Korea. METHODS Data on approval and reimbursement for drugs designated as ODs for the last 10 years (2012-2021) in South Korea were extracted. Among them, with 136 approved products as of 31 December 2022, the reimbursement rates and lead time to reimbursement between drugs for rare diseases (DRDs) and nondrugs for rare diseases (non-DRDs) were analyzed. The pricing and reimbursement (P&R) pathways between drugs for only rare diseases (DORDs) and drugs for rare and cancerous diseases (DRCDs) were compared. RESULTS The reimbursement rates for DRDs and non-DRDs were 54.8% and 33.3%, respectively, and the lead time to reimbursement for DRDs and non-DRDs were 16.1 months and 31.2 months, respectively. The P&R pathways for DORDs and DRCDs were pharmacoeconomic evaluation waivers (21.7% and 52.6%), weighted average price (52.2% and 13.2%), and risk-sharing agreement (30.4% and 81.6%). CONCLUSION The copayment reduction system may act as a driver and also barrier for the reimbursement of ODs. To expand treatment accessibility to ODs, it is necessary to consistently grants benefits in all processes from OD designation to market access.
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Affiliation(s)
- Se-Eun Hwang
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Minyoung Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Youngjun Hong
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Dongyun Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Taehyang Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jihee Park
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Junkyu Bae
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jong Hyuk Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
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34
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Cicolini I, Blasetti A, Chiarelli F. Ciliopathies in pediatric endocrinology. Ann Pediatr Endocrinol Metab 2023; 28:5-9. [PMID: 37015775 PMCID: PMC10073028 DOI: 10.6065/apem.2244288.144] [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: 12/22/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023] Open
Abstract
Ciliopathies are a group of disorders that involve many organs and systems. In this review, we consider the role of the cilium in multiorgan pathology with a focus on endocrinological aspects. Identification of new genes and mutations is the major challenge in development of a tailored and appropriate therapy. It is expected that new mutations will be identified to characterize ciliopathies and promote new therapies.
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Affiliation(s)
- Ilenia Cicolini
- Department of Pediatrics, University of Chieti, Chieti, Italy
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35
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Wang X, Gan M, Dong X, Lu Y, Zhou W. An Integrated Pipeline for Trio-Rapid Genome Sequencing in Critically Ill Infants. Curr Protoc 2023; 3:e706. [PMID: 36971344 DOI: 10.1002/cpz1.706] [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] [Indexed: 03/29/2023]
Abstract
Trio-rapid genome sequencing (trio-rGS) can assist the genetic diagnosis of critically ill infants given its ability to detect a broad range of pathogenic variants, as well as microbes, simultaneously with high efficiency. To achieve more comprehensive clinical diagnoses, it is essential to propose a recommended protocol in clinical practice. Here, we introduced an integrated pipeline to detect germline variants and microorganisms simultaneously from trio-RGS in critically ill infants, which provides step-by-step criteria for the semi-automatic processing procedures. With this pipeline in clinical application, only 1 ml of peripheral blood is needed for clinicians to provide both genetic and infectious causal information to a patient. The establishment and clinical practice of the method is of great significance for further mining of high-throughput sequencing data and for assisting clinicians in promoting diagnosis efficiency and accuracy. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Experimental pipeline for rapid whole-genome sequencing for the simultaneous detection of germline variants and microorganisms Basic Protocol 2: Computational pipeline for rapid whole-genome sequencing for the simultaneous detection of germline variants and microorganisms.
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Affiliation(s)
- Xiao Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Mingyu Gan
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Center for Big Data in Clinical Research, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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36
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Martínez-Barrios E, Grassi S, Brión M, Toro R, Cesar S, Cruzalegui J, Coll M, Alcalde M, Brugada R, Greco A, Ortega-Sánchez ML, Barberia E, Oliva A, Sarquella-Brugada G, Campuzano O. Molecular autopsy: Twenty years of post-mortem diagnosis in sudden cardiac death. Front Med (Lausanne) 2023; 10:1118585. [PMID: 36844202 PMCID: PMC9950119 DOI: 10.3389/fmed.2023.1118585] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
In the forensic medicine field, molecular autopsy is the post-mortem genetic analysis performed to attempt to unravel the cause of decease in cases remaining unexplained after a comprehensive forensic autopsy. This negative autopsy, classified as negative or non-conclusive, usually occurs in young population. In these cases, in which the cause of death is unascertained after a thorough autopsy, an underlying inherited arrhythmogenic syndrome is the main suspected cause of death. Next-generation sequencing allows a rapid and cost-effectives genetic analysis, identifying a rare variant classified as potentially pathogenic in up to 25% of sudden death cases in young population. The first symptom of an inherited arrhythmogenic disease may be a malignant arrhythmia, and even sudden death. Early identification of a pathogenic genetic alteration associated with an inherited arrhythmogenic syndrome may help to adopt preventive personalized measures to reduce risk of malignant arrhythmias and sudden death in the victim's relatives, at risk despite being asymptomatic. The current main challenge is a proper genetic interpretation of variants identified and useful clinical translation. The implications of this personalized translational medicine are multifaceted, requiring the dedication of a specialized team, including forensic scientists, pathologists, cardiologists, pediatric cardiologists, and geneticists.
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Affiliation(s)
- Estefanía Martínez-Barrios
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Simone Grassi
- Forensic Medical Sciences, Department of Health Science, University of Florence, Florence, Italy
| | - María Brión
- Family Heart Disease Unit, Cardiology Service, Santiago de Compostela University Hospital, Santiago de Compostela, Spain,Cardiovascular Genetics, Santiago de Compostela Health Research Institute, Santiago de Compostela, Spain,Genomic Medicine Group, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain
| | - Rocío Toro
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Sergi Cesar
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - José Cruzalegui
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mònica Coll
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Mireia Alcalde
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Cardiology Department, Hospital Josep Trueta, Girona, Spain
| | - Andrea Greco
- Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Department of Medical and Surgical Sciences of the Mother, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - María Luisa Ortega-Sánchez
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Spain
| | - Eneko Barberia
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Antonio Oliva
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Georgia Sarquella-Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,*Correspondence: Georgia Sarquella-Brugada,
| | - Oscar Campuzano
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Oscar Campuzano,
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Chevarin M, Alcantara D, Albuisson J, Collonge-Rame MA, Populaire C, Selmani Z, Baurand A, Sawka C, Bertolone G, Callier P, Duffourd Y, Jonveaux P, Bignon YJ, Coupier I, Cornelis F, Cordier C, Mozelle-Nivoix M, Rivière JB, Kuentz P, Thauvin C, Boidot R, Ghiringhelli F, O'Driscoll M, Faivre L, Nambot S. The "extreme phenotype approach" applied to male breast cancer allows the identification of rare variants of ATR as potential breast cancer susceptibility alleles. Oncotarget 2023; 14:111-125. [PMID: 36749285 PMCID: PMC9904323 DOI: 10.18632/oncotarget.28358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
In oncogenetics, some patients could be considered as "extreme phenotypes", such as those with very early onset presentation or multiple primary malignancies, unusually high numbers of cancers of the same spectrum or rare cancer types in the same parental branch. For these cases, a genetic predisposition is very likely, but classical candidate gene panel analyses often and frustratingly remains negative. In the framework of the EX2TRICAN project, exploring unresolved extreme cancer phenotypes, we applied exome sequencing on rare familial cases with male breast cancer, identifying a novel pathogenic variant of ATR (p.Leu1808*). ATR has already been suspected as being a predisposing gene to breast cancer in women. We next identified 3 additional ATR variants in a cohort of both male and female with early onset and familial breast cancers (c.7762-2A>C; c.2078+1G>A; c.1A>G). Further molecular and cellular investigations showed impacts on transcripts for variants affecting splicing sites and reduction of ATR expression and phosphorylation of the ATR substrate CHEK1. This work further demonstrates the interest of an extended genetic analysis such as exome sequencing to identify very rare variants that can play a role in cancer predisposition in extreme phenotype cancer cases unexplained by classical cancer gene panels testing.
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Affiliation(s)
- Martin Chevarin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Juliette Albuisson
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | | | - Céline Populaire
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Zohair Selmani
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Amandine Baurand
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Sawka
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Geoffrey Bertolone
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Philippe Jonveaux
- Laboratoire de Génétique Médicale, INSERM U954, Hôpitaux de Brabois, Vandoeuvre les Nancy, France
| | - Yves-Jean Bignon
- Laboratoire d’Oncologie Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - François Cornelis
- Université Bordeaux, IMB, UMR 5251, Talence, France
- Service d’imagerie diagnostique et interventionnelle de l’adulte, Hôpital Pellegrin, CHU de Bordeaux, France
| | | | | | - Jean-Baptiste Rivière
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Paul Kuentz
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Christel Thauvin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Romain Boidot
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | - François Ghiringhelli
- Département d’oncologie médicale, INSERM LNC U1231, Centre Georges François Leclerc, Dijon, France
| | - Marc O'Driscoll
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Laurence Faivre
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Sophie Nambot
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
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Jia A, Lei Y, Liu DP, Pan L, Guan HZ, Yang B. A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China. Pharmgenomics Pers Med 2023; 16:81-97. [PMID: 36755623 PMCID: PMC9901461 DOI: 10.2147/pgpm.s387767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Objective The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs). Methods Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated. Results Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES. Conclusion The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.
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Affiliation(s)
- An Jia
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China
| | - Yi Lei
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Dan-Ping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Lu Pan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Hui-Zhen Guan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Bicheng Yang
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China,Correspondence: Bicheng Yang, Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, People’s Republic of China, Tel +86 15350402147, Email
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Dembélé J, Liao JH, Liu TP, Chen YP. Overcoming Cytosolic Delivery Barriers of Proteins Using Denatured Protein-Conjugated Mesoporous Silica Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:432-451. [PMID: 36562665 PMCID: PMC9896485 DOI: 10.1021/acsami.2c17544] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Intracellular delivery of therapeutic proteins has increased advantages over current small-molecule drugs and gene therapies, especially in therapeutic efficacies for a broad spectrum of diseases. Hence, developing the protein therapeutics approach provides a needed alternative. Here, we designed a mesoporous silica nanoparticle (MSN)-mediated protein delivery approach and demonstrated effective intracellular delivery of the denatured superoxide dismutase (SOD) protein, overcoming the delivery challenges and achieving higher enzymatic activity than native SOD-conjugated MSNs. The denatured SOD-conjugated MSN delivery strategy provides benefits of reduced size and steric hindrance, increased protein flexibility without distorting its secondary structure, exposure of the cell-penetrating peptide transactivator of transcription for enhanced efficient delivery, and a change in the corona protein composition, enabling cytosolic delivery. After delivery, SOD displayed a specific activity around threefold higher than in our previous reports. Furthermore, the in vivo biosafety and therapeutic potential for neuron therapy were evaluated, demonstrating the biocompatibility and the effective antioxidant effect in Neuro-2a cells that protected neurite outgrowth from paraquat-induced reactive oxygen species attack. This study offers an opportunity to realize the druggable possibility of cytosolic proteins using MSNs.
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Affiliation(s)
- Julien Dembélé
- Graduate
Institute of Biomedical Materials & Tissue Engineering, College
of Biomedical Engineering, Taipei Medical
University, Taipei 11031, Taiwan
- Laboratory
of Toxicology, Environment and Health, Doctorate School of Health, University Joseph Ki-Zerbo, Ouaga 03 BP 7021, Burkina Faso
| | - Jou-Hsuan Liao
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Tsang-Pai Liu
- Department
of Surgery, Mackay Memorial Hospital, Taipei 10449, Taiwan
| | - Yi-Ping Chen
- Graduate
Institute of Nanomedicine and Medical Engineering, Taipei Medical University, Taipei 11031, Taiwan
- International
PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei 11031, Taiwan
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Kagan M, Semo-Oz R, Ben Moshe Y, Atias-Varon D, Tirosh I, Stern-Zimmer M, Eliyahu A, Raas-Rothschild A, Bivas M, Shlomovitz O, Chorin O, Rock R, Tzadok M, Ben-Zeev B, Heimer G, Bolkier Y, Gruber N, Dagan A, Bar Aluma BE, Pessach IM, Rechavi G, Barel O, Pode-Shakked B, Anikster Y, Vivante A. Clinical impact of exome sequencing in the setting of a general pediatric ward for hospitalized children with suspected genetic disorders. Front Genet 2023; 13:1018062. [PMID: 36699461 PMCID: PMC9868164 DOI: 10.3389/fgene.2022.1018062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Genetic conditions contribute a significant portion of disease etiologies in children admitted to general pediatric wards worldwide. While exome sequencing (ES) has improved clinical diagnosis and management over a variety of pediatric subspecialties, it is not yet routinely used by general pediatric hospitalists. We aim to investigate the impact of exome sequencing in sequencing-naive children suspected of having monogenic disorders while receiving inpatient care. Methods: We prospectively employed exome sequencing in children admitted to the general pediatric inpatient service at a large tertiary medical center in Israel. Genetic analysis was triggered by general and/or subspecialist pediatricians who were part of the primary inpatient team. We determined the diagnostic yield among children who were referred for exome sequencing and observed the effects of genetic diagnosis on medical care. Results: A total of fifty probands were evaluated and exome sequenced during the study period. The most common phenotypes included were neurodevelopmental (56%), gastrointestinal (34%), and congenital cardiac anomalies (24%). A molecular diagnosis was reached in 38% of patients. Among seven patients (37%), the molecular genetic diagnosis influenced subsequent clinical management already during admission or shortly following discharge. Conclusion: We identified a significant fraction of genetic etiologies among undiagnosed children admitted to the general pediatric ward. Our results support that early application of exome sequencing may be maximized by pediatric hospitalists' high index of suspicion for an underlying genetic etiology, prompting an in-house genetic evaluation. This framework should include a multidisciplinary co-management approach of the primary care team working alongside with subspecialties, geneticists and bioinformaticians.
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Affiliation(s)
- Maayan Kagan
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Rotem Semo-Oz
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Rheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yishay Ben Moshe
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Atias-Varon
- Pediatric Nephrology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Irit Tirosh
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Rheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Michal Stern-Zimmer
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Annick Raas-Rothschild
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Maayan Bivas
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Odelia Chorin
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Rachel Rock
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Michal Tzadok
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bruria Ben-Zeev
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gali Heimer
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Heart Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Noah Gruber
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Endocrinology and Diabetes Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Adi Dagan
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Pulmonology and National CF Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bat El Bar Aluma
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Pulmonology and National CF Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Itai M. Pessach
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Department of Pediatric Intensive Care, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ortal Barel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,The Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ben Pode-Shakked
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Pediatric Nephrology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,*Correspondence: Asaf Vivante,
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Cosma BM, Shirali Hossein Zade R, Jordan EN, van Lent P, Peng C, Pillay S, Abeel T. Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations. Gigascience 2022; 12:giad100. [PMID: 38000912 PMCID: PMC10673639 DOI: 10.1093/gigascience/giad100] [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: 01/30/2023] [Revised: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short read lengths specific to next-generation sequencing (NGS), third-generation sequencers are known to produce more error-prone reads, thereby generating a new set of challenges for assembly algorithms and pipelines. However, the introduction of HiFi reads, which offer substantially reduced error rates, has provided a promising solution for more accurate assembly outcomes. Since the introduction of third-generation sequencing technologies, many tools have been developed that aim to take advantage of the longer reads, and researchers need to choose the correct assembler for their projects. RESULTS We benchmarked state-of-the-art long-read de novo assemblers to help readers make a balanced choice for the assembly of eukaryotes. To this end, we used 12 real and 64 simulated datasets from different eukaryotic genomes, with different read length distributions, imitating PacBio continuous long-read (CLR), PacBio high-fidelity (HiFi), and ONT sequencing to evaluate the assemblers. We include 5 commonly used long-read assemblers in our benchmark: Canu, Flye, Miniasm, Raven, and wtdbg2 for ONT and PacBio CLR reads. For PacBio HiFi reads , we include 5 state-of-the-art HiFi assemblers: HiCanu, Flye, Hifiasm, LJA, and MBG. Evaluation categories address the following metrics: reference-based metrics, assembly statistics, misassembly count, BUSCO completeness, runtime, and RAM usage. Additionally, we investigated the effect of increased read length on the quality of the assemblies and report that read length can, but does not always, positively impact assembly quality. CONCLUSIONS Our benchmark concludes that there is no assembler that performs the best in all the evaluation categories. However, our results show that overall Flye is the best-performing assembler for PacBio CLR and ONT reads, both on real and simulated data. Meanwhile, best-performing PacBio HiFi assemblers are Hifiasm and LJA. Next, the benchmarking using longer reads shows that the increased read length improves assembly quality, but the extent to which that can be achieved depends on the size and complexity of the reference genome.
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Affiliation(s)
- Bianca-Maria Cosma
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
| | - Ramin Shirali Hossein Zade
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
| | - Erin Noel Jordan
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
- Technical Biochemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Paul van Lent
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
| | - Chengyao Peng
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
| | - Stephanie Pillay
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Intelligent Systems, Delft University of Technology, 2628 XE, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Zecca C, Tortelli R, Carrera P, Dell'Abate MT, Logroscino G, Ferrari M. Genotype-phenotype correlation in the spectrum of frontotemporal dementia-parkinsonian syndromes and advanced diagnostic approaches. Crit Rev Clin Lab Sci 2022; 60:171-188. [PMID: 36510705 DOI: 10.1080/10408363.2022.2150833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The term frontotemporal dementia (FTD) refers to a group of progressive neurodegenerative disorders characterized mainly by atrophy of the frontal and anterior temporal lobes. Based on clinical presentation, three main clinical syndromes have traditionally been described: behavioral variant frontotemporal dementia (bvFTD), non-fluent/agrammatic primary progressive aphasia (nfPPA), and semantic variant PPA (svPPA). However, over the last 20 years, it has been recognized that cognitive phenotypes often overlap with motor phenotypes, either motor neuron diseases or parkinsonian signs and/or syndromes like progressive supranuclear palsy (PSP) and cortico-basal syndrome (CBS). Furthermore, FTD-related genes are characterized by genetic pleiotropy and can cause, even in the same family, pure motor phenotypes, findings that underlie the clinical continuum of the spectrum, which has pure cognitive and pure motor phenotypes as the extremes. The genotype-phenotype correlation of the spectrum, FTD-motor neuron disease, has been well defined and extensively investigated, while the continuum, FTD-parkinsonism, lacks a comprehensive review. In this narrative review, we describe the current knowledge about the genotype-phenotype correlation of the spectrum, FTD-parkinsonism, focusing on the phenotypes that are less frequent than bvFTD, namely nfPPA, svPPA, PSP, CBS, and cognitive-motor overlapping phenotypes (i.e. PPA + PSP). From a pathological point of view, they are characterized mainly by the presence of phosphorylated-tau inclusions, either 4 R or 3 R. The genetic correlate of the spectrum can be heterogeneous, although some variants seem to lead preferentially to specific clinical syndromes. Furthermore, we critically review the contribution of genome-wide association studies (GWAS) and next-generation sequencing (NGS) in disentangling the complex heritability of the FTD-parkinsonism spectrum and in defining the genotype-phenotype correlation of the entire clinical scenario, owing to the ability of these techniques to test multiple genes, and so to allow detailed investigations of the overlapping phenotypes. Finally, we conclude with the importance of a detailed genetic characterization and we offer to patients and families the chance to be included in future randomized clinical trials focused on autosomal dominant forms of FTLD.
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Affiliation(s)
- Chiara Zecca
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari "Aldo Moro", Pia Fondazione Card G. Panico Hospital, Tricase, Italy
| | - Rosanna Tortelli
- Neuroscience and Rare Diseases Discovery and Translational Area, Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Paola Carrera
- Unit of Genomics for Human Disease Diagnosis and Clinical Molecular Biology Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Teresa Dell'Abate
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari "Aldo Moro", Pia Fondazione Card G. Panico Hospital, Tricase, Italy
| | - Giancarlo Logroscino
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari "Aldo Moro", Pia Fondazione Card G. Panico Hospital, Tricase, Italy.,Department of Basic Medicine Sciences, Neuroscience, and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
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Tang Y, Luo Y. Identification of a novel mutation in complement receptor 2 in Chinese familial systemic lupus erythematosus. Arch Rheumatol 2022; 37:566-573. [PMID: 36879571 PMCID: PMC9985375 DOI: 10.46497/archrheumatol.2022.9167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/23/2021] [Indexed: 03/08/2023] Open
Abstract
Objectives This study aims to analyze the relationship between complement receptor 2 (CR2) gene mutation and the clinical phenotype in Chinese familial systemic lupus erythematosus (SLE). Patients and methods A total of one Chinese familial SLE patients (median age: 30.25 years; range, 22 to 49 years) were included between January 2017 and December 2018. The clinical features and diagnoses of familial SLE patients were analyzed using whole-exome sequencing (WES) of genomic deoxyribonucleic acid (DNA) samples. Sanger sequencing was used to verify candidate mutations detected in the examined family. Results The mother and her three daughters were diagnosed with SLE. The clinical characteristics showed that the patient and her mother were diagnosed with lupus nephritis. The eldest daughter had decreased renal function and lower serum albumin levels. Immunological index analysis showed that all four patients were positive for anti-SSA and antinuclear antibody (ANA), but that only the second daughter was positive for anti-double-stranded DNA (dsDNA). Complement 3 (C3) was significantly decreased in all patients, while evaluation of the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) showed that the second and third daughters had mild active SLE. The mother and eldest daughter were treated with prednisolone combined with cyclophosphamide, while the other two daughters were treated with prednisolone alone. The WES and Sanger sequencing analyses revealed an unreported missense T>C mutation c.2804 in the 15th exon of the CR gene in all four patients. Conclusion We identified a novel c.2804 (exon 15) T>C mutation in the CR gene of Chinese familial SLE. This mutation was previously reported, suggesting that the CR gene c.2804 (exon 15) T>C mutation is the probable cause of SLE in this family.
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Affiliation(s)
- Yuewu Tang
- Department of Nephrology, Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, China
| | - Yi Luo
- Department of Blood Transfusion, Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, China
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Korth‐Bradley JM. Regulatory Framework for Drug Development in Rare Diseases. J Clin Pharmacol 2022; 62 Suppl 2:S15-S26. [DOI: 10.1002/jcph.2171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/13/2022] [Indexed: 12/04/2022]
Affiliation(s)
- Joan M. Korth‐Bradley
- Clinical Pharmacology Global Product Development, Pfizer Inc. Collegeville Pennsylvania USA
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Raimondi D, Orlando G, Verplaetse N, Fariselli P, Moreau Y. Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. FRONTIERS IN BIOINFORMATICS 2022; 2:1098941. [PMID: 36530385 PMCID: PMC9749061 DOI: 10.3389/fbinf.2022.1098941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/12/2023] Open
Affiliation(s)
| | | | | | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Torino, Italy
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CRISPR-Based Tools for Fighting Rare Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121968. [PMID: 36556333 PMCID: PMC9787644 DOI: 10.3390/life12121968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022]
Abstract
Rare diseases affect the life of a tremendous number of people globally. The CRISPR-Cas system emerged as a powerful genome engineering tool and has facilitated the comprehension of the mechanism and development of therapies for rare diseases. This review focuses on current efforts to develop the CRISPR-based toolbox for various rare disease therapy applications and compares the pros and cons of different tools and delivery methods. We further discuss the therapeutic applications of CRISPR-based tools for fighting different rare diseases.
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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Wang G, Xu Y, Wang Q, Chai Y, Sun X, Yang F, Zhang J, Wu M, Liao X, Yu X, Sheng X, Liu Z, Zhang J. Rare and undiagnosed diseases: From disease-causing gene identification to mechanism elucidation. FUNDAMENTAL RESEARCH 2022; 2:918-928. [PMID: 38933382 PMCID: PMC11197726 DOI: 10.1016/j.fmre.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Rare and undiagnosed diseases substantially decrease patient quality of life and have increasingly become a heavy burden on healthcare systems. Because of the challenges in disease-causing gene identification and mechanism elucidation, patients are often confronted with difficulty obtaining a precise diagnosis and treatment. Due to advances in sequencing and multiomics analysis approaches combined with patient-derived iPSC models and gene-editing platforms, substantial progress has been made in the diagnosis and treatment of rare and undiagnosed diseases. The aforementioned techniques also provide an operational basis for future precision medicine studies. In this review, we summarize recent progress in identifying disease-causing genes based on GWAS/WES/WGS-guided multiomics analysis approaches. In addition, we discuss recent advances in the elucidation of pathogenic mechanisms and treatment of diseases with state-of-the-art iPSC and organoid models, which are improved by cell maturation level and gene editing technology. The comprehensive strategies described above will generate a new paradigm of disease classification that will significantly promote the precision and efficiency of diagnosis and treatment for rare and undiagnosed diseases.
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Affiliation(s)
- Gang Wang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Yuyan Xu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qintao Wang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi Chai
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiangwei Sun
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fan Yang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Jian Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengchen Wu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xufeng Liao
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaomin Yu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Sheng
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhihong Liu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Jin Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, The First Affiliated Hospital, Zhejiang University School of Medicine; Center of Gene/Cell Engineering and Genome Medicine of Zhejiang Province, Hangzhou 310058, China
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von der Lippe C, Neteland I, Feragen KB. Children with a rare congenital genetic disorder: a systematic review of parent experiences. Orphanet J Rare Dis 2022; 17:375. [PMID: 36253830 PMCID: PMC9575260 DOI: 10.1186/s13023-022-02525-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Caring for a child with a chronic disease may be demanding and stressful. When a child has a rare condition, the impact of care on parents is amplified due to the rarity of the diagnosis. In order to address the lack of generalized and synthesized knowledge regarding parents' experiences of having a child with a rare genetic disorder, and give a holistic picture of these experiences, a systematic review of the available qualitative research was conducted. METHODS We performed a systematic review, including qualitative studies on parents of children with rare genetic disorders, published between 2000 and 2020. RESULTS The review included 33 qualitative studies. Findings were synthesized and categorized according to three main themes: Parents' experiences with health care, Responsibilities and challenges, and Factors promoting positive experiences in parents. The findings demonstrate that parents of children with rare genetic disorders share many common challenges, despite evident differences across conditions. CONCLUSION Coordinated care, and a more holistic approach in the follow up of children with rare genetic disorders is needed. International collaboration on research, diagnostics, producing scientific correct and understandable information available for health care professionals and lay people should be prioritized.
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Affiliation(s)
- Charlotte von der Lippe
- Centre for Rare Disorders, Rikshospitalet, Oslo University Hospital, P.B. 4950, 0424, Nydalen, Oslo, Norway.
| | - Ingrid Neteland
- Centre for Rare Disorders, Rikshospitalet, Oslo University Hospital, P.B. 4950, 0424, Nydalen, Oslo, Norway
| | - Kristin Billaud Feragen
- Centre for Rare Disorders, Rikshospitalet, Oslo University Hospital, P.B. 4950, 0424, Nydalen, Oslo, Norway
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Unni P, Friend J, Weinberg J, Okur V, Hochscherf J, Dominguez I. Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases. Front Mol Biosci 2022; 9:851547. [PMID: 36310603 PMCID: PMC9608649 DOI: 10.3389/fmolb.2022.851547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.
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Affiliation(s)
- Prasida Unni
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Jack Friend
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston University, Boston, MA, United States
| | - Volkan Okur
- New York Genome Center, New York, NY, United States
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
- *Correspondence: Isabel Dominguez,
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