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Bridges Y, de Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JO. Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598672. [PMID: 38915571 PMCID: PMC11195176 DOI: 10.1101/2024.06.13.598672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to measure and is impacted by many factors, for example, ontology structure, annotation completeness or changes to the underlying algorithm. Assertions of the capabilities of VGPAs are often not reproducible, in part because there is no standardised, empirical framework and openly available patient data to assess the efficacy of VGPAs - ultimately hindering the development of effective prioritisation tools. Results In this paper, we present our benchmarking tool, PhEval, which aims to provide a standardised and empirical framework to evaluate phenotype-driven VGPAs. The inclusion of standardised test corpora and test corpus generation tools in the PhEval suite of tools allows open benchmarking and comparison of methods on standardised data sets. Conclusions PhEval and the standardised test corpora solve the issues of patient data availability and experimental tooling configuration when benchmarking and comparing rare disease VGPAs. By providing standardised data on patient cohorts from real-world case-reports and controlling the configuration of evaluated VGPAs, PhEval enables transparent, portable, comparable and reproducible benchmarking of VGPAs. As these tools are often a key component of many rare disease diagnostic pipelines, a thorough and standardised method of assessment is essential for improving patient diagnosis and care.
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Affiliation(s)
- Yasemin Bridges
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Katherina G Cortes
- School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Melissa Haendel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel R Korn
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | | | - James A McLaughlin
- Samples, Phenotypes, and Ontologies (SPOT), European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Peter N Robinson
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Julius Ob Jacobsen
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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Wen C, Shen G, Fang C, Tian L. Insight into the research history and trends of total anomalous pulmonary venous connection: a bibliometric analysis. J Cardiothorac Surg 2024; 19:285. [PMID: 38730414 PMCID: PMC11088122 DOI: 10.1186/s13019-024-02787-8] [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: 09/16/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Total anomalous pulmonary venous connection (TAPVC) is a rare congenital heart disease characterized by the inability of all pulmonary veins to connect to the left atrium. Our previous bibliometric article summarized the characteristics of only the 100 most cited papers in TAPVC research. The purpose of this study was to use comprehensive bibliometric analysis to examine the development history, current status, and future trends in the field of TAPVC. METHODS All publications on TAPVC published between 2000 and 2023 were collected from the Web of Science Core Collection. The publication and citation data were quantitatively analyzed by publication year, country, institution, author, and journal. Co-authorship and co-occurrence analyses were performed using VOSviewer, and keyword and reference bursts were identified using CiteSpace. Pearson's test was used to examine the correlations between two continuous variables. RESULTS As of July 20, 2023, we identified 368 publications with 3320 citations. These publications were published in 132 journals and authored by 1835 researchers from 457 institutions in 47 countries. For the number of publications, the top country, top institution, top author, and top journals were the United States (n = 82), Shanghai Jiao Tong University (n = 13), Huiwen Chen (n = 9), and Annals of Thoracic Surgery and Pediatric Cardiology (n = 29 each), respectively. For the number of citations, the top country, top affiliation, top author, and top journal were the United States (n = 1348), University of Toronto (n = 250), Christopher A. Caldarone (n = 315), and Annals of Thoracic Surgery (n = 746), respectively. The number of national publications significantly correlated with GDP (R = 0.887, P < 0.001), research & development (R&D) expenditure (R = 0.375, P = 0.013), population (R = 0.694, P < 0.001), and journals (R = 0.751, P < 0.001). The number of national citations significantly correlated with GDP (R = 0.881, P < 0.001), R&D expenditure (R = 0.446, P = 0.003), population (R = 0.305, P = 0.037), and journals (R = 0.917, P < 0.001). International collaboration in the field of TAPVC was not well developed. The most commonly cited publication discussed era changes in mortality and reoperation rate in TAPVC patients. The most common keywords were "total anomalous pulmonary venous connection" and "congenital heart disease". The keyword "case report" appeared most recently, with an average occurrence year of 2021.8. The co-occurrence analysis grouped 26 keywords into six themes: surgical repair of TAPVC, postoperative pulmonary vein stenosis, surgical repair of TAPVC patients with heterotaxy, application of echocardiography in diagnosing TAPVC, application of echocardiography in the prenatal diagnosis of TAPVC, and application of the sutureless technique in the surgical repair of TAPVC patients with right atrial isomerism or a single ventricle. Citation burst detection identified 32 references with citation bursts, seven of which had ongoing citation bursts until 2023. CONCLUSIONS This study conducted a bibliometric analysis to provide a comprehensive overview of TAPVC research. We hope to offer new ideas for promoting development in the field of TAPVC.
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Affiliation(s)
- Chen Wen
- Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Geng Shen
- Division of Cardiology, Peking University First Hospital, Beijing, China
| | - Chenhao Fang
- Department of Neurosurgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Tian
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, China
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Choon YW, Choon YF, Nasarudin NA, Al Jasmi F, Remli MA, Alkayali MH, Mohamad MS. Artificial intelligence and database for NGS-based diagnosis in rare disease. Front Genet 2024; 14:1258083. [PMID: 38371307 PMCID: PMC10870236 DOI: 10.3389/fgene.2023.1258083] [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: 08/03/2023] [Accepted: 11/24/2023] [Indexed: 02/20/2024] Open
Abstract
Rare diseases (RDs) are rare complex genetic diseases affecting a conservative estimate of 300 million people worldwide. Recent Next-Generation Sequencing (NGS) studies are unraveling the underlying genetic heterogeneity of this group of diseases. NGS-based methods used in RDs studies have improved the diagnosis and management of RDs. Concomitantly, a suite of bioinformatics tools has been developed to sort through big data generated by NGS to understand RDs better. However, there are concerns regarding the lack of consistency among different methods, primarily linked to factors such as the lack of uniformity in input and output formats, the absence of a standardized measure for predictive accuracy, and the regularity of updates to the annotation database. Today, artificial intelligence (AI), particularly deep learning, is widely used in a variety of biological contexts, changing the healthcare system. AI has demonstrated promising capabilities in boosting variant calling precision, refining variant prediction, and enhancing the user-friendliness of electronic health record (EHR) systems in NGS-based diagnostics. This paper reviews the state of the art of AI in NGS-based genetics, and its future directions and challenges. It also compare several rare disease databases.
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Affiliation(s)
- Yee Wen Choon
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | - Yee Fan Choon
- Faculty of Dentistry, Lincoln University College, Petaling Jaya, Selangor, Malaysia
| | - Nurul Athirah Nasarudin
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fatma Al Jasmi
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Muhamad Akmal Remli
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | | | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Liu X, Chen H, Zhong Y, Lee TY, Han W, Yu D, Liu H, Ji J. Diet therapy in patients with rare diseases: a scoping review. J Hum Nutr Diet 2022; 36:742-753. [PMID: 36448617 DOI: 10.1111/jhn.13116] [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: 04/25/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND This scoping review presents existing research evidence regarding diet therapy in patients with rare diseases (RDs). METHODS Using the five-stage scoping review framework proposed by Arksey, O'Malley and Levac, we searched the published literature in PubMed, Web of Science, Royal Society of Chemistry, China National Knowledge Infrastructure, VIP Database and Wan Fang Database from January 2010 to November 2022. We selected diet therapy studies on 121 RDs, as categorised by the National Health Commission of China in 2018. Charts for research analysis were developed and used to categorise the data. RESULTS We ultimately included 34 diet therapy studies from 19 countries and territories for 10 RDs and 3 RD groups. RD diet therapy studies have mainly focused on inborn errors of metabolism (92.3%) and are common in Western countries. Most studies focused on diet therapy methods for RDs (44%). In addition, 29% of studies included diet therapy management, 15% included guidelines for diet therapy and 12% included the impact of diet therapy on patients. CONCLUSIONS Current diet therapies for RDs lack specificity and present with limited characteristics. Therefore, it is necessary to expand the scope and depth of future research and explore evidence-based recommendations and new diet therapies focused on patient needs and family support to provide a reference for improving the efficacy and safety of diet therapies for RDs.
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Affiliation(s)
- Xuehua Liu
- College of Nursing, Guangzhou Medical University, Guangzhou, China
| | - Huifang Chen
- College of Nursing, Guangzhou Medical University, Guangzhou, China
| | - Yaping Zhong
- College of Nursing and Midwifery, Monash University, Clayton Campus, Clayton, Victoria, Australia
| | - Tsorng-Yeh Lee
- College of Nursing, York University, Toronto, Ontario, Canada
| | - Wenxuan Han
- College of Nursing, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Dafang Yu
- Department of Nursing, Jinan Maternal and Child Care Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Huaxia Liu
- College of Nursing, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Ji Ji
- College of Nursing, Guangzhou Medical University, Guangzhou, China.,Department of Nursing, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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5
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Kańduła MM, Aldoshin AD, Singh S, Kolaczyk ED, Kreil D. ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification. Nucleic Acids Res 2022; 51:e6. [PMID: 36395816 PMCID: PMC9841426 DOI: 10.1093/nar/gkac988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
With more and more data being collected, modern network representations exploit the complementary nature of different data sources as well as similarities across patients. We here introduce the Variation of information fused Layers of Networks algorithm (ViLoN), a novel network-based approach for the integration of multiple molecular profiles. As a key innovation, it directly incorporates prior functional knowledge (KEGG, GO). In the constructed network of patients, patients are represented by networks of pathways, comprising genes that are linked by common functions and joint regulation in the disease. Patient stratification remains a key challenge both in the clinic and for research on disease mechanisms and treatments. We thus validated ViLoN for patient stratification on multiple data type combinations (gene expression, methylation, copy number), showing substantial improvements and consistently competitive performance for all. Notably, the incorporation of prior functional knowledge was critical for good results in the smaller cohorts (rectum adenocarcinoma: 90, esophageal carcinoma: 180), where alternative methods failed.
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Affiliation(s)
- Maciej M Kańduła
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Swati Singh
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Eric D Kolaczyk
- Correspondence may also be addressed to Eric D. Kolaczyk. Tel: +1 514 398 3805;
| | - David P Kreil
- To whom correspondence should be addressed. Tel: +43 1 47654 79009;
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Kundu J, Ghosh A, Ghosh U, Das A, Nagar D, Pattanayak S, Ghose A, Sinha S. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. J Org Chem 2022; 87:9466-9478. [PMID: 35839125 DOI: 10.1021/acs.joc.2c00265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) constitute 3 out of the 11 FDA-approved oligonucleotide-based drugs in the last 6 years. PMOs can effectively silence disease-causing genes and modify splicing. However, PMO synthesis has remained challenging for a variety of reasons: inefficient deprotection and coupling methods and instability of monomers. Here, we report the development of a suitable combination of resin supports, deblocking and coupling reagents for synthesizing PMOs using either trityl or Fmoc-protected chlorophosphoramidate monomers. The synthesized PMOs using both the methods on a solid support have been validated for gene silencing in a zebrafish model. The protocol was successfully transferred into an automated DNA synthesizer to make several sequences of PMOs, demonstrating for the first time the adaptation of regular PMOs in a commercial DNA synthesizer. Moreover, PMOs with longer than 20-mer sequences, including FDA-approved Eteplirsen (30-mer), were achieved in >20% overall yield that is superior to previous reports. Hybridization study shows that PMOs exhibit a higher binding affinity toward complementary DNA relative to the DNA/DNA duplex (>6 °C). Additionally, the introduction of Fmoc chemistry into PMOs opens up the possibility for PMO synthesis in commercial peptide synthesizers for future development.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Dhriti Nagar
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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A population-based study of mortality due to muscular dystrophies across a 36-year period in Spain. Sci Rep 2022; 12:3750. [PMID: 35260676 PMCID: PMC8904487 DOI: 10.1038/s41598-022-07814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/22/2022] [Indexed: 12/02/2022] Open
Abstract
Muscular dystrophies (MD) are a group of rare hereditary degenerative diseases. Our aim was to analyze the mortality pattern in Spain from 1981 to 2016 to assess the temporal trend and discern possible geographic differences using population-based data. Annual deaths related to MD were obtained from the National Statistics Institute with codes 359.1 of the ICD-9 (1981–1998) and G71.0 of the ICD-10 (1999–2016). Age-adjusted mortality rates were calculated and changes in mortality trends were identified. The standardized mortality ratios (SMR) and their respective 95% confidence intervals were calculated by district for 1999–2016. Smoothed SMRs and posterior probability were also assessed and then mapped to look for patterns or geographic distribution. All rates were expressed per 1,000,000 inhabitants. A total of 2,512 deaths (73.8% men) were identified. The age-adjusted mortality rates varied from 0.63 (95% CI 0.40–0.95) in 1981 to 1.51 (95% CI 1.17–1.93) in 2016. MD mortality showed a significant increase of 8.81% per year (95% CI 5.0–12.7) from 1981 to 1990, remaining stable afterwards. Areas with risk of death higher than expected for Spain as a whole were identified, not showing a specific regional pattern. In conclusion, the rising trend in MD mortality might be attributable to advanced improvements in diagnostic techniques leading to a rise in prevalence. Further research on the districts with the highest mortality would be necessary.
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8
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Gresky J, Dorn J, Teßmann B, Petiti E. How rare is rare? A literature survey of the last 45 years of paleopathological research on ancient rare diseases. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2021; 33:94-102. [PMID: 33813348 DOI: 10.1016/j.ijpp.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVE This paper aims to provide a quantitative estimation of the representation of diseases defined as rare today in the bioarchaeological literature and to outline the reasons for this. MATERIALS A 45-year bibliometric study of publications in seven bioarchaeological journals, along with two journals and editorial groups of broader scientific focus. METHODS Analyses of distribution patterns of the search hits and diachronic trends for achondroplasia, autosomal-dominant osteopetrosis, osteogenesis imperfecta, and osteopoikilosis, compared to those for tuberculosis as control measure of coverage. RESULTS Studies of ancient rare diseases (ARD) are mostly published as case reports in specialized journals and their number did not benefit from the introduction of biomolecular studies. The higher frequency of cases of achondroplasia suggests that not all rare diseases are equally under-represented. CONCLUSIONS Rare diseases are still largely under-represented in bioarchaeological literature. Their marginality likely results from a combination of taphonomic, methodological and public visibility factors. SIGNIFICANCE This article is the first attempt to provide a quantitative assessment of the under-representation of ARD and to outline the factors behind it. LIMITATIONS Rare diseases are an etiologically heterogeneous group. The number of surveyed journals and articles, as well as targeted diseases might be limiting factors. SUGGESTIONS FOR FURTHER RESEARCH Increasing collection and dissemination of data on ARD; opening a wide-ranging debate on their definition; implementation of biomolecular studies.
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Affiliation(s)
- Julia Gresky
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany.
| | - Juliane Dorn
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, Berlin, Germany
| | - Emmanuele Petiti
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany
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Radu R, Hernández-Ortega S, Borrega O, Palmeri A, Athanasiou D, Brooke N, Chapí I, Le Corvec A, Guglieri M, Perera-Lluna A, Garrido-Aguirre J, Ryll B, Nafria Escalera B. Global Collaborative Social Network (Share4Rare) to Promote Citizen Science in Rare Disease Research: Platform Development Study. JMIR Form Res 2021; 5:e22695. [PMID: 33779572 PMCID: PMC8088870 DOI: 10.2196/22695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/22/2020] [Accepted: 12/20/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Rare disease communities are spread around the globe and segmented by their condition. Little research has been performed on the majority of rare diseases. Most patients who are affected by a rare disease have no research on their condition because of a lack of knowledge due to absence of common groups in the research community. OBJECTIVE We aimed to develop a safe and secure community of rare disease patients, without geographic or language barriers, to promote research. METHODS Cocreation design methodology was applied to build Share4Rare, with consultation and input through workshops from a variety of stakeholders (patients, caregivers, clinicians, and researchers). RESULTS The workshops allowed us to develop a layered version of the platform based on educating patients and caregivers with publicly accessible information, a secure community for the patients and caregivers, and a research section with the purpose of collecting patient information for analysis, which was the core and final value of the platform. CONCLUSIONS Rare disease research requires global collaboration in which patients and caregivers have key roles. Collective intelligence methods implemented in digital platforms reduce geographic and language boundaries and involve patients in a unique and universal project. Their contributions are essential to increase the amount of scientific knowledge that experts have on rare diseases. Share4Rare has been designed as a global platform to facilitate the donation of clinical information to foster research that matters to patients with rare conditions. The codesign methods with patients have been essential to create a patient-centric design.
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Affiliation(s)
| | | | | | - Avril Palmeri
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle, United Kingdom
| | - Dimitrios Athanasiou
- Stichting United Parent Projects Muscular Dystrophy, World Duchenne Organization, Amsterdam, Netherlands
| | | | | | | | - Michela Guglieri
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle, United Kingdom
| | - Alexandre Perera-Lluna
- Center for Biomedical Engineering Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Jon Garrido-Aguirre
- Center for Biomedical Engineering Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Bettina Ryll
- Melanoma Patient Network Europe, Uppsala, Sweden
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Li H, Fang F, Xu M, Liu Z, Zhou J, Wang X, Wang X, Han T. Clinical Assessments and EEG Analyses of Encephalopathies Associated With Dynamin-1 Mutation. Front Pharmacol 2019; 10:1454. [PMID: 31920647 PMCID: PMC6915043 DOI: 10.3389/fphar.2019.01454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
Epileptic encephalopathy, caused by mutations in the dynamin-1 (DNM1; NM_004408) gene, is a newly identified neurologic disorder in children. Thus far, the full clinical and electroencephalographic features of children with DNM1 mutation-related epileptic encephalopathy have not been established. The aim of this study is to characterize the phenotypic, genetic, and electroencephalographic features of children with DNM1 mutation-related epileptic encephalopathy. Here, we investigated a patient with a novel pathogenic DNM1 variant, who received treatment in Beijing Children's Hospital and had detailed clinical, EEG, and genetic information. Conversely, we performed an extensive literature search in PubMed, EMBASE, Cochrane Central Register of Controlled Trials, Chinese BioMedical Literature Database, China National Knowledge Infrastructure, and Wanfang Database using the term "DNM1" and were able to find 32 cases reported in nine articles (in English) from January 2013 to December 2018. The clinical features of 33 cases with pathogenic DNM1 variants were analyzed and the results showed that patients carrying pathogenic variants in the GTPase or middle domains present with epileptic encephalopathy and severe neurodevelopmental symptoms. Patients carrying pathogenic variants in both domains exhibited comparable phenotypes.
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Affiliation(s)
- Hua Li
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Manting Xu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhimei Liu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ji Zhou
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaohui Wang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaofei Wang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tongli Han
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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11
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Lin H, Qiu JW, Rauf YM, Lin GZ, Liu R, Deng LJ, Deng M, Song YZ. Sodium Taurocholate Cotransporting Polypeptide (NTCP) Deficiency Hidden Behind Citrin Deficiency in Early Infancy: A Report of Three Cases. Front Genet 2019; 10:1108. [PMID: 31788003 PMCID: PMC6856633 DOI: 10.3389/fgene.2019.01108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022] Open
Abstract
Sodium taurocholate cotransporting polypeptide (NTCP), a carrier protein encoded by the gene SLC10A1, is expressed in the basolateral membrane of the hepatocyte to uptake bile acids from plasma. As a new inborn error of bile acid metabolism, NTCP deficiency remains far from being well understood in terms of the clinical and molecular features. Citrin deficiency is a well-known autosomal recessive disease arising from SLC25A13 mutations, and in neonates or infants, this condition presents as transient intrahepatic cholestasis which usually resolves before 1 year of age. All the three patients in this paper exhibited cholestatic jaundice and elevated total bile acids in their early infancy, which were attributed to citrin deficiency by SLC25A13 genetic analysis. In response to feeding with lactose-free and medium-chain triglycerides-enrich formula, their clinical and laboratory presentations disappeared gradually while the hypercholanemia persisted, even beyond 1 year of age. On subsequent SLC10A1 analysis, they were all homozygous for the well-known pathogenic variant c.800C > T (p.Ser267Phe), and NTCP deficiency was thus definitely diagnosed. The findings in this paper indicated that NTCP deficiency could be covered up by citrin deficiency during early infancy; however, in citrin-deficient patients with intractable hypercholanemia following resolved cholestatic jaundice, NTCP deficiency should be taken into consideration.
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Affiliation(s)
- Hui Lin
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jian-Wu Qiu
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yaqub-Muhammad Rauf
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Gui-Zhi Lin
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Rui Liu
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Li-Jing Deng
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Mei Deng
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yuan-Zong Song
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
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12
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Shi J, Ren M, Jia J, Tang M, Guo Y, Ni X, Shi T. Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease. Front Pharmacol 2019; 10:1200. [PMID: 31680973 PMCID: PMC6803541 DOI: 10.3389/fphar.2019.01200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
Osteogenesis imperfecta (OI), mainly caused by structural abnormalities of type I collagen, is a hereditary rare disease characterized by increased bone fragility and reduced bone mass. Clinical manifestations of OI mostly include multiple repeated bone fractures, thin skin, blue sclera, hearing loss, cardiovascular and pulmonary system abnormalities, triangular face, dentinogenesis imperfecta (DI), and walking with assistance. Currently, 20 causative genes with 18 subtypes have been identified for OI, of them, variations in COL1A1 and COL1A2 have been demonstrated to be major causative factors to OI. However, the complexity of the bone formation process indicates that there are potential new pathogenic genes associated with OI. To comprehensively explore the underlying mechanism of OI, we conducted association analysis between genotypes and phenotypes of OI diseases and found that mutations in COL1A1 and COL1A2 contributed to a large proportion of the disease phenotypes. We categorized the clinical phenotypes and the genotypes based on the variation types for those 155 OI patients collected from literature, and association study revealed that three phenotypes (bone deformity, DI, walking with assistance) were enriched in two variation types (the Gly-substitution missense and groups of frameshift, nonsense, and splicing variations). We also identified four novel variations (c.G3290A (p.G1097D), c.G3289C (p.G1097R), c.G3289A (p.G1097S), c.G3281A (p.G1094D)) in gene COL1A1 and two novel variations (c.G2332T (p.G778C), c.G2341T (p.G781C)) in gene COL1A2, which could potentially contribute to the disease. In addition, we identified several new potential pathogenic genes (ADAMTS2, COL5A2, COL8A1) based on the integration of protein–protein interaction and pathway enrichment analysis. Our study provides new insights into the association between genotypes and phenotypes of OI and novel information for dissecting the underlying mechanism of the disease.
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Affiliation(s)
- Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Meng Ren
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Muxue Tang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
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13
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Fu Y, Jia J, Yue L, Yang R, Guo Y, Ni X, Shi T. Systematically Analyzing the Pathogenic Variations for Acute Intermittent Porphyria. Front Pharmacol 2019; 10:1018. [PMID: 31572191 PMCID: PMC6753391 DOI: 10.3389/fphar.2019.01018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
The rare autosomal dominant disorder acute intermittent porphyria (AIP) is caused by the deficient activity of hydroxymethylbilane synthase (HMBS). The symptoms of AIP are acute neurovisceral attacks which are induced by the dysfunction of heme biosynthesis. To better interpret the underlying mechanism of clinical phenotypes, we collected 117 HMBS gene mutations from reported individuals with AIP and evaluated the mutations' impacts on the corresponding protein structure and function. We found that several mutations with most severe clinical symptoms are located at dipyromethane cofactor (DPM) binding domain of HMBS. Mutations on these residues likely significantly influence the catalytic reaction. To infer new pathogenic mutations, we evaluated the pathogenicity for all the possible missense mutations of HMBS gene with different bioinformatic prediction algorithms, and identified 34 mutations with serious pathogenicity and low allele frequency. In addition, we found that gene PPARA may also play an important role in the mechanisms of AIP attacks. Our analysis about the distribution frequencies of the 23 variations revealed different distribution patterns among eight ethnic populations, which could help to explain the genetic basis that may contribute to population disparities in AIP prevalence. Our systematic analysis provides a better understanding for this disease and helps for the diagnosis and treatment of AIP.
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Affiliation(s)
- Yibao Fu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lishu Yue
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Ruiying Yang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Biobank for Clinical Data and Samples in Pediatrics, Beijing Children’s Hospital, National Center for Children’s Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, China
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14
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Yan B, Wang C, Zhang K, Zhang H, Gao M, Lv Y, Li X, Liu Y, Gai Z. Novel Neonatal Variants of the Carbamoyl Phosphate Synthetase 1 Deficiency: Two Case Reports and Review of Literature. Front Genet 2019; 10:718. [PMID: 31507628 PMCID: PMC6713721 DOI: 10.3389/fgene.2019.00718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/09/2019] [Indexed: 12/31/2022] Open
Abstract
Carbamoyl phosphate synthetase I (CPS1) deficiency (CPS1D), is a rare autosomal recessive disorder, characterized by life-threatening hyperammonemia. In this study, we presented the detailed clinical features and genetic analysis of two patients with neonatal-onset CPS1D carrying two compound heterozygous variants of c.1631C > T (p.T544M)/c.1981G > T (p.G661C), and c.2896G > T (p.E966X)/c622-3C > G in CPS1 gene, individually. Out of them, three variants are novel, unreported including a missense (c.1981G > T, p.G661C), a nonsense (c.2896G > T, p.E966X), and a splicing change of c.622-3C > G. We reviewed all available publications regarding CPS1 mutations, and in total 264 different variants have been reported, with majority of 157 (59.5%) missense, followed by 35 (13.2%) small deletions. This study expanded the mutational spectrum of CPS1. Moreover, our cases and review further support the idea that most (≥90%) of the mutations were "private" and only ∼10% recurred in unrelated families.
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Affiliation(s)
- Beibei Yan
- Neonatology Department, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Chao Wang
- Shandong Freshwater Fisheries Research Institute, Ji’nan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Min Gao
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Xiaoying Li
- Neonatology Department, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
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15
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Jia J, An Z, Ming Y, Guo Y, Li W, Liang Y, Guo D, Li X, Tai J, Chen G, Jin Y, Liu Z, Ni X, Shi T. eRAM: encyclopedia of rare disease annotations for precision medicine. Nucleic Acids Res 2019; 46:D937-D943. [PMID: 29106618 PMCID: PMC5753383 DOI: 10.1093/nar/gkx1062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/24/2017] [Indexed: 01/12/2023] Open
Abstract
Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM). eRAM was built by text-mining nearly 10 million scientific publications and electronic medical records, and integrating various data in existing recognized databases (such as Unified Medical Language System (UMLS), Human Phenotype Ontology, Orphanet, OMIM, GWAS). eRAM systematically incorporates currently available data on clinical manifestations and molecular mechanisms of rare diseases and uncovers many novel associations among diseases. eRAM provides enriched annotations for 15 942 rare diseases, yielding 6147 human disease related phenotype terms, 31 661 mammalians phenotype terms, 10,202 symptoms from UMLS, 18 815 genes and 92 580 genotypes. eRAM can not only provide information about rare disease mechanism but also facilitate clinicians to make accurate diagnostic and therapeutic decisions towards rare diseases. eRAM can be freely accessed at http://www.unimd.org/eram/.
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Affiliation(s)
- Jinmeng Jia
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhongxin An
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yue Ming
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, The Ministry of Education Key Laboratory of Major Diseases in Children, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yunxiang Liang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dongming Guo
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xin Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jun Tai
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Zhimei Liu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xin Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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16
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Wang D, Gao M, Zhang K, Jin R, Lv Y, Liu Y, Ma J, Wan Y, Gai Z, Liu Y. Molecular Genetics Analysis of 70 Chinese Families With Muscular Dystrophy Using Multiplex Ligation-Dependent Probe Amplification and Next-Generation Sequencing. Front Pharmacol 2019; 10:814. [PMID: 31404137 PMCID: PMC6669794 DOI: 10.3389/fphar.2019.00814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Muscular dystrophy (MD) includes multiple types, of which dystrophinopathies caused by dystrophin (DMD) mutations are the most common types in children. An accurate identification of the causative mutation at the genomic level is critical for genetic counseling of the family, and analysis of genotype-phenotype correlations, as well as a reference for the development of gene therapy. Methods: Totally, 70 Chinese families with suspected MD probands were enrolled in the study. The multiplex ligation-dependent probe amplification (MLPA) was first performed to screen large deletions/duplications of DMD exons in the patients, and then, next-generation sequencing (NGS) was carried out to detect small mutations in the MLPA-negative patients. Results: Totally, 62 mutations of DMD were found in 62 probands with DMD/BMD, and two compound heterozygous mutations in LAMA2 were identified in two probands with MDC1A (a type of congenital MD), indicating that the diagnostic yield was 91.4% by MLPA plus NGS for MD diagnosis in this cohort. Out of the mutations, 51 large mutations encompassing 47 (75.8%) deletions and four duplications (6.5%) were identified by MLPA; 11 small mutations including six (9.7%) nonsense, two (3.2%) small deletions, two splice-site mutations (3.2%), and one small insertion (1.6%) were found by NGS. Large mutations were found most frequently in the hotspot region between exons 45 and 55 (70.6%). Out of the 11 patients harboring point mutations in DMD, 8 were novel mutations. Additionally, one novel mutation in LAMA2 was identified. All the novel mutations were analyzed and predicted as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guideline. Finally, 34 DMD, 4 BMD, 24 BMD/DMD, and 2 MDC1A were diagnosed in the cohort. Conclusion: Our data indicated that the MLPA plus NGS can be a comprehensive and effective tool for precision diagnosis and potential treatment of MD and is particularly necessary for the patients at very young age with only two clinical indicators (persistent hyperCKemia and typical myopathy performance on electromyogram) but no definite clinical manifestations.
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Affiliation(s)
- Dong Wang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Min Gao
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ruifeng Jin
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yong Liu
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Jian Ma
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ya Wan
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
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Identification of a novel COL4A5 mutation in the proband initially diagnosed as IgAN from a Chinese family with X-linked Alport syndrome. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1572-1579. [PMID: 31209800 DOI: 10.1007/s11427-018-9545-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023]
Abstract
Alport syndrome (AS) is a hereditary progressive nephropathy characterized by hematuria, ultrastructural lesions of the glomerular basement membrane, ocular lesions and sensorineural hearing loss. Germline mutations of COL4A5 are associated with X-linked AS with an extreme phenotypic heterogeneity. Here, we investigated a Chinese family with Alport syndrome. The proband was a 9-year-old boy with hematuria and proteinuria. Based on the test results of renal biopsy and immunofluorescence, the proband was initially diagnosed as IgA nephropathy and the treatment was recommended accordingly. Meanwhile, we found that the treatment outcome was poor. Therefore, for proper clinical diagnosis and appropriate treatment, targeted exome-based next-generation sequencing has been undertaken. We identified a novel hemizygous single nucleotide deletion c.1902delA in COL4A5 gene. Segregation analysis identified that this novel mutation is co-segregated among the affected family members but absent in unaffected family members. The clinical diagnosis of the proband was revised as AS accompanied by IgA nephropathy, which has been rarely reported. Our findings demonstrated the significance of the application of Genetic screening, expanded the mutation spectrum of COL4A5 associated AS patients with atypical renal phenotypes and provided a good lesson to be learned from our detour during the diagnosis.
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18
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Ren XT, Wang XH, Ding CH, Shen X, Zhang H, Zhang WH, Li JW, Ren CH, Fang F. Next-Generation Sequencing Analysis Reveals Novel Pathogenic Variants in Four Chinese Siblings With Late-Infantile Neuronal Ceroid Lipofuscinosis. Front Genet 2019; 10:370. [PMID: 31105743 PMCID: PMC6494930 DOI: 10.3389/fgene.2019.00370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022] Open
Abstract
Neuronal Ceroid Lipofuscinoses (NCLs) are progressive degenerative diseases mainly affect brain and retina. They are characterized by accumulation of autofluorescent storage material, mitochondrial ATPase subunit C, or sphingolipid activator proteins A and D in lysosomes of most cells. Heterogenous storage material in NCLs is not completely disease-specific. Most of CLN proteins and their natural substrates are not well-characterized. Studies have suggested variants of Late-Infantile NCLs (LINCLs) include the major type CLN2 and minor types CLN5, CLN6, CLN7, and CLN8. Therefore, combination of clinical and molecular analysis has become a more effective diagnosis method. We studied 4 late-infantile NCL siblings characterized by seizures, ataxia as early symptoms, followed by progressive regression in intelligence and behavior, but mutations are located in different genes. Symptoms and progression of 4 types of LINCLs are compared. Pathology of LINCLs is also discussed. We performed Nest-Generation Sequencing on these phenotypically similar families. Three novel variants c.1551+1insTGAT in TPP1, c.244G>T in CLN6, c.554-5A>G in MFSD8 were identified. Potential outcome of the mutations in structure and function of proteins are studied. In addition, we observed some common and unique clinical features of Chinese LINCL patient as compared with those of Western patients, which greatly improved our understanding of the LINCLs.
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Affiliation(s)
- Xiao-Tun Ren
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiao-Hui Wang
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chang-Hong Ding
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | | | | | - Wei-Hua Zhang
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jiu-Wei Li
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chang-Hong Ren
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Fang Fang
- Department of Neurology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
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19
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Zhao X, Song Y, Chen S, Wang X, Luo F, Yang Y, Chen L, Chen R, Chen H, Su Z, Wu D, Gong C. Growth Pattern in Chinese Children With 5α-Reductase Type 2 Deficiency: A Retrospective Multicenter Study. Front Pharmacol 2019; 10:173. [PMID: 30930770 PMCID: PMC6429988 DOI: 10.3389/fphar.2019.00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/11/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND 5α-reductase type 2 deficiency (5αRD) is an autosomal recessive hereditary disease of the group of 46, XY disorders of sex development (DSD). OBJECTIVE To study the growth pattern in Chinese pediatric patients with 5αRD. SUBJECTS Data were obtained from 141 patients with 5αRD (age: 0-16 years old) who visited eight pediatric endocrine centers from January 2010 to December 2017. METHODS In this retrospective cohort study, height, weight, and other relevant data were collected from the multicenter hospital registration database. Baseline luteinizing hormone (LH), follicle stimulating hormone (FSH), testosterone (T), and dihydrotestosterone (DHT) after human chorionic gonadotropin (HCG) stimulation test were measured by enzyme enhanced chemiluminescence assay. Bone age (BA) was assessed using the Greulich-Pyle (G-P) atlas. Growth curve was constructed based on λ-median-coefficient of variation method (LMS). RESULTS The height standard deviation scores (HtSDS) and weight standard deviation scores (WtSDS) in 5αRD children were in the normal range as compared to normal boys. Significantly higher HtSDS was observed in patients with 5αRD who were <1 year old (t = 3.658, 2.103, P = 0.002, 0.048, respectively), and higher WtSDS in those <6 months old (t = 2.756, P = 0.012). Then HtSDS and WtSDS decreased gradually and fluctuated near the median of the same age until 13 years. WtSDS in 5αRD children from northern China were significantly higher than those from the south (Z = -2.670, P = 0.008). The variation tendency of HtSDS in Chinese 5αRDs was consistent with the trend of stimulating T. HtSDS and stimulating T in the external masculinization score (EMS) <7 group were slightly higher than those in EMS ≥ 7 group without significant difference. Additionally, the ratio of BA over chronological age (BA/CA) was significantly <1 in children with 5αRD. CONCLUSION Children with 5αRD had a special growth pattern that was affected by high levels of T, while DHT played a very small role in it. Their growth accelerated at age <1 year, followed by slowing growth and fluctuating height near normal median boys' height. The BA was delayed in 5αRD children. Androgen treatment, which may be considered anyway for male 5αRD patients with a micropenis, may also be beneficial for growth.
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Affiliation(s)
- Xiu Zhao
- Center of Endocrinology, Genetics and Metabolism, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Department of Endocrinology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yanning Song
- Center of Endocrinology, Genetics and Metabolism, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Shaoke Chen
- Genetic and Metabolic Central Laboratory, Maternal and Children Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiumin Wang
- Department of Endocrinology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, Shanghai, China
| | - Feihong Luo
- Department of Endocrinology, Children’s Hospital of Fudan University, Fudan University, Shanghai, China
| | - Yu Yang
- Department of Endocrinology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Linqi Chen
- Department of Endocrinology, Children’s Hospital of Soochow University, Suzhou, China
| | - Ruimin Chen
- Department of Endocrinology, Fuzhou Children’s Hospital, Fuzhou, China
| | - Hui Chen
- Department of BME, Capital Medical University, Beijing, China
| | - Zhe Su
- Department of Endocrinology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Di Wu
- Center of Endocrinology, Genetics and Metabolism, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Chunxiu Gong
- Center of Endocrinology, Genetics and Metabolism, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
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20
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Liu Z, Zhang L, Shen D, Ding C, Yang X, Zhang W, Li J, Deng J, Gong S, Liu J, Qian S, Fang F. Compound Heterozygous CHAT Gene Mutations of a Large Deletion and a Missense Variant in a Chinese Patient With Severe Congenital Myasthenic Syndrome With Episodic Apnea. Front Pharmacol 2019; 10:259. [PMID: 30914958 PMCID: PMC6422987 DOI: 10.3389/fphar.2019.00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/28/2019] [Indexed: 01/28/2023] Open
Abstract
Congenital myasthenic syndromes (CMSs) are a group of inherited disorders caused by genetic defects in neuromuscular junctions. Mutations in CHAT, encoding choline acetyltransferase, cause congenital myasthenic syndrome with episodic apnea (CMS-EA), a rare autosomal recessive disease characterized by respiratory insufficiency with cyanosis and apnea after infections, fever, vomiting, or excitement. To date, no studies have reported deletions comprised of multiple exons. Here, using next generation sequencing, we identified compound heterozygous mutations, namely a large maternally inherited deletion, including exons 4, 5, and 6, and a paternally inherited missense variant (c.914T>C [p.Ile305Thr]) in CHAT in a Chinese patient with a severe phenotype of CMS-EA. Furthermore, the large deletion was also validated by real-time fluorescence quantitative polymerase chain reaction. The patient was a 10-month-old boy, who presented with a weak cry and feeding difficulties soon after birth, ptosis at 4 months old, episodic apnea after fever at 9 months old, and respiratory insufficiency with cyanosis and apnea that required intubation after a respiratory tract infection at 10 months old. Unfortunately, he died in the Pediatric Intensive Care Unit soon after hospitalization. The patient's elder sister had similar clinical manifestations, and she died prior to the age of 2 months old without a diagnosis. Genotype-phenotype correlation analysis revealed that loss-of-function mutations in exons 4-6 of CHAT might cause more severe CMS-EA. To our knowledge, this is the first study to show compound heterozygous CHAT mutations consisting of a large deletion and missense mutation in a patient with CMS-EA.
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Affiliation(s)
- Zhimei Liu
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- School of Statistics, Faculty of Economics and Management, East China Normal University, Shanghai, China
| | - Danmin Shen
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Changhong Ding
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xinying Yang
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Weihua Zhang
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jiuwei Li
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jie Deng
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Shuai Gong
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jun Liu
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Suyun Qian
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Fang
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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21
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Lu X, Chen W, Li L, Zhu X, Huang C, Liu S, Yang Y, Zhao Y. Two Novel AGXT Mutations Cause the Infantile Form of Primary Hyperoxaluria Type I in a Chinese Family: Research on Missed Mutation. Front Pharmacol 2019; 10:85. [PMID: 30787879 PMCID: PMC6372570 DOI: 10.3389/fphar.2019.00085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare metabolic disorder characterized by a defect in the liver-specific peroxisomal enzyme alanine-glyoxylate and serine-pyruvate aminotransferase (AGT). This disorder results in hyperoxaluria, recurrent urolithiasis, and nephrocalcinosis. Three forms of PH1 have been reported. Data on the infantile form of PH1 are currently limited in literature. Despite the fact that China is the most populated country in the world, only a few AGXT mutations have been reported in several Chinese PH1 patients. In the present study, we investigated a Chinese family in which two siblings are affected by the infantile form of PH1. Sanger sequencing was carried out on the proband, but the results were misleading. Two novel missense mutations (c.517T > C/p.Cys173Arg and c.667A > C/p.Ser223Arg) of the AGXT gene were successfully detected through whole-exome sequencing. These two mutations occurred in the highly conserved residues of the AGT. Four software programs predicted both mutations as the cause of the disease. A postmortem examination was performed and revealed the occurrence of global nephrocalcinosis on both kidneys. The crystals were collected and analyzed as calcium oxalate monohydrate. This study extends the knowledge on the clinical phenotype-genotype correlation of the AGXT mutation. That is, (i) two novel missense mutations were identified for the infantile form of PH1 and (ii) the same AGXT genotype caused the same infantile form of PH1 within the family.
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Affiliation(s)
- Xiulan Lu
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
- Pediatric Intensive Care Unit, Hunan Children’s Hospital, University of South China, Changsha, China
| | - Weijian Chen
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
- Department of Pathology, Hunan Children’s Hospital, University of South China, Changsha, China
| | - Liping Li
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
| | - Xinyuan Zhu
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
| | - Caizhi Huang
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
| | | | - Yongjia Yang
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
| | - Yaowang Zhao
- The Laboratory of Genetics and Metabolism, Hunan Children’s Research Institute (HCRI), Hunan Children’s Hospital, University of South China, Changsha, China
- Department of Urinary Surgery, Hunan Children’s Hospital, University of South China, Changsha, China
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22
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Zhang L, Jin Y, Zheng K, Wang H, Yang S, Lv C, Han W, Yu Y, Yang Y, Geng D, Yang H, Shi T, Guo Y, Ni X. Whole-Genome Sequencing Identifies a Novel Variation of WAS Gene Coordinating With Heterozygous Germline Mutation of APC to Enhance Hepatoblastoma Oncogenesis. Front Genet 2018; 9:668. [PMID: 30619485 PMCID: PMC6305990 DOI: 10.3389/fgene.2018.00668] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Hepatoblastoma (HB), a leading primary hepatic malignancy in children, originates from primitive hepatic stem cells. This study aimed to uncover the genetic variants that are responsible for HB oncogenesis. One family, which includes the healthy parents, and two brothers affected by HB, was recruited. Whole-genome sequencing (WGS) of germline DNA from all the family members identified two maternal variants, located within APC gene and X-linked WAS gene, which were harbored by the two brothers. The mutation of APC (rs137854573, c.C1606T, p.R536X) could result in HB carcinogenesis by activating Wnt signaling. The WAS variant (c.G3T, p.M1-P5del) could promote HB cell proliferation and inhibit T-cell-based immunity by activating PLK1 signaling and inactivating TCR signaling. Further analysis reflected that WAS deficiency might affect the antitumor activity of natural killer and dendritic cells. In summary, the obtained results imply that an APC mutant together with an X-linked WAS mutant, could lead to HB tumorigenesis by activating Wnt and PLK1 signaling, inhibiting TCR signaling, and reducing the antitumor activity of natural killer and dendritic cells.
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Affiliation(s)
- Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kai Zheng
- Department of General Surgery, Wuhan Children's Hospital, Wuhan, China
| | - Huanmin Wang
- Department of Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shen Yang
- Department of Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chenkai Lv
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wei Han
- Department of Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yongbo Yu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yeran Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Di Geng
- Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hui Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xin Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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23
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Jia J, Wang R, An Z, Guo Y, Ni X, Shi T. RDAD: A Machine Learning System to Support Phenotype-Based Rare Disease Diagnosis. Front Genet 2018; 9:587. [PMID: 30564269 PMCID: PMC6288202 DOI: 10.3389/fgene.2018.00587] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/15/2018] [Indexed: 01/21/2023] Open
Abstract
DNA sequencing has allowed for the discovery of the genetic cause for a considerable number of diseases, paving the way for new disease diagnostics. However, due to the lack of clinical samples and records, the molecular cause for rare diseases is always hard to identify, significantly limiting the number of rare Mendelian diseases diagnosed through sequencing technologies. Clinical phenotype information therefore becomes a major resource to diagnose rare diseases. In this article, we adopted both a phenotypic similarity method and a machine learning method to build four diagnostic models to support rare disease diagnosis. All the diagnostic models were validated using the real medical records from RAMEDIS. Each model provides a list of the top 10 candidate diseases as the prediction outcome and the results showed that all models had a high diagnostic precision (≥98%) with the highest recall reaching up to 95% while the models with machine learning methods showed the best performance. To promote effective diagnosis for rare disease in clinical application, we developed the phenotype-based Rare Disease Auxiliary Diagnosis system (RDAD) to assist clinicians in diagnosing rare diseases with the above four diagnostic models. The system is freely accessible through http://www.unimd.org/RDAD/.
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Affiliation(s)
- Jinmeng Jia
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ruiyuan Wang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhongxin An
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, The Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xi Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, The Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- National Center for International Research of Biological Targeting Diagnosis and Therapy/Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research/Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
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