In 1994, an initiative began to form a community of those interested in genetic mutations and their documentation with a view to developing a considered, integrated, and systematic approach to the. Jisc Research Data Registry and Discovery Service DCC http://www.dcc.ac.uk/projects/research-data-registry-pilot (2014). Lopes, P., Dalgleish, R. & Oliveira, J. L. WAVe: web analysis of the variome. Cooperative control of striated muscle mass and metabolism by MuRF1 and MuRF2. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. 2021 Nov 9;13(1):174. doi: 10.1186/s13073-021-00976-x. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. 14, 295300 (2013). This consortium comprises rare disease researchers and funding organizations and promotes the goal of developing 200 new therapies for rare diseases and a means to diagnose most rare diseases by the year 2020. Two novel fibrillin-2 mutations in congenital contractural arachnodactyly. Javed, A., Agrawal, S. & Ng, P. C. Phen-Gen: combining phenotype and genotype to analyze rare disorders. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. A generic software called UMD (Universal Mutation Database) was developed as a generic software to create locusspecific databases (LSDBs) with the 4th Dimension package from ACI, which includes an optimized structure to assist and secure data entry and to allow the input of various clinical data. sharing sensitive information, make sure youre on a federal UMD (Universal Mutation Database): 2005 update - Wiley Online Library Genet. To facilitate comparison of identified mutations in these two genes and search for specific functional areas, we created an LSDB for the FBN2 gene: the UMD-FBN2 database. Here we report the new release (September 2004) of this freely available tool (www.umd.be), which allows the creation of LSDBs for virtually any gene and includes a large set of new analysis tools. The final section offers advice on database construction. eCollection 2021. 45, 11131120 (2013). FOIA Broud C, Collod-Broud G, Boileau C, Soussi T, Junien C. Hum Mutat. A report on an ethical framework for responsible data sharing developed in conjunction with a wide spectrum of the bioethics, genomics and clinical communities, under the auspices of the GA4GH. Genet. 2022 Jan 19;12:768342. doi: 10.3389/fgene.2021.768342. Genet. 2000;15(1):105-13. doi: 10.1002/(SICI)1098-1004(200001)15:1<105::AID-HUMU19>3.0.CO;2-G. Broud C, Hamroun D, Collod-Broud G, Boileau C, Soussi T, Claustres M. Hum Mutat. An initial description of the Human Genome Variation Society's nomenclature standard for naming sequence variants. Thompson, R. et al. RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research. A generic software called UMD (Universal Mutation Database), developed as a generic software to create locusspecific databases (LSDBs) with the 4th Dimension package from ACI, has been successfully adapted to nine genes either involved in cancer or in genetic diseases. Mutat. This tool is freely available. J. Hum. The authors also acknowledge the many key insights provided by attendees of an IRDiRC workshop dedicated to this topic, and expert suggestions made by colleague R. Dalgleish (University of Leicester, UK). UMD (LSDBs) - Database Commons - National Genomics Data Center Cheng, W. C. et al. Med. Beck, T., Hastings, R. K., Gollapudi, S., Free, R. C. & Brookes, A. J. GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. 9, e1003143 (2013). The collection of these mutations will be critical for researchers and clinicians to establish genotype/phenotype correlations. National Library of Medicine den Dunnen, J., Cutting, G. R. & Paalman, M. H. Mandatory variant submission our experiences. The percentages of genetic variance explained by a specific locus, ranging from less than 1% for many common traits up to 100% for some Mendelian diseases. Li, M. X. et al. eCollection 2023. J. Med. The proportion of persons who carry a pathogenic germline variation and also show signs of a disease irrespective of the clinical severity. Transl. Bragin, E. et al. INFEVERS: The repertory of Familial Mediterranean Fever (FMF) and Heredit. Observ-OM and Observ-TAB: universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. Bethesda, MD 20894, Web Policies Would you like email updates of new search results? Edlund, K., et al.. (2012). UMD (Universal Mutation Database): A generic software to build and Rev. Hum. The second section deals with submitting data. & Biesecker, L. G. Databases of genomic variation and phenotypes: existing resources and future needs. Mutat. Zhang L, Qin Z, Huang T, Tam B, Ruan Y, Guo M, Wu X, Li J, Zhao B, Chian JS, Wang X, Wang L, Wang SM. Pharmacogenomics knowledge for personalized medicine. 2002 Dec 7;146(49):2354-8. The authors declare no competing financial interests. In the present context, federation involves connecting genotypephenotype databases across networks to allow combined searches for information about variations or diseases. Genet. Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy. Genet. Other fields such as molecular epidemiology will also be developed using these new data. Hum Mol Genet. Nat. Nucleic Acids Res 41, D962-D969. 7, 36 (2015). Nucleic Acids Res. Nature 467, 10611073 (2010). The human genome is thought to contain about 80,000 genes and presently only 3,000 are known to be implicated in genetic . Hum. The .gov means its official. Hum. Chinese Medicine Phenomics (Chinmedphenomics): Personalized, Precise and Promising, VariantStore: an index for large-scale genomic variant search, http://www.dcc.ac.uk/projects/research-data-registry-pilot, ACO2 clinicobiological dataset with extensive phenotype ontology annotation, Identifying disease-causing mutations in genomes of single patients by computational approaches. Polvi, A. et al. Germline and Somatic mutations in postmenopausal breast cancer patients. 5R24OD011883), and the Bundesministerium fr Bildung und Forschung (BMBF; project no. Mutat. PubMed An approach to patient care that subdivides patients into groups that are defined on the basis of expected risk of developing disease or the expected response to a certain treatment. The FBN2 gene: new mutations, locus-specific database (Universal DNA sequence analysis and genotype-phenotype assessment in 71 patients with syndromic hearing loss or auditory neuropathy. TLDR. Hum. Enhancing discoverability of public health and epidemiology research data. Improved exome prioritization of disease genes through cross-species phenotype comparison. Nucleic Acids Res. UMD (Universal Mutation Database): A generic software to build and analyze locus-specific databases Authors: Christophe Beroud Aix-Marseille Universit Gwenalle Collod-Broud French Institute. Array-CGH has become a standard diagnostic tool for the identification of copy number variants. 2, 24 (2010). PubMed Central (1998) p53 gene mutation: software and database, A new locus-specific database (LSDB) for mutations in the TGFBR2 gene: UMD- TGFBR2, A new locus-specific database (LSDB) for mutations in the folliculin ( FLCN ) gene, 108th ENMC International Workshop, 3rd Workshop of the MYO-CLUSTER project: EUROMEN, 7th International Emery-Dreifuss Muscular Dystrophy (EDMD) Workshop, 1315 September 2002, Naarden, The Netherlands, Guidelines for establishing locus specific databases, UMD-CFTR: A Database Dedicated to CF and CFTR-Related Disorders, Recommendations for locus-specific databases and their curation, Soussi, (2014) Locus-Specific Databases in Cancer: What Future in a Post-Genomic Era? 40, D1308D1312 (2012). Carey, J. C., Allanson, J. E., Hennekam, R. C. & Biesecker, L. G. Standard terminology for phenotypic variations: The elements of morphology project, its current progress, and future directions. We also created specific tools for infrequent mutations such as gross deletions and duplications, and deep intronic mutations. 369, 15021511 (2013). Genet. Many registries collect information about individuals over time or are used to track information regarding the response of patients to treatments. HHS Vulnerability Disclosure, Help Mutat. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Waldrop MA, Moore SA, Mathews KD, Darbro BW, Medne L, Finkel R, Connolly AM, Crawford TO, Drachman D, Wein N, Habib AA, Krzesniak-Swinarska MA, Zaidman CM, Collins JJ, Jokela M, Udd B, Day JW, Ortiz-Guerrero G, Statland J, Butterfield RJ, Dunn DM, Weiss RB, Flanigan KM. Genet. It was developed as a generic software to create locus-specific databases (LSDBs) with the 4(th) Dimension(R) package from ACI. Bareil C, Thze C, Broud C, Hamroun D, Guittard C, Ren C, Paulet D, Georges Md, Claustres M. Hum Mutat. Rath, A. et al. et al. Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Anthony J. Brookes. Other fields such as molecular epidemiology will also be developed using these new data. Unauthorized use of these marks is strictly prohibited. Clin. To facilitate comparison of identified mutations in these two genes and search for specific functional areas, we created an LSDB for the FBN2 gene: the UMD-FBN2 database. Knowledge about these mutations and their association with clinical and biological data is essential for clinicians, geneticists, and researchers. Genome Med. Mutations in the human gene for fibrillin-1 (FBN1) in the Marfan syndrome and related disorders. (33.378%), 495/776 This site needs JavaScript to work properly. Google Scholar. Conley, J. M., Cook-Deegan, R. & Lzaro-Muoz, G. Myriad after Myriad: the proprietary data dilemma. Nat. Res. official website and that any information you provide is encrypted UMD (Universal Mutation Database): A generic software to build and sharing sensitive information, make sure youre on a federal ORCID provides a persistent digital identifier (for example, orcid.org/0000-0002-0736-9199) for each researcher that can be used to streamline workflows such as manuscript and grant submission and to unambiguously identify researchers in databases. PMC https://doi.org/10.1038/nrg3932. Genome Med. A CRISPR prime editing approach corrects all types of G12 and G13 oncogenic KRAS mutations using a universal pegRNA, demonstrating the potential of applying this system to KRAS gene therapy . UMD-MLH1/MSH2/MSH6 databases: description and analysis of genetic 22, R27R31 (2013). View 2 excerpts, references background and methods. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). 38, 17671771 (2010). Mol Clin Oncol. Human mutation. The TP53 LSDB paradigm, Significance of TP53 mutations in human cancer: A critical analysis of mutations at CpG dinucleotides, Identification of 23 TGFBR2 and 6 TGFBR1 gene mutations and genotype-phenotype investigations in 457 patients with Marfan syndrome type I and II, Loeys-Dietz syndrome and related disorders, p53 Website and analysis of p53 gene mutations in human cancer: Forging a link between epidemiology and carcinogenesis, Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases, UMD-DYSF, a novel locus specific database for the compilation and interactive analysis of mutations in the dysferlin gene, The molecular genetics of Marfan syndrome and related disorders, Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase, The molecular genetics of Marfan syndrome and related microfibrillopathies, Identification of the minimal combination of clinical features in probands for efficient mutation detection in the FBN1 gene, Prognosis Factors in Probands With an FBN1 Mutation Diagnosed Before the Age of 1 Year, Planning the human variome project: the Spain report, Functional implications of the p.Cys680Arg mutation in the MLH1 mismatch repair protein, Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: proposed guidelines for improving data collection, distribution, and integration, Human Splicing Finder: an online bioinformatics tool to predict splicing signals, Severe Marfan syndrome due to FBN1 exon deletions. Schaefer, C. & RPGEH GO Project Collaboration. Analysis of publicly available LDLR, APOB, and PCSK9 variants - Nature Ruiz-Pesini, E. et al. 12, 417428 (2011). Nucleic Acids Res. Med. Mol. Kohane, I. S. Using electronic health records to drive discovery in disease genomics. Mutat. Niels Wind, Mef Nilbert, Christina Therkildsen, American Journal of Medical Genetics Part A, Current Opinion in Genetics & Development, Journal of Occupational Medicine and Toxicology, Locus-specific mutation databases: pitfalls and good practice based on the p53 experience. The consequential shift in focus from single-gene variants towards large gene panels, exomes, whole genomes and myriad observable characteristics creates new challenges and opportunities in database design, interpretation of variant pathogenicity and modes of data representation and use. The variant call format and VCFtools. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Currently, the volume and the quality of phenotype data compared with genotype data held in genotypephenotype databases is lower, possibly owing to practical, financial, ethical, legal and organizational challenges that must be overcome to produce good phenotypic data on large numbers of individuals. The UMD-LDLR database: additions to the software and 490 new entries to the database. 24, 356364 (2014). Hum. PLoS Genet. DECIPHER has a large suite of tools to facilitate the interpretation of candidate variants. Hum. Eur. Characterizing race/ethnicity and genetic ancestry for 100,000 subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. Int. Nat. 33, 13451351 (2012). sharing sensitive information, make sure youre on a federal The study provided a strong case for uniformity of data to make the content maximally useful and derived a community structure that would enhance the chances of mutation capture rather than being left unpublished in a patient's report. With the completion of the Human Genome Project, our vision of human genetic diseases has changed. Hum Mutat. Nucleic Acids Res. Mutat. UMD: UNIVERSAL MUTATION DATABASE 87 sis is rather difficult due to the size of the target gene. Yagi H, Takiguchi H, Takeda N, Inuzuka R, Taniguchi Y, Porto KJ, Ishiura H, Mitsui J, Morita H, Komuro I. Clin Case Rep. 2022 Feb 9;10(2):e05335. PubMed 84, 524533 (2009). J Transl Med. Nature Reviews Genetics The .gov means its official. Ploski, R. et al. Hum. UMD (Universal Mutation Database): 2005 update - Semantic Scholar 33, 803808 (2012). Recent developments of the UMDp53 database are described, which include new fields and routines that will help users not only for molecular epidemiology and pharmacogenetic studies but also for patientbased studies. Clipboard, Search History, and several other advanced features are temporarily unavailable. In biomedicine, especially high-throughput omics data such as whole-genome sequencing, as well as ever increasing amounts of clinical data available in electronic health care records, are often regarded as big data. Ten novel FBN2 mutations in congenital contractural arachnodactyly: delineation of the molecular pathogenesis and clinical phenotype. Pharmacol. Hoang CQ, Duong HQ, Nguyen NT, Nguyen SAH, Nguyen C, Nguyen BD, Phung LT, Nguyen DT, Pham CTM, Le Doan T, Tran MH. J. Hum. Hum. It was developed as a generic software to create locus-specific databases (LSDBs) with the 4th Dimension package from 4D. Hu L, Li H, Sun G, Wu K, Luan Z, Xiang Y, Tang S. Mol Genet Genomic Med. The degree of clinical expression and severity of a disease in individuals who have inherited a given germline variation. Before Clipboard, Search History, and several other advanced features are temporarily unavailable. A generic software called UMD (Universal Mutation Database), developed as a generic software to create locusspecific databases (LSDBs) with the 4th Dimension package from ACI, has been successfully adapted to nine genes either involved in cancer or in genetic diseases. 14 October 2022, Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz EMBO J. eCollection 2022 Feb. Qiu J, Lou Y, Zhu Y, Wang M, Peng H, Hao Y, Jiang H, Mao Y.
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