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ClinVar: public archive of relationships among sequence variation and human phenotype

Melissa J. Landrum, Jennifer M. Lee, George R. Riley, Wonhee Jang, Wendy S. Rubinstein, Deanna M. Church, Donna R. Maglott
2013 Nucleic Acids Research  
ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) provides a freely available archive of reports of relationships among medically important variants and phenotypes.  ...  ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation.  ...  Variation Variation is a key component of ClinVar's data model, especially to be able to represent the relationship of variation to phenotype.  ... 
doi:10.1093/nar/gkt1113 pmid:24234437 pmcid:PMC3965032 fatcat:ons2vfjgnfdr3hjadgnu6rki7a

ClinVar: improving access to variant interpretations and supporting evidence

Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Karen Karapetyan, Kenneth Katz (+10 others)
2017 Nucleic Acids Research  
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes  ...  ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants).  ...  ClinVar useful for the clinical genetics community.  ... 
doi:10.1093/nar/gkx1153 pmid:29165669 pmcid:PMC5753237 fatcat:ngbthvyavvejjdkin52xwrjmua

ClinVar: public archive of interpretations of clinically relevant variants

Melissa J. Landrum, Jennifer M. Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover, Wonhee Jang, Kenneth Katz (+7 others)
2015 Nucleic Acids Research  
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported  ...  Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.  ...  make ClinVar useful for the clinical genetics community.  ... 
doi:10.1093/nar/gkv1222 pmid:26582918 pmcid:PMC4702865 fatcat:x4b6xdfj65ebtnpinz3m2mcm6u

tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine

Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu, Jonathan Wren
2017 Bioinformatics  
variants curated in ClinVar.  ...  Our method, in benchmarking results, demonstrates a high F-measure of 90% and compared favorably to the state of the art.  ...  Funding This work was supported by the National Institutes of Health intramural research program, National Library of Medicine. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btx541 pmid:28968638 pmcid:PMC5860583 fatcat:ym74zidyt5dyvefjsrpusno57q

Databases of genomic variation and phenotypes: existing resources and future needs

J. J. Johnston, L. G. Biesecker
2013 Human Molecular Genetics  
The purpose of this review is to summarize the state of the art of variation and genotype -phenotype databases, how they can be used, and opportunities to improve these resources.  ...  Accurate variation and genotype -phenotype databases are critical in our ability to make sense of the vast amount of information that MPS generates.  ...  ACKNOWLEDGEMENT The authors thank Michael Bamshad, Lisa Brooks, David Cooper, Ada Hamosh, Melissa Landrum, Donna Maglott, David Ng, Roberta Pagon and Larry Singh for thoughtful comments on this review.  ... 
doi:10.1093/hmg/ddt384 pmid:23962721 pmcid:PMC3782073 fatcat:ieu6foaplvblvojafhb7zuksvu

circVAR database: genome-wide archive of genetic variants for human circular RNAs

Min Zhao, Hong Qu
2020 BMC Genomics  
Genetic variation of circRNAs may affect complex traits/diseases by changing their binding efficiency to target miRNAs and proteins.  ...  We found that, based on mapping to the 1000 Genomes and ClinVAR databases, chromosome 17 has a relatively large number of circRNAs and associated common and health-related genetic variants.  ...  Richard Burns for review and comments on this manuscript.  ... 
doi:10.1186/s12864-020-07172-y pmid:33121433 fatcat:r7jhttealrhbnbe3455755uqqe

Available resources and challenges for the clinical annotation of somatic variations

Catherine I. Dumur
2014 Cancer Cytopathology  
Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology.  ...  The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology.  ...  ClinVar ClinVar (http://www.ncbi.nlm.nih.gov/clinvar) 10 was launched in 2012, with the first public release in April 2013, and is a freely accessible public archive for reports of the relationship of  ... 
doi:10.1002/cncy.21471 pmid:25111663 pmcid:PMC4231254 fatcat:6urfq3ycznfapgm5xcsikestzi

ClinGen — The Clinical Genome Resource

Heidi L. Rehm, Jonathan S. Berg, Lisa D. Brooks, Carlos D. Bustamante, James P. Evans, Melissa J. Landrum, David H. Ledbetter, Donna R. Maglott, Christa Lese Martin, Robert L. Nussbaum, Sharon E. Plon, Erin M. Ramos (+2 others)
2015 New England Journal of Medicine  
The patient's family pursues genetic testing that shows a "likely pathogenic" variant for the condition on the basis of a study in an original research publication.  ...  An immediate clinical workup detects evidence of cardiomyopathy, and an intracardiac defibrillator is implanted to reduce the risk of sudden cardiac death.  ...  and interpretation of genomic and phenotypic variation.  ... 
doi:10.1056/nejmsr1406261 pmid:26014595 pmcid:PMC4474187 fatcat:sc5t4l5csnfodfpzmpfinr6zai

Critical assessment of secondary findings in genes linked to primary arrhythmia syndromes

Isabel Diebold, Ulrike Schön, Florentine Scharf, Anna Benet‐Pages, Andreas Laner, Elke Holinski‐Feder, Angela Abicht
2020 Human Mutation  
Comparison of the databases ClinVar, LOVD and HGMD showed impactful differences (0.2% to 1.3%) in variant interpretation improvable by expert-curation depending on database and classification system used  ...  Since IPAS account for a significant proportion of sudden cardiac deaths (SCD) in young and apparently healthy individuals, variant interpretation has great impact on diagnosis and prevention of disease  ...  ClinVar is a freely accessible, public archive of reports of the relationship among human variations and phenotypes, with supporting evidence (Landrum et al., 2016) .  ... 
doi:10.1002/humu.23996 pmid:32048431 fatcat:6kurx7l4rbdepl7a35ih7sahke

Pleiotropic Phenotypes Associated With PKP2 Variants

Valeria Novelli, Kabir Malkani, Marina Cerrone
2018 Frontiers in Cardiovascular Medicine  
In this review, we will provide a summary of all the currently available genetic information related to the Pkp2 gene, including different phenotypes, ClinVar annotations and data from large control database  ...  However, the assessment of pathogenicity regarding the genetic variations associated with Pkp2 is still a challenging task: the gene has a positive Residual Variation Intolerance Score and the potential  ...  The goal of this repositories is to provide information on the expected human variation frequency.  ... 
doi:10.3389/fcvm.2018.00184 pmid:30619891 pmcid:PMC6305316 fatcat:ngp6tlr3cfbz5ivdpnmkruxjae

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+31 others)
2011 Nucleic Acids Research  
Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.  ...  chemicals (Biosystems and the Pub-Chem suite of small molecule databases).  ...  Variation viewer The Variation Viewer (www.ncbi.nlm.nih.gov/variation/ view) displays human variations from dbSNP, dbVar and ClinVar in the context of the current and previous human reference genome assemblies  ... 
doi:10.1093/nar/gkr1184 pmid:22140104 pmcid:PMC3245031 fatcat:zxmwupa435gfzcpusnv7oe3qnm

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2004 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources  ...  for the data in GenBank and other biological data made available through the NCBI Web site.  ...  RECENT DEVELOPMENTS ClinVar ClinVar (www.ncbi.nlm.nih.gov/clinvar/) is a new medical genetics resource that collects assertions of the relationships between human sequence variations and phenotypes (2  ... 
doi:10.1093/nar/gki062 pmid:15608222 pmcid:PMC540016 fatcat:pxy5l62n65d2pmslx3noinamya

Using Long-Term Follow-Up Data to Classify Genetic Variants in Newborn Screened Conditions

Kevin Wilhelm, Mathew J. Edick, Susan A. Berry, Michael Hartnett, Amy Brower
2022 Frontiers in Genetics  
We found 564 genetic variants with accompanying phenotypic data and identified that 161 of the 564 variants (29%) were not included in ClinVar.  ...  genotype and phenotype.  ...  ACKNOWLEDGMENTS The following individuals were members of the IBEMC:  ... 
doi:10.3389/fgene.2022.859837 pmid:35692825 pmcid:PMC9178101 fatcat:fguv76qxebb35n7pac2kbqzsp4

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Lishuang Shen, Maria Angela Diroma, Michael Gonzalez, Daniel Navarro-Gomez, Jeremy Leipzig, Marie T. Lott, Mannis van Oven, Douglas C. Wallace, Colleen Clarke Muraresku, Zarazuela Zolkipli-Cunningham, Patrick F. Chinnery, Marcella Attimonelli (+3 others)
2016 Human Mutation  
diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants.  ...  PhenoTips is used for phenotypic data submission on de-identified patients using human phenotype ontology terminology.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. MSeqDR  ... 
doi:10.1002/humu.22974 pmid:26919060 pmcid:PMC4846568 fatcat:bzp3d5hrffb7hb4dupropvddka

Genomic Information Systems applied to Precision Medicine: Genomic Data Management for Alzheimer's Disease Treatment

Ana León Palacio, Ignacio Pascual Fernández, Oscar Pastor López
2018 Information Systems Development  
With these fundamentals in mind, this paper introduces a particular example to bear the methodological treatment of the search, filter and load of genomic variations related to Alzheimer's Disease for  ...  The study of the genetic characteristics of every patient, makes possible the study of significant DNA variations in order to ease an early diagnosis, essential to stop the progression of the disorder.  ...  Acknowledgements The authors would like to thank the members of the PROS Research Centre Genome group for the fruitful discussions regarding the application of CM in the medicine field.  ... 
dblp:conf/isdevel/PalacioFL18 fatcat:pnl42smlmjgitp2qak62rx4xhq
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