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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 continues to make improvements to its search and retrieval functions.  ...  Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report.  ...  ACKNOWLEDGEMENTS We thank our partners in the ClinGen group, most notably Heidi Rehm, Christa Martin, Steven Harrison, Erin Riggs and Danielle Azzariti, for their continued feedback and guidance to make  ... 
doi:10.1093/nar/gkx1153 pmid:29165669 pmcid:PMC5753237 fatcat:ngbthvyavvejjdkin52xwrjmua

ClinVar: improvements to accessing data

2019 Nucleic Acids Research  
The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file.  ...  ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH  ...  ACKNOWLEDGEMENTS The authors thank the ClinVar users who have participated in user experience interviews. We welcome feedback from the community.  ... 
doi:10.1093/nar/gkz972 pmid:31777943 pmcid:PMC6943040 fatcat:iwsisqgnovh3lc4c5z22v3l3oi

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  
Interpretations are aggregated by variantcondition combination and assigned an accession number prefixed with RCV.  ...  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.  ...  ACKNOWLEDGEMENTS We thank our partners in the ClinGen group, most notably Heidi Rehm, Christa Martin, Steven Harrison, Erin Riggs and Danielle Metterville, for their continued feedback and guidance to  ... 
doi:10.1093/nar/gkv1222 pmid:26582918 pmcid:PMC4702865 fatcat:x4b6xdfj65ebtnpinz3m2mcm6u

Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database

2019 Nucleic Acids Research  
Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists.  ...  Here, we present Simple ClinVar (http://simple-clinvar.broadinstitute.org/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar  ...  ACKNOWLEDGEMENTS We thank the researchers and clinicians involved in the generation of clinical data contained in ClinVar.  ... 
doi:10.1093/nar/gkz411 pmid:31114901 pmcid:PMC6602488 fatcat:lsac4eplingtvnqvkle2isnr4q

ClinVar database of global familial hypercholesterolemia-associated DNA variants

Michael A. Iacocca, Joana R. Chora, Alain Carrié, Tomáš Freiberger, Sarah E. Leigh, Joep C. Defesche, C. Lisa Kurtz, Marina T. DiStefano, Raul D. Santos, Steve E. Humphries, Pedro Mata, Cinthia E. Jannes (+11 others)
2018 Human Mutation  
Collaborating to provide thorough, reliable evidence-based variant interpretation will ultimately improve the care of FH patients.  ...  To further reform interpretation of FH-associated variants, areas for improvement in variant submissions were identified and addressed; these include a need for more detailed submissions and submission  ...  TF was supported by the Ministry of Health of the Czech Republic, Grants nr. 16-29084A and 15-28277A (all rights reserved).  ... 
doi:10.1002/humu.23634 pmid:30311388 pmcid:PMC6206854 fatcat:voevcng4sjepzmqpbkqy4c2v4i

Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts

Robert R. Butler III, Pablo V. Gejman
2018 F1000Research  
of the evidence supporting the variant clinical significance.  ...  With the rapidly growing body of variant evidence, most submitters and researchers have limited resources to devote to variant curation.  ...  We would also like to thank Mr. Alex Henrie, Ms. Sarah Hemphill, Dr. Karen Eilbeck and Dr. Heidi Rehm for advanced access to their upcoming publication on the ClinVar Miner software and web utility.  ... 
doi:10.12688/f1000research.14470.1 pmid:29862020 pmcid:PMC5941247 fatcat:63wndzm6dfasddokzuv3s6pexa

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 accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation.  ...  accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations.  ...  , interpretation of functional and clinical significance, methodology used to capture variant calls and supporting evidence.  ... 
doi:10.1093/nar/gkt1113 pmid:24234437 pmcid:PMC3965032 fatcat:ons2vfjgnfdr3hjadgnu6rki7a

Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts

Robert R. Butler III, Pablo V. Gejman
2018 F1000Research  
of the evidence supporting the variant clinical significance.  ...  With the rapidly growing body of variant evidence, most submitters and researchers have limited resources to devote to variant curation.  ...  We would also like to thank Mr. Alex Henrie, Ms. Sarah Hemphill, Dr. Karen Eilbeck and Dr. Heidi Rehm for advanced access to their upcoming publication on the ClinVar Miner software and web utility.  ... 
doi:10.12688/f1000research.14470.2 fatcat:vtjkbqifxnemjfxslhhynxdjiq

Reinterpretation of common pathogenic variants in ClinVar revealed a high proportion of downgrades

Jiale Xiang, Jiyun Yang, Lisha Chen, Qiang Chen, Haiyan Yang, Chengcheng Sun, Qing Zhou, Zhiyu Peng
2020 Scientific Reports  
This study aimed to interpret and reclassify common pathogenic (P) and likely pathogenic (LP) variants in ClinVar and to identify indicators linked with reclassification.  ...  ClinVar provides a universal platform for users who intend to share the classification variants, resulting in the improved concordance of variant interpretation.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1038/s41598-019-57335-5 pmid:31942019 pmcid:PMC6962394 fatcat:dxvdhc7as5b2bnzdg5uzf45bcy

Sources of discordance among germ-line variant classifications in ClinVar

Shan Yang, Stephen E Lincoln, Yuya Kobayashi, Keith Nykamp, Robert L Nussbaum, Scott Topper
2017 Genetics in Medicine  
Ongoing improvements to ClinVar may make it easier to use, particularly for nonexpert users.  ...  ClinVar can be a reliable resource supporting variant interpretation, quality assessment, and clinical practice when factors uncovered in this study are taken into account.  ...  ACKNOWLEDGMENTS We are deeply grateful to the laboratories and other groups who are working to advance medical care by submitting data to the ClinVar database.  ... 
doi:10.1038/gim.2017.60 pmid:28569743 pmcid:PMC5632819 fatcat:ubzwwe4s25fjhak5ytp2s7orhi

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar

Steven M. Harrison, Jill S. Dolinsky, Amy E. Knight Johnson, Tina Pesaran, Danielle R. Azzariti, Sherri Bale, Elizabeth C. Chao, Soma Das, Lisa Vincent, Heidi L. Rehm
2017 Genetics in Medicine  
identify the basis of interpretation differences and to investigate if data sharing and reassessment resolves interpretation differences by analyzing a subset of variants.  ...  Purpose-Data sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories.  ...  We thank all ClinVar submitters for sharing their data and Jim Carver and Jessica Burgess for creating the figures.  ... 
doi:10.1038/gim.2017.14 pmid:28301460 pmcid:PMC5600649 fatcat:mhjrpwp7evhurhkikw7ct4tg44

Variability in gene-based knowledge impacts variant classification: an analysis of FBN1 missense variants in ClinVar

Linnea M. Baudhuin, Michelle L. Kluge, Katrina E. Kotzer, Susan A. Lagerstedt
2019 European Journal of Human Genetics  
In order to assess variability in classification of FBN1 variants, 674 FBN1 missense variants from 18 ClinVar submitters were compared and reanalyzed using FBN1-specific criteria and ACMG/AMP 2015 guidelines  ...  Non-cysteine critical residue variants were less likely to be classified as (L)P [55.3% (78/141)] than cysteine variants [91.3% (283/310)] and were more likely to lack evidence citing the functional significance  ...  as ClinVar, an NIH open-access database of clinically observed variants and their classifications.  ... 
doi:10.1038/s41431-019-0440-3 pmid:31227806 pmcid:PMC6777626 fatcat:a6ayra4qjvaqjk7rgy3esqekqe

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar

M L Famiglietti, A Estreicher, L Breuza, S Poux, N Redaschi, I Xenarios, A Bridge
2019 Database: The Journal of Biological Databases and Curation  
We show that existing interpretations of variant pathogenicity in UniProtKB/Swiss-Prot and ClinVar are highly concordant, with 88% of variants that are common to the two resources having interpretations  ...  We have now incorporated ACMG guidelines and ClinGen tools into the UniProt Knowledgebase (UniProtKB) curation workflow and routinely submit variant data from UniProtKB/Swiss-Prot to ClinVar.  ...  Acknowledgements We are grateful to the development team of the ClinGen pathogenicity calculator for generating the files for submission to ClinVar. Conflict of interest. None declared.  ... 
doi:10.1093/database/baz040 pmid:30937429 pmcid:PMC6444058 fatcat:oel3w3qdszeuxc3b5ldpwfxrbe

Points to consider for sharing variant-level information from clinical genetic testing with ClinVar

Danielle R. Azzariti, Erin Rooney Riggs, Annie Niehaus, Laura Lyman Rodriguez, Erin M. Ramos, Brandi Kattman, Melissa J. Landrum, Christa L. Martin, Heidi L. Rehm
2018 Molecular Case Studies  
We propose specific data elements from interpreted genomic variants that are appropriate for submission to ClinVar when direct patient consent was not sought and describe situations in which obtaining  ...  ClinGen has collaborated with ClinVar and the National Human Genome Research Institute to develop points to consider for clinical laboratories on sharing de-identified variant-level data in light of both  ...  Acknowledgments We thank the many ClinVar submitters for sharing their data as well as Elyse Galloway and Kate Saylor, formerly of the NHGRI Division of Policy, Communications, and Education.  ... 
doi:10.1101/mcs.a002345 pmid:29437798 pmcid:PMC5793773 fatcat:4pewasfjmzbs3cec3y2g7l7sea

In-silico Analysis of NF1 Missense Variants in ClinVar: Translating Variant Predictions into Variant Interpretation and Classification

Accetturo, Bartolomeo, Stella
2020 International Journal of Molecular Sciences  
Methods: Here, we analyzed three different computational methods, VEST3, REVEL and ClinPred, and after extracting predictions scores for 1585 NF1 missense variants listed in ClinVar, evaluated their performances  ...  With the advent of next-generation sequencing in genetic testing, predicting the pathogenicity of missense variants represents a major challenge potentially leading to misdiagnoses in the clinical setting  ...  Conclusions The focus of our study was to improve NF1 missense variants interpretation and classification, considering that 66.2% (1045/1579) of missense variants listed at ClinVar were reported by single  ... 
doi:10.3390/ijms21030721 pmid:31979111 pmcid:PMC7037781 fatcat:5nwqyygxzrgg5ohwydjc3fhieq
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