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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.  ...  useful for the clinical genetics community.  ... 
doi:10.1093/nar/gkv1222 pmid:26582918 pmcid:PMC4702865 fatcat:x4b6xdfj65ebtnpinz3m2mcm6u

ClinVar data parsing

Xiaolei Zhang, Eric V. Minikel, Anne H. O'Donnell-Luria, Daniel G. MacArthur, James S. Ware, Ben Weisburd
2017 Wellcome Open Research  
.: Using high-resolution variant frequencies to empower clinical genome interpretation. Genet Med. 2017. PubMed Abstract | Publisher Full Text  ...  Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants.  ...  Software availability The pipeline, its fully parsed data files and example data files are available: https://github.com/macarthur-lab/clinvar Archived source code as at the time of publication: https:  ... 
doi:10.12688/wellcomeopenres.11640.1 pmid:28630944 pmcid:PMC5473414 fatcat:ahkz2duzebdtnoeaksockxplc4

ClinVar: improvements to accessing data

2019 Nucleic Acids Research  
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  ...  Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools  ...  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

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  
ClinVar provides a universal platform for users who intend to share the classification variants, resulting in the improved concordance of variant interpretation.  ...  Most of the reclassifications were of variants with a low rank, an older classification, a higher allele frequency, or which were collected through methods other than clinical testing.  ...  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

Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts

Robert R. Butler III, Pablo V. Gejman
2018 F1000Research  
While ClinVar has become an indispensable resource for clinical variant interpretation, its sophisticated structure provides it with a daunting learning curve.  ...  of the evidence supporting the variant clinical significance.  ...  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

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  
Methods-ClinVar variants with submissions from at least two of the four participating laboratories were compared.  ...  identify the basis of interpretation differences and to investigate if data sharing and reassessment resolves interpretation differences by analyzing a subset of variants.  ...  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

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  
Motivation: Despite significant efforts in expert curation, clinical relevance about most of the 154 million dbSNP reference variants (RS) remains unknown.  ...  variants curated in ClinVar.  ...  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

Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach

Steven M. Harrison, Jill S. Dolinksy, Wenjie Chen, Christin D. Collins, Soma Das, Joshua L. Deignan, Kathryn B. Garber, John Garcia, Olga Jarinova, Amy E. Knight Johnson, Juha W. Koskenvuo, Hane Lee (+14 others)
2018 Human Mutation  
Outliers were identified by first comparing ClinVar submissions from 41 clinical laboratories to detect variants with medically significant differences between the laboratories (650 variants).  ...  Next, medically significant differences were filtered for variants with ≥3 classifications (244 variants), of which 87.6% (213 variants) had a majority consensus in ClinVar, thus allowing for identification  ...  Acknowledgments Research reported in this publication was supported in part by the National Human Genome Research Institute (NHGRI) under award U41HG006834.  ... 
doi:10.1002/humu.23643 pmid:30311378 pmcid:PMC6188667 fatcat:ihljhckrl5g3datno34pnwu5yu

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  ...  Databases provide conflicting results for the purpose of identifying pathogenic variants in SF associated with IPAS at a level of sufficient evidence for clinical return.  ...  public archive of interpretations of clinically relevant variants (ClinVar), Leiden Open-source Variant Database (LOVD), or by Medical Genetics Center (MGZ)-curators were listed DIEBOLD ET AL. | 1027 benign  ... 
doi:10.1002/humu.23996 pmid:32048431 fatcat:6kurx7l4rbdepl7a35ih7sahke

Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup

CL Overby, B Heale, S Aronson, JM Cherry, S Dwight, A Milosavljevic, T Nelson, A Niehaus, MA Weaver, EM Ramos, MS Williams
2015 Clinical Pharmacology and Therapeutics  
Acknowledgments The ClinGen Consortium is funded by The National Human Genome Research Institute (NHGRI), in conjunction with additional funding from The Eunice Kennedy Shriver National Institute of Child  ...  ClinVar archives assertions of clinical significance for variants related to specific conditions, and thus, relies on voluntary submissions from clinical testing labs, researchers, locus-specific databases  ...  clinically relevant variants" (www.clinicalgenome.org) [1] .  ... 
doi:10.1002/cpt.270 pmid:26418054 pmcid:PMC4724305 fatcat:bjy2m7rrcjecnnoyauuehpv5xi

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  
Five years later, during a routine clinic visit of one of the genotype-positive family members, the cardiologist queries a database for current knowledge on the genetic variant and discovers that the variant  ...  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.  ...  The first is ClinVar, which is a database at the National Center for Biotechnology Information that archives information submitted about variants with medical relevance.  ... 
doi:10.1056/nejmsr1406261 pmid:26014595 pmcid:PMC4474187 fatcat:sc5t4l5csnfodfpzmpfinr6zai

Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML

Henrik Banck, Martin Dugas, Carsten MÜller-Tidow, Sarah Sandmann
2021 Cancer Genomics & Proteomics  
Public databases provide decision support for interpreting variants but there is still need for manual curation.  ...  We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia. Clinical implications were found for 13% of all variants.  ...  We are also grateful to Albina Caetano da Silva and Nicolette Banck for moral support and proof-reading of the article.  ... 
doi:10.21873/cgp.20250 pmid:33608312 pmcid:PMC7943210 fatcat:iofshvy3anheveotehixitehxa

Genetic variant interpretation: a primer for clinicians

Varun Kaushik, John‐Paul Plazzer, Ingrid Winship, Finlay Macrae
2021 Internal medicine journal (Print)  
Understanding these advances in genetic variant interpretation may allow practising clinicians to develop a more nuanced appreciation of the role genetic variant interpretation can play in the diagnosis  ...  In this article, we consider genetic variant interpretation with reference to efforts to better understand variation in the mismatch repair genes and their relation to Lynch syndrome - the most common  ...  The keystone database for ClinGen is ClinVar, a free public archive of variants and corresponding interpretations.  ... 
doi:10.1111/imj.15485 pmid:34541770 fatcat:ufocrxckqvan5ogtp22646nrbu

DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES

SHAN YANG, MELISSA CLINE, CAN ZHANG, BENEDICT PATEN, STEPHEN E. LINCOLN
2016 Biocomputing 2017  
Open sharing of clinical genetic data promises to both monitor and eventually improve the reproducibility of variant interpretation among clinical testing laboratories.  ...  A significant public data resource has been developed by the NIH ClinVar initiative, which includes submissions from hundreds of laboratories and clinics worldwide.  ...  Recently, the National Institutes of Health established ClinVar, "a freely available archive for interpretations of clinical significance of variants for reported conditions" [Landrum 2016 ].  ... 
doi:10.1142/9789813207813_0017 pmid:27896972 pmcid:PMC5340191 fatcat:3pmowpgrtvgmfpjtgszqghzesu

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.  ...  This work demonstrates that secondary analysis of longitudinal data collected as part of NBS finds unreported genetic variants and the accompanying clinical information can inform the relationship between  ...  ACKNOWLEDGMENTS The following individuals were members of the IBEMC:  ... 
doi:10.3389/fgene.2022.859837 pmid:35692825 pmcid:PMC9178101 fatcat:fguv76qxebb35n7pac2kbqzsp4
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