ClinVar: improvements to accessing data

By M. Landrum, Shanmuga Chitipiralla, Garth R. Brown, Chao Chen, Baoshan Gu, Jennifer Hart, Douglas Hoffman, W. Jang, Kuljeet Kaur, Chunlei Liu and 12 more. 2019

810 citations recorded by the source corpus.

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 such as NCBI's E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. 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's search engine has been fine-tuned for improved retrieval of search results.

Subfields: Cancer Research, Genetics

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. David Haussler
2. Kate R. Rosenbloom
3. Mark Diekhans

In Genetics

1. David Haussler
2. Mark Diekhans
3. Robert M. Kuhn

Citations in the corpus

• The next-generation Open Targets Platform: reimagined, redesigned, rebuilt (2022, methodology): “In collaboration with the European Variation Archive, we have also included complex structural variants in Clin-Var such as insertions, deletions, and small tandem repeats, aiming to cover a broader range of disease-causing mechanisms (27).”
• The Reactome Pathway Knowledgebase 2024 (2023, background): “Catalogs like ClinVar ( 14 ) and COSMIC ( 15 ) classify variants by their likely effects on protein structure and function, association with known disease phenotypes, and evidence quality.”
• Genenames.org: the HGNC and VGNC resources in 2021 (2020, background): “HGNC nomenclature data is displayed by many external resources including NCBI Gene (7), Ensembl (8), UniProt (9), GeneCards (10), RNAcentral (11) and the UCSC genome browser (12), as well as resources focused on human disease and phenotypes such as Decipher (13), OMIM (14), ClinGen (15), ClinVar (16”
• miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions (2021, methodology): “Tate,J.G., Bamford,S., Jubb,H.C., Sondka,Z., Beare,D.M., Bindal,N., Boutselakis,H., Cole,C.G., Creatore,C., Dawson,E. et al. (2019) COSMIC: the Catalogue Of Somatic Mutations In Cancer.”
• The UCSC Genome Browser database: 2021 update (2020, background): “An example of collapsed track items is showcased in Figure 4 with the ClinVar CNVs track for hg38.”