What is ClinVar? A database for variant interpretation! [Today's paper]
- 1. Today’s paper D1062–D1067 Nucleic Acids Research, 2018, Vol. 46, Database issue Published online 20 November 2017 doi: 10.1093/nar/gkx1153 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, Chunlei Liu, Zenith Maddipatla, Adriana Malheiro, Kurt McDaniel, Michael Ovetsky, George Riley, George Zhou, J. Bradley Holmes, Brandi L. Kattman and Donna R. Maglott National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Received September 26, 2017; Revised October 27, 2017; Editorial Decision October 28, 2017; Accepted November 17, 2017 ABSTRACT ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic vari- ants and interpretations of their significance to dis- ease, maintained at the National Institutes of Health. cance of a variant or set of variants are submitted to Clin- Var by clinical testing laboratories, research laboratories, locus-specific databases, expert panels and other groups. Submissions include a description of the variant(s); the con- dition for which the variant was interpreted; the interpre- tation of the clinical significance of the variant, with the Downloadedfromhttps://academic.oup.com doi: 10.1093/nar/gkx1153
- 3. Backgrounds > 800,000 variation records
- 4. Data structure VCV (Variation in ClinVar) : variant information RCV (Reference ClinVar) : variant-condition information SCV (Submitted record ClinVar) : variant-condition-submission information Accession IDs
- 5. Data structure VCV000422345 RCV001089682 RCV000507978 RCV000485626 SCV001245166 SCV001245166 SCV000571792 SCV000571792 `
- 6. Provided data: XML ClinVarVariationRelease : VCV-centric data of ClinVar ClinVarFullRelease : RCV-centric data of ClinVar * example XML file
- 7. Provided data: VCF * example VCF file • Clinical significance • Allele frequency data • Allele identifier • HGVS expression • variant in other databases • types of variation • molecular consequences • Allele origin
- 8. Phenotype-rich submissions Variant-disease information Patient-associated phenotypes with interpretations ‘Provider interpretation’ Collection method Clinical providers Patient registries Patient-associated phenotypes ‘Phenotypes only’
- 9. Searching ClinVar • Gene symbols • HGVS expressions • Protein changes • rs numbers • Diseases • Clinical features/phenotypes • Submitters • A location on a chromosome • The date that the clinical significance was last evaluated • HGNC ID or Gene ID • HPO ID Filters applicable to variants • Clinical significance • Review status • Allele origin • Method type • Molecular consequences • Variation type • Variant length • Variant-gene relationship
- 10. Summary
- 11. 1. ClinVar is a publicly available archive for sharing variant interpretation and supporting evidences. 2. ClinVar aggregates data by variant-disease pairs and by variants. 3. ClinVar data can be accessed through the website and downloaded in XML or VCF formats. 4. Submission with detailed phenotypic information of patients may be included. 5. Search function at the ClinVar website have been improved. Summary
- 12. Thanks for watching! Made by Heonjong Han Email: hhj6212@gmail.com