Today's paper is about ClinVar, a widely used database for variant interpretation. Today I covered "ClinVar: improving access to variant interpretations and supporting evidence." published in 2017, Nucleic Acids Research. Thanks for watching! doi: 10.1093/nar/gkx1153

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

2. Backgrounds
Genetic disease
?

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