ClinVar News and Announcements

Data release: Partners Healthcare/Harvard Medical School

Thu, 16 May 2013 08:00:00 EST

We are pleased to announce the release earlier this month of a major data set in ClinVar, namely submissions from Partners Healthcare/Harvard Medical School.

This release includes approximately 7000 interpretations of allele-phenotype relationships for about 40 disorders and 160 genes. More than 6500 alleles are novel to ClinVar.

The data can be retrieved using this URL:

http://www.ncbi.nlm.nih.gov/clinvar?term=%22partners%20healthcare%22[Submitter]

ClinVar XML and VCF Updated May 9, 2013

Tue, 14 May 2013 15:00:00 EST

The ClinVar XML and VCF files were updated on the ClinVar FTP site on 5/9/2013 (ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/) based on a data freeze on May 6, 2013. The current files are ClinVarFullRelease_2013-05.xml.gz accessed at ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ and clinvar_20130506.vcf.gz and clinvar_20130506.vcf.gz.tbi accessed at ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/. The most recent version of the XML and VCF files can be obtained by downloading ClinVarFullRelease_00-latest.xml.gz and clinvar_00-latest.vcf.gz (and .tbi).

At present, the ClinVar XML and VCF files will be updated monthly. We will post to this RSS feed when the data are released.

If you have any questions, please contact clinvar@ncbi.nlm.nih.gov

ClinVar Database Preview

Thu, 15 Nov 2012 07:00:00 EST

The ClinVar Database may be previewed at the "Try our preview site" link available on the ClinVar Homepage: http://www.ncbi.nlm.nih.gov/clinvar/. The preview site allows you to browse the preliminary ClinVar Database release by variant, gene, location, submitter, and other categories. Searchable fields are listed in the "Advanced" Search in the "Fields" dropdown. Before we release ClinVar as a fully-fledged database via the www URL, we will add website access to the evidence for both submission (SCV) and reference (RCV) accessions, and the date the clinical significance was last re-assessed. We welcome feedback and suggestions for improvement.

The link to the preview site is http://preview.ncbi.nlm.nih.gov/clinvar.

If you have any questions about ClinVar, please contact us as clinvar@ncbi.nlm.nih.gov

ClinVar data in VCF and XML formats and special reports

Thu, 15 Nov 2012 06:30:00 EST

ClinVar data are available in three formats:
1. As structured XML(ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml), which contains the detailed representation of each submission (ClinVarAccession), the aggregation of data across from multiple submissions (ReferenceClinVarAccession) , and content such as database identifiers and links added from other NCBI databases. Aggregation includes an explicit report of conflict in interpretations of pathogenicity. The xsd for this XML extraction is ftp.ncbi.nlm.nih.gov/pub/clilnvar/clinvar_public.xsd. ClinVar will make a complete XML extraction of the current database each month, with a cumulative weekly update file.
2. In VCF format, as a range of subsets of variants, such as clinical channel variants, variants with no known pathogenicity, etc. The different files are described in detail at http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/. The VCF files are available at either ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/ or ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/.
3. As reports from NCBI's Variation Reporter tool (http://www.ncbi.nlm.nih.gov/variation/tools/reporter). This tool allows you to submit your variation calls, and determine if any variation you find has a record in ClinVar. The underlying data are refreshed weekly.

Please note the data available for ftp are also in a 'preview' mode. In other words, there will be large-scale updates before the end of 2012 to process data submitted to dbSNP not yet processed in ClinVar, and to act on suggestions from the user community during this ‘preview’ time. The accessions are stable, but we will not start assignments of stable versions or unique identifiers until December. We will post to this feed when versions and uids are stable.

If you have any questions about ClinVar, please contact us as clinvar@ncbi.nlm.nih.gov

A Unified Clinical Genomics Database U41 grant proposal

Thu, 15 Nov 2012 06:00:00 EST

The U41 grant "A Unified Clinical Genomics Database," submitted by David Ledbetter, Christa Lese Martin, Joyce Mitchell, Robert Nussbaum and Heidi Rehm on 07/03/12 to the National Human Genome Research Institute has been posted on 11/14/12 on the ClinVar community documents FTP site and can be viewed at: http://www.ncbi.nlm.nih.gov/clinvar/community/.

ClinVar Community Policy papers and the Rehm-Martin-Nussbaum U41 Grant Proposal

Mon, 19 Dec 2011 12:00:00 EST

The Development and Curation of a Universal Human Genomic Variant Database U41 grant submitted on 09/27/11 to the National Human Genome Research Institute and two policy proposals arising from the ad hoc ClinVar Community Group meetings were posted 12/6/11 on the ClinVar community documents FTP site and can be viewed at: http://www.ncbi.nlm.nih.gov/clinvar/community/.

ASHG Posters and ClinVar Community documents posted on ClinVar website

Mon, 21 Nov 2011 11:00:00 EST

The NCBI ClinVar poster and the ClinVar Community poster presented at the ASHG meeting are available on the ClinVar website on the ClinVar documents FTP site and the ClinVar Community documents pages.