Next Wednesday, November 14, 2018, NCBI staff will show you how to use NCBI’s genome browsers and other resources to interpret variants. The graphical displays of Genome Data Viewer (GDV) and Variation Viewer offer an interactive experience that allows you to explore NCBI’s rich collection of annotations, datasets and literature for deciphering your variant-associated data. In this presentation, we’ll step through case studies and show you how to quickly display relevant NCBI track sets — including the new RefSeq Functional Elements track, upload a file or remotely-hosted dataset and display these as a track, and use browser tracks to identify known variants, then assess variant functional and clinical significance and allele frequency. You will also learn how to navigate from the browsers to NCBI resources such as ClinVar, dbSNP and PubMed, for additional variant information.
Date and time: Wed, Nov 14, 2018 12:00 PM – 12:45 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
The new services are faster, better at handling variants in repeat regions, and scalable to accommodate the continued explosive growth of variation volume. You can find more information about the services in the initial blog post and online SPDI document.
If you would like to report any issues related to these new services and/or would like to provide comments, please write to firstname.lastname@example.org.
The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.
ClinVar, NCBI’s database of clinically relevant genetic variations with supporting evidence, has redesigned its variation display, and welcomes your feedback. The new Variation in ClinVar (VCV) pages provide a better-organized, more-intuitive web display that makes it easy to quickly find the information you need.
In this blog post, we’ll take you through the new design using the example of a coding region variant (VCV000256160.1) in the ABCB4 gene.
The redesign brings the most important information to the top of the display. There are two new fields: (1) the VCV accession number and version used to cite the record, and (2) a short description of the variation (e.g., 11.3 kb deletion, or haplotype) to make it easy to quickly see what type of variation the record represents.
Starting in March 2018, SNP variation features will no longer be in RefSeq genome assembly records – chromosome and contig records with NC_, NT_, NW_ and AC_ accession prefixes. This change affects both the ASN.1 and flatfile records. Because the number of variants is already enormous and still growing, removing SNP features from these large genomic records will significantly reduce the size of RefSeq FTP files and make downloading and processing easier. We will continue to include SNPs on NG_-prefixed genomic records, and transcript (NM_, NR_, XM_, XR_) and protein (NP_, XP_, YP_) sequences.
NCBI dbSNP is pleased to announce a newly designed Reference SNP (RefSNP, rs) Report webpage to provide enhanced performance and presentation for access to individual RefSNP records. This Alpha version of the report enables browsing of submitted and computed RefSNP variant data from the redesigned dbSNP build system.
Figure 1. The dbSNP RefSNP Report Alpha for rs268.
ClinVar, NCBI’s archive of submitted associations between alleles in the human genome and diseases or phenotypes, is now producing XML files that aggregate all submitted disease/phenotype information by variant (or set of variants) for public release via FTP bulk download. The new product, called ClinVarVariationRelease, is currently in beta release and will move to full release in early September 2017.
NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.