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.
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.
Reminder: As of September 2017, NCBI has stopped accepting submissions for non-human SNPs in dbSNP and dbVar. RefSeq flatfiles will stop presenting non-human variant data in November 2017.
Subscribe to the refseq-announce listserv for regular updates on RefSeq.
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.
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.
This blog post is directed toward people who use dbSNP and dbVar, particularly those who submit non-human data to the two databases.
dbSNP and dbVar archive, process, display and report information related to germline and somatic variations from multiple species. These two databases have grown rapidly as sequencing and other discovery technologies have evolved, and now contain nearly two billion variants from over 360 species.
Based on projected growth and the resources required to archive and distribute the data, continued support for all organisms will become unsustainable for NCBI in the near future. Therefore, NCBI will phase out support for all non-human organisms in dbSNP and dbVar, and will support only human variation.
This blog post is intended for geneticists and dataflow engineers who need to compare genetic variants.
Have you ever tried to determine if two genetic variants are the same? If so, you’re not alone. There are competing ways to represent variants, handling ambiguous assignments, as well as reconciling updates to underlying sequence models. To help you with these problems, we’re introducing a new set of web services for comparing and grouping variants.