MedGen is a free, comprehensive resource for one-stop access to essential information on phenotypic health topics related to medical genetics as collected from established high-quality sources. It integrates terminology from multiple primary ontologies (or nomenclatures) to facilitate standardization and more accurate results from search queries.
Next week, NCBI staff will be at the NSGC 2018 conference in Atlanta, GA. While there, you can chat in person with us at booth #700 to learn about our medical genetics resources and pick up helpful material. We’d also love to hear any other questions or feedback to help support you.
Next Wednesday, October 10, 2018, NCBI staff will show you how to use the NCBI resources MedGen, ClinVar, and GTR to locate records for a specified list of symptoms or clinical features, explore specific disease-causing variants, see the review status of the clinical significance for a genetic variant, and find tests relevant to a clinical feature, gene or disease. You will also learn which resource works best for different types of searches.
Date and time: Wed, Oct 10, 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 email@example.com.
A study (PMID: 28158543) published in the July 2017 issue of Bioinformatics collects, classifies and analyzes single nucleotide variants (SNVs) that may affect response to currently approved drugs. They identified 2,640 SNVs of interest, most of which occur rarely in populations (minor allele frequency <0.01).
The researchers used protein sequence alignment tools and mined open data from multiple information resources accessed through E-utilities including PubChem Compound (Kim et al., 2016 PMID: 26400175), NCBI Gene (Maglott D, et al., 2014. PMID: 25355515), NCBI Protein (Sayers, 2013), MMDB (Madej et al., 2012 PMID: 22135289), PDB (Berman et al., 2000 PMID: 10592235), dbSNP (Sherry et al., 2001 PMID: 11125122), and ClinVar (Landrum et al., 2016 PMID: 26582918).
Questions, comments, and other feedback may be sent to Yanli Wang.
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.