Bioinformatics paper uses NCBI open data to analyze drug response


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.

5 NCBI articles in 2018 Nucleic Acids Research database issue


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.

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ClinVar Unveils New, More Intuitive Variation Display


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.

ClinVar variation page alpha view. Accession number & feedback tab are circled to highlight them.

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.

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NCBI releases newly designed dbSNP RefSNP Report – Alpha version


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.

The new RefSNP report (alpha version). You can see all of the sections described in the blog post, like the summary section and the sidebar menu.

Figure 1. The dbSNP RefSNP Report Alpha for rs268.

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ClinVar Allele-Based Summaries Now Available for FTP Download


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.

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NCBI Facilitates Hackathons at the Bio-IT World Conference and Silicon Valley Artificial Intelligence


NCBI usually participates in hackathons as direct organizers and planners. However, NCBI staff recently functioned as facilitators in two hackathons organized by outside groups: one at the Bio-IT World conference, and one at the Silicon Valley Artificial Intelligence (SVAI) incubator.

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Questions about GTR, ClinVar, or MedGen? Ask us at ASCO 2017!


NCBI will be exhibiting at the ASCO Annual Meeting 2017 from June 2-6.

Exhibit Hall Booth #3046

ASCO attendees can get navigation tips and hands-on help with GTR and ClinVar submissions, take handout materials and meet with Adriana Malheiro, MS* at Booth #3046.

Booth times:

Saturday, June 3 – 9AM–5PM
Sunday, June 4 – 9AM–5PM
Monday, June 5 – 9AM–5PM

*Contact us to schedule a meeting with Adriana Malheiro, MS.

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NCBI’s 3 Newest Medical Genetics Resources: GTR, MedGen & ClinVar


GTR_ClinVar_MedGen imageNCBI has three relatively new online resources for information about genetic tests, genetic conditions, and genetic variations:

  • The Genetic Testing Registry, or GTR – a registry of genetic tests for heritable and somatic changes in humans
  • MedGen – a medical genetics portal that focuses on information about medical conditions with a genetic component
  • ClinVar – an archival database that contains reported assertions about the relationship between genetic variations and phenotypes

This blog will provide a very brief overview of the three resources by outlining some of their content features. For a more thorough introduction to the three resources, including the types of information available in each and how to use them, we recommend viewing this approximately hour-long webinar that we conducted in June 2014.

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