November 14 Webinar: Variant Interpretation using NCBI Resources


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

Register

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.

 

 

NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials


Would you like to compare and analyze your data with known structural variants (SV) in NCBI’s database of genomic structural variation (dbVar)? Now there are easy-to-use files containing non-redundant (NR) deletions, duplications, and insertions aggregated from across studies in dbVar.  The files are available for human assembly versions GRCh37 and GRCh38.   Descriptions of the NR data are available on GitHub.

The NR files are available for FTP download in BED, BEDPE, and custom tab-separated formats, designed to be compatible with many popular tools and browsers. To help users get started, we have developed tutorials for UCSC Genomic Browser, Galaxy web-based analysis platform, NCBI Sequence Viewer, and command-line BEDtools.

An upcoming release will include annotations including genes, regulatory regions, and more. Have a favorite annotation you’d like to see? Send us your suggestions by contacting dbVar directly or open a GitHub issue. We also welcome comments and other improvement suggestions.

Discover GTR at AMP 2018 (Nov 1-3)


Starting this Thursday, November 1st, NCBI staff from projects like ClinVar, GTR, MedGen, Medical Genetics Summaries and OSIRIS will be ready to hear your feedback at the Association for Molecular Pathology (AMP) 2018 Annual Meeting & Expo in San Antonio, Texas. Come to booth #1810 and tell us how to make our resources better for you or ask questions about how to participate and use these resources!

Staff will also present on their current work at AMP 2018. We will present our analyses of current GTR tests and discuss how GTR data aims to reflect the current genetic testing landscape.

Below is a sneak peek on two different presentations to learn about “The NIH Genetic Testing Registry (GTR): Test Methodologies as a Sensor of the Precision Medicine Environment”:

  • Poster TT046 – Friday, November 2 from 2:30 – 3:30 PM
  • Technical Topics Platform Presentation – Saturday, November 3 from 7:45 – 8:00 AM

Continue reading

Improved search for eukaryotic and viral proteins and gene names


NCBI previously announced improved search functionality to provide users with better results for common language queries. We have expanded this search capability beyond queries for species-qualified gene symbols (e.g. human GhrI) to support species-qualified protein names (e.g. human obestatin) and gene names (e.g. human ghrelin and obestatin prepropeptide) in eukaryotes and viruses. Whether you are searching for a gene, transcript, or protein, our updated featured results panel displays the relevant information. The results panel for the selected gene includes quick links to many resources including transcripts, protein products, and publications.
Search results for peptide hormone 'rat obestatin' in NCBI's All Databases search page
Figure 1. Search results for peptide hormone ‘rat obestatin’ in NCBI’s All Databases search page
Try these example queries to see the improved search results.

Join NCBI at ASHG 2018, October 16-20


Putting your schedule together for ASHG? Don’t forget to look at all of NCBI’s activities, which include 1 GRC Workshop, 1 Booth (#315), 2 Co-Labs, and 10 Poster presentations. We created a handy schedule below, with links to posts where we’ve highlighted events.

Booth #315, Exhibit Hall:

  • Wednesday, October 17, 10:00 AM – 4:30 PM
  • Thursday, October 18, 10:00 AM – 4:30 PM
  • Friday, October 19, 10:00 AM – 4:30 PM

Visit us at the booth to provide feedback, have questions answered or just to chat!

Continue reading

Matched Annotation by NCBI and EMBL-EBI (MANE): a new joint venture to define a set of representative transcripts for human protein-coding genes


The RefSeq project at the NCBI and the Ensembl/GENCODE project at EMBL-EBI have provided independent high-quality human reference gene datasets to biologists since the sequencing of the human genome. Now we’re joining together on an exciting new project we’re calling Matched Annotation from the NCBI and EMBL-EBI or MANE, to provide a matched set of well-supported transcripts for human protein-coding genes and define one representative transcript for each gene. Both RefSeq and Ensembl will continue to provide a rich set of alternate transcripts per gene.

The MANE project builds on the successful CCDS collaboration (PMCID: PMC5753299) and incorporates feedback from RefSeq and Ensembl/GENCODE users who requested a common reference transcript dataset including one or a few key transcripts for each gene where the RefSeq and Ensembl/GENCODE transcripts are identical in length and sequence, and completely match the human reference genome sequence. We expect to later expand the project to include a larger subset of full-length transcripts that more fully represent the functional complexity of many genes. We’re leveraging public deep sequencing datasets to optimize 5’ and 3’ UTR endpoints to more accurately reflect transcriptional processes. To pick representative transcripts, we’ve developed computational methods to evaluate and integrate transcript expression levels, protein conservation, support from archived transcript submissions, clinical relevance, and other factors. Complex genes are subject to review by annotation experts from both groups to agree on a representative transcript and often make improvements to both annotation sets.

The unified, high-quality transcript set provided by the MANE project will simplify the task of choosing a transcript for comparative genomics, clinical reporting, and basic research. When integrated across different public genome resources, this minimal, identically annotated transcript set will eliminate the need to choose between RefSeq and Ensembl/GENCODE datasets for genomic analyses. This will also make it easy for researchers who currently prefer one dataset over the other to exchange data or translate coordinates (or HGVS variation expressions) between RefSeq and Ensembl annotation results. Furthermore, the perfect alignment of all MANE transcripts to GRCh38 will make the set compatible with NGS-based sequencing technologies and other resources that use the latest and highest-quality reference human genome assembly available.

Our goal is for the final MANE dataset to be stable, although individual sequences and the dataset as a whole will be versioned and allow for future updates and expansions as needed to incorporate significant new data and additional curation. We plan to release a partial “beta” transcript set by the end of the year for testing, and a large sequence update in the next few months to refine 5’ and 3’ RefSeq transcript ends and match the GRCh38 sequence. Ensembl plans to release similar updates in spring 2019.

We’re looking forward to your feedback! Next week, we will be presenting the project at the annual American Society for Human Genetics (ASHG) meeting in San Diego, CA, USA. Please attend our talks scheduled in the Genome Reference Consortium (GRC) workshop on Tuesday, October 16, at 1:00 PM, and in the Importance of Isoform Expression in Variant Interpretation Session (#94) on Saturday, October 20th at 9:15 AM.  You can also visit us at the NCBI or Ensembl booths and posters throughout the meeting or send us feedback at info@ncbi.nlm.nih.gov. We’re looking forward to your valuable input on our new initiative!

See improvements in NCBI’s genome visualization and analysis tools at ASHG


GDV_homepage

In 2016, NCBI introduced the Genome Data Viewer (GDV). This past May, the GDV replaced the aging Map Viewer. Over the past year, NCBI has kept you updated about GDV through announcements, webinars, and blogs. Now you can gather information and get an overview of all the changes to GDV in person at ASHG!

Check out Poster 1670F “What’s new with NCBI tools for genome visualization and analysis.” on Friday, Oct. 19 from 3 PM to 4 PM
(Exhibit Hall, Ground Level)

Continue reading

NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources


As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

Continue reading

October 10 Webinar: Using NCBI Medical Genetics Resources: MedGen, ClinVar, GTR


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

Register

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.