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!
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 email@example.com. We’re looking forward to your valuable input on our new initiative!
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)
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!
NCBI staff will share knowledge on various topics at the American Society of Human Genetics (ASHG) conference this month in San Diego. Here, on NCBI Insights, we feature some preliminary details for one of NCBI’s dbSNP posters.
You can visit poster 1692W “Improving dbSNP Data Quality and Annotation for Variant Interpretation” on Wednesday, Oct. 17 from 3 PM to 4 PM at ASHG.
As the American Society of Human Genetics (ASHG) conference is around the corner, the NCBI staff begin to prep for their presentations in San Diego. Here is some background for dbGaP’s poster about their process to improve data storage and accessibility.
Visit Poster 1435T “Storage and use of dbGaP data in the cloud” Thursday, October 18 from 2 PM to 3PM. (Exhibit Hall, Ground Floor)
This October, some NCBI staff will head out to present at the American Society of Human Genetics (ASHG) conference in sunny San Diego. Below, we give you an inside scoop on the ClinVar poster that we’ll present at ASHG.
Want to learn more about how you can submit phenotype and functional data? Or access the data?
Have we hooked you yet?
Head to Poster 1492T “Increasing phenotypic and functional evidence in ClinVar” on Thursday, Oct. 18 from 3 PM to 4 PM. (Exhibit Hall, Ground Floor)