Ensembl & Friends at ASHG

Excited for ASHG? So are we. You can find several representatives of Ensembl at the conference, as well as some of our close collaborators at the European Bioinformatics Institute (EBI), including GENCODE, the GWAS Catalog, HGNC, the IGSR and the LRG. Read on to find out more about where and when you can see our workshops, talks or posters (listed in chronological order). We would all be very happy to chat with anyone, so if you see us around please do say “hi”!

Workshops

Ensembl Genome Browser

Who? Erin Haskell, Ensembl
What? Interactive invited Workshop
When? Tues, Oct 16, 2:30pm – 4:00pm
Where? Room 31, Upper Level
Twitter: @ensembl and @mycoacia
Title: “Interactive Invited Workshop: Analysing Clinical Variation Data Using the Ensembl Tools and Resources”
Summary:

A brief introduction to Ensembl will be followed by hands-on demonstrations and exercises, including:

  1. using the Ensembl Variant Effect Predictor (VEP) tool to predict the functional consequences of a set variants identified from sequencing a clinical sample;
  2. exploring protein sequence haplotypes in this individual using the new Haplosaurus tool;
  3. working through a deep dive exploration of a single variant identified from the VEP analysis;
  4. exploring a single gene from the list of genes affected by the variant of interest.

Workshop materials can be found online at the Ensembl training portal.

The new MANE project – Matched Annotation from NCBI and EBI

Who? Joannella Morales, MANE LRG & GWAS Catalog (jointly with Terence Murphy, NCBI)
What? Talk, GRC hosted workshop
When? Tues, Oct 16, 1:00pm – 4:00pm
Where? Room 28B, Upper Level
Twitter: @GWASCatalog
Title: “Getting the Most from the Reference Assembly and Reference Materials: Updates and Developments from the Genome Reference Consortium (GRC) and Genome in a Bottle (GIAB)”
Summary:

We will discuss the MANE project (Matched Annotation from NCBI and EBI), which aims to release a genome-wide transcript set that contains one well-supported transcript per protein coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl transcript (ENST). We will also discuss the intersection between the MANE and LRG projects.

The NHGRI-EBI Genome Wide Association Study (GWAS) Catalog

Who? Jackie MacArthur and Joannella Morales, GWAS Catalog
What? Interactive Invited Workshop
When? Thurs, Oct 18, 7:15am – 8:45pm
Where? Room 33, Upper Level
Twitter: @GWASCatalog
Title: “Beyond “Other”: Working Toward a Standard Ontology for Diverse Populations”
Summary:

There is currently no standard ontology to describe diverse human populations, although diversity is crucial to human genomics research. This workshop will harmonise complimentary, parallel efforts across disciplines to accurately and responsibly describe human populations. The NHGRI-EBI Genome-Wide Association Study (GWAS) Catalog will present their work alongside other resources and share their process and experience on curating GWAS studies through a standardised framework of sample ancestry. Workshop participants will engage in an interactive session to understand these proposed ontologies, provide feedback, and build consensus toward widespread adoption.

Talks

The new MANE project – Matched Annotation from NCBI and EBI

Who? Jane Loveland, GENCODE Project
What? Talk, Session 94: 302
When? Sat, Oct 20, 9:15am-9:30am (Concurrent platform session G: 94. Importance of Isoform expression in Variant Interpretation)
Where? Room 6C, Upper Level
Twitter: @GencodeGenes
Title: “Converging on transcript annotation from Ensembl/GENCODE and RefSeq.”
Summary (full abstract here):
Building on the success of the collaborative CCDS project, Ensembl/GENCODE and RefSeq are collaboratively working to identify a representative transcript that captures most information about each protein-coding gene.  The annotation of that selected transcript in the RefSeq and GENCODE sets will be revised so that they completely match in overall exon structure, precise 5’ and 3’ transcript boundaries, and at the nucleotide sequence level. Our goals for 2018/2019 include convergence on key high value annotations to provide a common minimal set of transcripts per gene.

GWAS Catalog and Open Targets

Who? Annalisa Buniello GWAS catalog, Open Targets
What? Talk, Session 101: 336
When? Sat, Oct 20th, 10:30am-10:45am (Concurrent platform session H: 101. Novel Approaches for Conducting Genome-wide Association Studies)
Where? Room 6A, Upper Level
Title: “Expanding the scope of the GWAS catalog to improve drug target identification and prioritisation”
Summary (full abstract here):

Open Targets have therefore collaborated with the GWAS Catalog to expand the scope of the Catalog to include specific prioritised association studies carried out using targeted arrays such as MetaboChip, ImmunoChip and Exome array. Annalisa will be sharing details about new datasets available through GWAS.

Posters

The NHGRI-EBI GWAS Catalog

Who? Jackie MacArthur & Daniel Suveges, GWAS Catalog
What? Poster 2571W
When? Wed, Oct 17, 2:00pm – 4:00pm (Complex Traits and Polygenic Disorders)
Where? Exhibit Hall, Ground Level
Twitter: @GWASCatalog 
Title: “The enhanced GWAS Catalog: Catalysin discovery with the new REST API and improved web interface”
Summary (full abstract here):

The mission of the NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is to provide a highly curated, comprehensive collection of all GWAS publications and the discovered associations.  Here we introduce our RESTful API that provides programmatic access to the GWAS Catalog data, enabling users to retrieve data from our database in a high-throughput manner. To advance the accessibility of GWAS Catalog data we have also enhanced the Catalog’s web interface to better support common user queries. Our new publication, trait and variant-specific pages are designed to provide structured GWAS Catalog data and visualisations, along with links related to external data. Come along to find out about these new developments.

The International Genome Sequence Resource (IGSR), including the 1000 genomes project.

Who? Susan Fairley, IGSR
What? Poster 1563W
When? Wed, Oct 17, 2:00pm – 4:00pm (Bioinformatics and Computational Approaches)
Where? Exhibit Hall, Ground Level
Title: “Updating and expanding the resources from the 1000 Genomes Project in the International Genome Sample Resource (IGSR)”
Summary (full abstract here):

The 1000 Genomes Project generated the largest fully public catalogue of human genetic variation and produced a set of valuable reference resources that remain widely used. Through the International Genome Sample Resource (IGSR), we provide continued access and support to users of the 1000 Genomes data resources, while also building on those resources. IGSR is working to add populations that were not represented in 1000 Genomes. As the data sets in IGSR grow, we are developing the project website, which includes a data portal, to aid discoverability, navigation and interpretation of the data sets. Come along to find out more about the IGSR.

The HUGO Gene Nomenclature Committee (HGNC)

Who? Paul Denny, HGNC
What? Poster 1558T
When? Thurs, Oct 18, 3:00pm-4:00pm (Bioinformatics and Computational Approaches)
Where? Exhibit Hall, Ground Level
Twitter: @genenames
Title: “A balancing act: Aiming for stability in human gene nomenclature.”
Summary (full abstract here):
HGNC has always tried to minimise changes to gene symbols, but we are now actively working towards this aim, in collaboration with the the Transforming Genetic Medicine Initiative (TGMI) consortium. Our initial focus is on genes causing disease, and we are utilising several different criteria, such as literature usage of the symbol and gene family membership, to assess the potential long-term stability of individual gene symbols and names. Come along to find out more about the HGNC.

Locus Reference Genomic (LRG)

What? Poster 1583F
When? Fri, Oct 19, 2:00pm-4:00pm (Bioinformatics and Computational Approaches)
Where? Exhibit Hall, Ground Level
Title: “Locus Reference Genomic (LRG): A resource for reporting clinically relevant sequence variants”
Summary (full abstract here):
The Locus Reference Genomic (LRG) is a manually curated resource designed specifically for the reporting of clinically relevant variants. Each LRG record provides a stable and non-versioned genomic DNA sequence for a region of the human genome, establishing a coordinate system that is independent from upgrades to the reference assembly. Come along to learn more about the LRG project.

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