Skip to main content

Workshop 2024

First community workshop on standards and infrastructure for predicted effector gene lists

📍 Dates & Locations

  • September 16–17, 2024
  • In-person: Broad Institute (Cambridge, MA, USA) & European Bioinformatics Institute (Hinxton, UK)
  • Virtual: By videoconference

ℹ️ Get more details at the communnity page

Background​

Researchers who perform genome-wide association studies (GWAS) often aggregate and integrate multiple evidence types in order to predict the effector (causal) genes at GWAS loci (examples).

These predictions are a valuable outcome of GWAS, but in 2024 there were no community standards for organizing or sharing them. The proliferation of evidence types, methods, and formats carried the risk of confusion.

To address this gap, we held a community workshop on the standards, infrastructure, and incentives required to promote:

  • Sharing
  • Interoperability
  • Updating of predicted effector gene lists

📊 A community survey was conducted in preparation (see results).

👥 The workshop had 80+ participants from diverse institutions and career stages.
📝 A manuscript describing the proceedings is in preparation.

Aims of the Workshop​

  • Raise awareness of the diversity of approaches to creating predicted effector gene (PEG) lists
  • Identify challenges in sharing, maintaining, and updating PEG lists
  • Ensure that PEG lists with supporting evidence and metadata are FAIR and relevant to the community
  • Begin to discuss a community standard for reporting PEG lists
  • Define strategies for evaluation and collation of PEG lists
  • Identify strategies for incentivizing adoption of the proposed standards

Agenda​

Day 1 — Monday, September 16, 2024​

🕘 9am–1pm EDT / 2pm–6pm BST | View video recording

  • 09:00 EDT / 14:00 BST – Introduction and welcome
    Noël Burtt, Knowledge Portal Network [slides]

  • 09:20 EDT / 14:20 BST – Who’s that causal gene? Lessons learned in annotating 100,000 GWAS SNPs
    Eric Fauman, Pfizer Inc. [slides]

  • 10:20 EDT / 15:20 BST – Open Targets as an end user of PEG lists
    Yakov Tsepilov, Open Targets [slides]

  • 10:35 EDT / 15:35 BST – Open discussion

  • 10:45 EDT / 15:45 BST – Break

  • 10:55 EDT / 15:55 BST – Overview of current gene prioritization efforts and PEG lists
    Maria Costanzo, Knowledge Portal Network [slides]

  • 11:25 EDT / 16:25 BST – 10-minute presentations of gene prioritizations

    • Cassandra Spracklen (UMass) [slides]
    • Brent Richards (McGill)
    • Adam Butterworth (Cambridge) [slides]

  • 12:05 EDT / 17:05 BST – Open discussion: key features of each approach and comparisons

  • 12:30 EDT / 17:30 BST – How ClinGen handles framework standardization with broad input
    Marina DiStefano, ClinGen [slides]

  • 13:00 EDT / 18:00 BST – Adjourn

Day 2 — Tuesday, September 17, 2024​

🕘 9am–1pm EDT / 2pm–6pm BST | View video recording

  • 09:00 EDT / 14:00 BST – GWAS Catalog’s experience developing GWAS standards
    Laura Harris, GWAS Catalog [slides]

  • 09:15 EDT / 14:15 BST – Curation & display of PEG lists in Knowledge Portals
    Maria Costanzo, Knowledge Portal Network [slides]

  • 09:25 EDT / 14:25 BST – Curation of gold standard lists at Open Targets
    Xiangyu Jack Ge, Open Targets [slides]

  • 09:35 EDT / 14:35 BST – Open discussion: advantages & disadvantages of PEG list presentations

  • 09:50 EDT / 14:50 BST – Results of community survey
    Maria Costanzo, Knowledge Portal Network [slides]

  • 10:00 EDT / 15:00 BST – Standardization requirements for computational & AI methods
    Jason Flannick, Boston Children’s Hospital [slides]

  • 10:15 EDT / 15:15 BST – Break

  • 10:25 EDT / 15:25 BST – Proposal for PEG list standards
    Yue Ji & Laura Harris, GWAS Catalog [slides]

  • 10:40 EDT / 15:40 BST – Breakout group discussions on proposed standards
    (40 minutes, guiding questions provided)

  • 11:20 EDT / 16:20 BST – Breakout reports + larger group discussion

  • 12:40 EDT / 17:40 BST – Wrap up
    All organizers

  • 13:00 EDT / 18:00 BST – Adjourn

Meeting Materials​

📑 Presentations​

📝 Workshop Notes​

💬 Breakout Group Discussions​

📂 Other Materials​