1 of 12

Future Plans for Predicted Effector Gene Working Group

Julie Jurgens

Broad Institute of MIT and Harvard

5/8/25

2 of 12

What now?

  • Move from minimal recommendations to standards
  • Evaluate strawman
    • In-house assessments
    • Community feedback
  • Refine current framework
  • Distribute to the community & encourage adoption

​

3 of 12

PEG WG Meeting Structure

  • Frequency: Monthly
  • Duration: 1 hour
  • Blocks of meetings focused around a single topic

​

​

​

​

Define question, strategy, and delegation of tasks

Present initial results/ next steps

Iterate to develop mature results and recommendations

4 of 12

Future PEG Working Group Meeting Topics

  • Solidifying Data/ Metadata Standards
  • Benchmarking
  • Defining use cases
  • Comparing prioritization approaches
  • Creating community recommendations

5 of 12

Benchmarking

  • Identify gaps in the proposed strawman by fitting existing PEG lists into it
    • 149 PEG lists from Predicted Effector Genes Knowledge Portal
    • Where are the gaps?
    • How can we refine our framework?

​

6 of 12

Defining use cases

  • Submission to a knowledgebase
  • Input to bioinformatic pipeline
  • Hypothesis generation
  • Confirmation of independent findings
  • Gene-drug target prioritization
  • Reuse/computational ingest
    • AI/ML/KG readiness
  • Validation with AI
  • Enable others to compare validation approaches

​

​

7 of 12

Creating community recommendations

Engage with professional societies to develop endorsed recommendations

Public pilot launch: Coordinated community efforts to identify new datasets and apply standards (like ACMG/AMP)

Develop iterative versions of framework

8 of 12

Longer-Term: Comparing results obtained by different prioritization approaches?

  • Challenge: lack of standards
  • Identify dataset(s), apply/compare various approaches
    • Positive and negative controls
    • Rubric to assess scoring systems
  • Requirements:
    • Volunteer data contributor(s)
    • Community WG members to test
  • Ultimate aim: enabling metaanalysis to define gold standard lists

​

9 of 12

Other discussion topics?

10 of 12

Meta-data

Data

The Working Group starts now!

11 of 12

Planning our next WG meeting

  • June 2025
  • Doodle poll:

https://doodle.com/group-poll/participate/bWoKRYnb

  • Topic: decided today by group

�

12 of 12

Summary and Next Steps

  • The community has a strong interest and need for PEG list standards
  • Need to develop roadmap to enable discovery
  • The many purposes and evidence types integrated by PEG list require input from multidisciplinary experts
  • We need an engaged community of stewards
    • YOU!

​

​