GA4GH Connect 2021 Meeting Report
The 2021 GA4GH Connect Meeting brought online 344 participants across 23 countries. The four-day meeting enabled active contributors to collaborate and advance cross-Work Stream initiatives and key deliverables on the GA4GH Strategic Roadmap.
Opening Remarks and Meeting Goals
Ewan Birney (EMBL-EBI) presented on the GA4GH Starter Kit and its goals for building momentum on the implementation of GA4GH standards and lowering the barrier to genomics interoperability. Ewan also announced the addition of Susan Fairley who is the new CSO joining GA4GH. Participants then heard brief presentations from the Work Streams, the Federated Analysis Systems Project (FASP), and the Equity, Diversity and Inclusion (EDI) Advisory Group outlining their goals and of Connect and what participants can expect out of their sessions.
Opportunities for Collaboration: External Initiatives Presentations
Three large-scale consortia — the Medical Genome Initiative (MGI), the Human Pangenome Reference Consortium (HPRC), and the International Hundred-thousand Cohorts Consortium (IHCC) — gave presentations on their work, highlighting opportunities for collaboration with the GA4GH Work Streams.
Beacon V2
The Beacon v2 team showcased progress on advanced features on the product. Tim Beck presented on Beacon v2 filters, which aims to enable filtering of Beacon responses by certain biomedical properties and procedural metadata; Michael Baudis presented on the representation of structural variants; and Lauren Fromont presented on the schema for representing cohorts in Beacon v2. The team aims to continue work on Beacon v2 in order to prepare the standard for submission through the GA4GH product approval process this year.
Cloud Work Stream
The Cloud Work Stream meeting began with a roundtable check in with GA4GH Driver Projects and other implementers regarding the status of Cloud API implementations and suggestions for improvement of those APIs to better fit their needs. Subsequently, the group discussed the major issues being addressed in 2021 for each API: Workflow Execution Service, Task Execution Service, Data Repository Service, and Tool Registry Service. Finally, the meeting chairs summarized ongoing collaborative discussions with other projects and Work Streams (Federated Analysis Systems Project, Data Use and Researcher Identity, and Discovery).
Data Access Committee Review Standards (DACReS)
Ted Dove (University of Edinburgh), Vasiliki Rahimzadeh (Stanford), Jonathan Lawson (Broad Institute) led a discussion on the early stages of the Data Access Committee Review Standards (DACReS) Policy, specifically the Guiding Principles and Purpose sections. Contributors will continue to work on a first draft of the policy.
Data Security Work Stream
David Bernick (Broad Institute) introduced new potential deliverables for the Data Security Work Stream, including “Malfeasance Rules”: rulesets that could help institutions detect policy problems and understand if someone is exceeding mandates of research. The Work Stream also revisited the Breach Response Protocol, which it intends to polish off as a deliverable in 2021.
Data Security: Federated Analytics and Cloud Security
Jean-Pierre Hubaux and Francesco Marino (EPFL) delivered an in-depth presentation of the state of affairs for privacy-conscious data sharing, emphasizing that multi-party homomorphic encryption (MHE) provides a response to this challenge. The Data Security Work Stream will join efforts with the Cloud Work Stream to support refinement of APIs, notably of DRS, TRS and WES, to let them support federated analysis.
Discovery Work Stream
The Discovery Work Stream met to focus on alignment from all the different Discovery products: Search API, Beacon API, Networks, and Schemablocks. The team used this session to hear feedback from Driver Projects and use cases to help steer direction of product updates and developments.
DRS Alignment with Beacon and Search
The Data Repository Service (DRS) API of the Cloud Work Stream met with the Discovery Work Stream standards—Search API and Beacon API—to discuss areas of alignment. All teams gave brief introductions to their standards and identified key areas for collaboration: Search as a mechanism to discover DRS URLs for files of interest; collaboration on a method for defining metadata; and addressing the handover mechanism from Beacon API to DRS.
DRS and Passports Alignment
Kurt Rodarmer (NIH) gave a presentation on the DRS implementation with Passports and the proposed steps forward. Max Barkley (DNAstack), Craig Voisin (Google), Kurt Rodarmer (NIH), and Sarion Bowers (Sanger Institute) then led a discussion on the existing DRS and Passport spec change proposal and solicited community feedback to discuss stakeholder use cases.
EDI Workshop: Building a Diverse and Inclusive GA4GH
The Equity, Diversity, and Inclusion (EDI) Advisory Group and the Regulatory and Ethics Work Stream hosted a workshop and whiteboarding session to focus on building a more inclusive and diverse GA4GH community, in order to build standards that can benefit the global community. The team brainstormed a series of project ideas falling into the categories of Onboarding into GA4GH, Participation Levels within GA4GH, and Equity by Design in our standards. The project ideas were presented at the end of the meeting, and the community voted on which projects may have the most impact to the GA4GH community. The EDI and REWS teams will use this feedback to advance and develop guidance on key projects.
Federated Analysis Systems Project (FASP) Updates
The FASP team presented accomplishments from 2020 and heard lightning talks on scientific use cases for FASP. Participants then discussed FASP-scripts, the use cases supported, areas for exploration and how people can contribute to the repo. The team identified obstacles for the project’s next steps and solutions which include discussing particular API integration problems and solutions and engagement through hackathons.
Genetic Discrimination Observatory (GDO)
Yann Joly (CGP/McGill) and Gratien Dalpé (CPG/McGill) introduced attendees to the Genetic Discrimination Observatory (GDO), a global network of stakeholders dedicated to researching and preventing genetic discrimination. Attendees explored how the GDO could collaborate with GA4GH, leading to a resolution to prepare an activity plan proposal.
Key Management in the Cloud
The Crypt4GH encrypted file format is targeted at individual researchers working with secure data. This session sought to provide a space for attendees to exchange ideas and to discuss ways to enable Crypt4GH-encrypted files to be processed in the cloud natively, particularly within the standards developed by the Cloud Work Stream (DRS, WES, CWL, etc.).
Large Scale Genomics Work Stream
The Large Scale Genomics Work Stream meeting began with presentations from each individual task team, including brief introductions to the ongoing work of each as well as opportunities for involvement and future plans. Subsequently, the Work Stream leads chaired a discussion about the future of the Variant Call File (VCF) format as the community scales to massively large scale genomics datasets.
Phenopackets & Pedigree Integration with Beacon
The Clinical and Phenotypic Data Capture and Discovery Work Streams came together to discuss progress and opportunities for collaboration between the Phenopackets, Pedigree, Beacon API and Search API teams. The Work Streams confirmed that Beacon API and Search API will be able to support Phenopackets and Pedigree, and will continue to explore JSON schema representation.
Phenopackets & VA/VR Integration
The Clinical and Phenotypic Data Capture and Genomic Knowledge Standards Work Streams came together to define the scope and requirements for Variant Annotation and Variation Representation Specification objects within the Phenopacket schema, specifically which elements are in and out of scope. The Work Streams will continue to collaborate to develop an integration solution that involves a descriptor pattern, eventually working to build an “interpretation packet”.
Phenopackets & Pedigree Integration with Beacon API and Search API
The Clinical and Phenotypic Data Capture and Discovery Work Streams came together to discuss progress and opportunities for collaboration between the Phenopackets, Pedigree, Beacon API and Search API teams. The Work Streams confirmed that Beacon API and Search API will be able to support Phenopackets and Pedigree, and will continue to explore JSON schema representation.
REWS Return of Results Policy
Anna Lewis (Harvard) and Bartha Knoppers (CGP/McGill) led attendees through a review of the motivation, starting point and background of the Return of Results (RoR) Policy, as well as an in-depth discussion on particular policy considerations. The RoR team will work to integrate comments received from GA4GH community and present a finalised Policy to the GA4GH Steering Committee for approval.
Regulatory & Ethics Work Stream
Schemablocks
The Schemablocks team is reviving discussions and will aim to expand participation in the future. Specifically he team will focus on building a library of data models, collaborating with TASC under new CSO leadership to define a process for what will be accepted as part of the “core” Schemablocks, and to explore use cases through the Search API and Phenopackets.
Sequence Annotation
The Sequence Annotation team began its meeting by introducing the scope of the current project and then opened up to a community whiteboarding session to understand what features the community needs to see in a Sequence Annotation standard, how they would like to see these features described, and what relationships exist between features.
Variant Annotation
Matthew Brush (OHSU) and Javier Lopez (Genomics England) led a session focused on defining the work to be for the delivery of the v0 release and roll-out. Driver Projects were invited to provide their feedback on the Statement Models, documentation about the foundational SEPIO information model, and how they would like to be involved in testing the v0 spec.
VCF/VRS/refget Alignment Meeting
VRS 1.3 Planning and Implementation Guidelines
Larry Babb (Broad Institute) and Alex Wagner (Nationwide Children’s Hospital) presented a brief progress report for VRS 1.2, plans and next steps for VRS 1.3, and implementation guidance using the VRSATILE approach. The session included an open discussion on process, design, implementation strategies, and improvements for VRS.
Closing Remarks & Report Backs
To wrap up the GA4GH Connect 2021 Meeting, the Work Streams, the Federated Analysis Systems Project (FASP), and the Equity, Diversity and Inclusion (EDI) Advisory Group presented a report back of key takeaways from their sessions and the work that is expected to happen between now and the 9th Plenary Meeting.