Welcome to the Global Alliance for Genomics and Health (GA4GH) Updates report. In this document, you can learn about progress from across the GA4GH community, including key achievements, next steps, and opportunities for community input and engagement. Work Stream and GA4GH community meetings can be found on the new GA4GH calendar. Contact the relevant GA4GH staff member to access the Zoom details.

Table of Contents

Work Stream updates

Clinical & Phenotypic Data Capture (Clin/Pheno)

Clin/Pheno meeting minutes
The Clin/Pheno Work Stream helps clinicians and researchers store, describe, and send data about observable traits (phenotypes) and clinical care. Learn more.

Key updates

• To date, the Pedigree team has prepared the following materials:

• recommendations for a common data set for family health history;
• a conceptual model for representing pedigree data;
• KINship, an ontology for family history relationships;
• guides for implementing Pedigree in FHIR and Phenopackets;
• validation and conversion tooling (in progress) with support from the GA4GH technical team.

• The Phenopackets team has a manuscript in preprint, entitled “A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery.”

Coming up next

• The Clin/Pheno Work Stream will hold two sessions at the September Connect 2024 meeting:

• Collaborative development of a FHIR-based family health history standard: leveraging KIN Ontology and Phenopackets with HL7, G2MC, and the US CDC/NCI
• Bridging challenges and new implementations in GA4GH Clin/Pheno standards

Cloud

Cloud meeting minutes
The Cloud Work Stream standardises how researchers bring algorithms to data — or define, share, and execute portable workflows in any cloud environment, securely and easily. Learn more.

Key achievements

• The TES team is publishing a paper on the TES specification. TES is also now officially supported in the NextFlow engine.
• The TRS team has had constructive conversations with representatives from Seqera-Nextflow. The TRS and Nextflow teams identified potential areas for collaboration and cooperation, and welcome more discussions on how the two communities can share workflows.
• The Workflow Execution Service (WES) team conducted a survey to collect feedback on the product, providing valuable insights for future versions.

Coming up next

• The Cloud Work Stream is continuing maintenance on all of its main products.

• The DRS team is working to address specific topics, such as location constraints, stats endpoints, and cold storage objects.
• The TES and WES teams will work on connecting their specifications to authorisation and authentication systems. This includes reaching out to the Data Security Work Stream and other experts in the field to understand the needs.
• The TRS team will aim to collect feedback to shape the future direction of the product.
• The WES team will continue product enhancements, based on feedback collected from implementers.

• The Cloud Work Stream will hold two sessions at the September Connect 2024 meeting:

• DRS v1.6 and beyond: DRS access options for compute tools
• Cloud Work Stream in 2025

Data Use & Researcher Identities (DURI)

DURI meeting minutes
The DURI Work Stream creates tools to communicate who can access datasets for which purposes. The tools help  confirm user identity and match researcher type to data permissions. Learn more.

Key achievements

• We are excited to welcome Jonathan Lawson of the Broad Institute of MIT and Harvard as the new Co-Lead of the DURI Work Stream! Learn more about Jonathan and the DURI Work Stream in this press release.
• DURI and the Regulatory & Ethics Work Stream (REWS) have been working on standardising Data Access Agreement clauses. The product is nearly ready for approval — stay tuned!

Coming up next

• DURI leadership is excited to roll out a new road map and begin regular product meetings to address known challenges and rising opportunities to make compliant data use faster within a federated ecosystem. Look out for forthcoming invitations and join us!

Discovery

Discovery meeting minutes 
The Discovery Work Stream helps researchers and clinicians explore the wealth of worldwide genomic variations through products developed for searching and exchanging genomic data. Learn more.

Key achievements

• Beacon

• There are several latest releases with Beacon: Beacon v2.1.0 minor version and Beacon v2.0 Reference Implementation, which has a new user interface.
• The Beacon team is currently collaborating with the RNAget team, an approved product of the Large-Scale Genomics (LSG) Work Stream, to include the tool in the Beacon v2.0 extension model. RNAget API provides a common set of communication channels that allows researchers to efficiently retrieve RNA data of interest.
• The Beacon team’s latest publication, “Twelve quick tips for deploying Beacon,” gives simple tips for the community to keep in mind when deploying Beacon with their datasets.

• Data Connect

• Over the last few months, the Data Connect team has worked to increase adoption and support more implementations. Through DNAstack’s Omics AI, GA4GH standards, including Data Connect, are powering a number of data sharing collaborations and tools: the Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network Cloud, the MSSNG database, and the Target ALS Data Portal.

• Experiments Metadata

• The Experiments Metadata team hosted a hackathon during the Genomics Standards Consortium Annual Meeting to review and enhance the core genomics metadata developed by the GA4GH Experiments Metadata Standard Group. You can find the recording, slides, minutes, and meeting summary available here.

Coming up next

• Beacon

• Beacon Scouts will continue to actively collaborate with the community to expand the specification. The team also plans to work with ELIXIR nodes and the Genomic Data Infrastructure (GDI) project to support their adoption of the Beacon v2.0 API.
• Beacon v2.0 and its reference implementation will be showcased in a workshop titled “From zero to federated discovery: beaconise your biomedical data” at ECCB24 on 17 September, in Turku, Finland.

• Data Connect

• The Data Connect team is looking to collaborate with other Work Streams to integrate with other standards, such as Passports. The team is also looking to work with more user groups to implement Data Connect.
• Data Connect provides a way to organise data into tables, and to describe their data model using JSON schema. The team is investigating adding the capability to capture relationships between tables, and reference standards and units of measurement. 

• Experiments Metadata

• The team aims to finalise the core list of experiment metadata properties during their September Connect session. Concurrently, they are seeking domain champions to assist in developing tailored property lists for various experiment types.

• The Discovery Work Stream will hold several sessions at the September Connect 2024 meeting:

• Service Info and Service Registry: present and future
• Future of Data Connect standard
• Beacon down under: pioneering practical cohort building in genomic research
• Improving data interoperability across GA4GH: Data Model Consensus (DaMaSC) study group
• Global Beacon showcase: advancing data discoverability across platforms
• Experiments Metadata Standard

• The Discovery Work Stream will have a booth during the 12th Plenary meeting to gather feedback on community needs and invite attendees to get involved. Come visit the Discovery booth to learn more about Beacon, DaMaSC, and Data Connect!

Genomic Knowledge Standards (GKS)

GKS meeting minutes
The GKS Work Stream designs technical standards that enable computer-to-computer exchange of information about genomes, improving the search and application of genomic knowledge. Learn more.

Key achievements

• Two new GKS Work Stream leads have been selected and will be announced at the end of August.
• GKS worked with the Technical Alignment Subcommittee (TASC) to foster technical alignment on Schema URI definitions. GKS has implemented this for the VRS, Variant Annotation specification (VA-spec), and GKS commons products.
• VRS v2.0 draft documentation is live and available for public review. It includes support for structural variation using the new adjacency, terminus, and derived molecule classes.
  

Coming up next

• The Cat-VRS team aims to have a draft version of the specification up for product review in Q1 2025.
• GKS will start regular public calls across the GKS Work Stream to showcase current or prospective implementations of the GKS specifications and a high-level overview of product development activities.
• The GKS Work Stream is developing a road map for the next phase of development for all GKS products, in addition to working on a community perspective manuscript. Contributors with a new or long-standing interest in GKS development and application are welcome and encouraged to participate in setting this vision.
• The GKS Work Stream will host several sessions at the September Connect 2024 meeting:

• Mad GKS 2.0: the Implementation Warrior
• Mad GKS: beyond maturity

• Join the GKS Work Stream at its hackathon at the American Society of Human Genetics (ASHG) 2024 Annual Meeting in Denver, USA on 4 November. Please contact Beatrice Amos for registration details.

Large-Scale Genomics (LSG)

LSG meeting minutes
The LSG Work Stream develops products to describe, compress, store, encrypt, and transfer genomic data in a scalable way. Learn more.

Key achievements

• The WGS QC team is creating a framework for reporting quality control metrics for whole genome sequencing, in order to facilitate the exchange of results across initiatives and establish confidence in the data quality. The team has put together a document describing key metrics, and has released a reference implementation on dockstore.
• VCF v4.5 is now live! Key features of this version include support for calling base modifications and improved scalability for large cohorts. The v4.5 spec improves scalability of the VCF format for multiple samples by introducing the novel concept of local alleles at variant sites with several alternative alleles.
• The RNAget team is collaborating with the ELIXIR Beacon Driver Project on an “RNA Beacon” extension.

Coming up next

• The Crypt4GH team is working on a second version of the specification. The new version will include:

• better checks for file integrity, making it impossible to change an encrypted file without the changes being detected;
• improvements to make it easier to serve files remotely;
• and the addition of certificates so the data source can be verified.

• The WGS Quality Control Standards team aims to release an improved reference implementation on dockstore, to include variant calling level QC metrics.
• The “RNA Beacon” extension, a collaboration between the RNAget and Beacon teams, will be available for review and comment soon.
• The Future of VCF Working Group is developing a benchmarking challenge to test and compare approaches to scale the VCF format even further. Please get in touch if you are interested in this endeavour.
• The LSG Work Stream will host two sessions at the September Connect 2024 meeting.

• What’s new in VCF v4.5
• File Formats Working Practices

Data Security

Data Security meeting minutes 
The Data Security Work Stream develops products and guidelines to safeguard privacy, data integrity, and service availability. The Work Stream also assesses GA4GH outputs for risk or security implications. Learn more.

Key achievements

• The Data Security Work Stream welcomed a new lead, Jaime Delgado Learn more about the lead and the Work Stream in this GA4GH press release.
• The team presented the Passports standard at the ISO Technical Committee 215/SC 1 Conference to explore the potential for an open Ad Hoc Group (AHG). Delgado will lead AHG-2, renewing an open call for participants to join.
• To facilitate cross-Work-Stream collaboration, the Data Security Work Stream provided an overview of the Passports specification at a Data Connect meeting.

Coming up next

• To advance product development, the team is looking at the following topics for future investigation:

• Passport Visas as verifiable credentials: OpenID for Verifiable Credentials (OID4VC) is an upcoming standard similar to the GA4GH AAI OIDC Profile. It defines a digital wallet, which collects verifiable credentials from credential issuers and provides them to verifiers. The Data Security Work Stream seeks to collaborate with ISO to determine if Passport Visas, or equivalent information, could be standardised for use within OID4VC.
• Trusted Research Environment Initiative: This initiative seeks to establish a Trusted Research Environment Registry for use by the global genomics community. This registry is intended to serve as a source of trust for the genomics community when accessing data through platforms using the Data Repository Service (DRS) and Passports credentials.
• Security issues in Beacon v2.0: DSWS is exploring a collaboration with the Beacon team to conduct an in-depth analysis on the security and privacy needs and restrictions of Beacon v2.0.

• The Data Security Work Stream will host a Passports & AAI session at the September Connect 2024 meeting.

Regulatory & Ethics (REWS)

REWS meeting minutes 
REWS develops community-driven policies and tools that address regulatory and ethical considerations in genomic research and international data sharing. Learn more.

Key achievements

• REWS has continued to work across various regulatory and ethical challenges within genomics over the last few months. These include:

• submitting comments on behalf of GA4GH on the WHO’s draft principles for human genome access, use, and sharing — read more in this GA4GH press release;
• publishing a new Public Attitudes for Genomic Policy Brief on genomic data sharing in Singapore, written by Marthe Smedinga, Research Fellow at the National University of Singapore;
• publishing a new Health Data Sharing, Privacy, and Regulatory Forum Brief on synthetic health data, written by Elizabeth Redrup Hill, Senior Policy Analyst, and Colin Mitchell, Head of Humanities, at the PHG Foundation;
• and publishing several academic papers, including:

• providing clarification and consistent term usage and application of Genetic Discrimination in Nature Genetics and JAMA Network Open (in press);
• Paediatric Pharmacogenomics;
• a paper on the Diversity in Datasets policy, which has been accepted by  Nature Genetics.

• REWS has also moved forward in establishing the foundations for teams engaging in cutting edge research, including pathogen data sharing and ethical, legal, and social implications (ELSI) impact measurement tools. Stay tuned for more information about these groups on ga4gh.org!
• REWS is evaluating the impact of the BioSecure Act on data sharing practices.
• A survey on clinical data sharing was completed; results will be shared with the American College of Medical Genetics and Genomics (ACMG) committee.

Coming up next

• REWS is developing guidance to help technical teams address regulatory and ethical considerations while completing the product approval process, providing clarity on REWS requirements.
• REWS has also unveiled its 2024-2025 road map, addressing relevant topics in the field of genomics. These include public attitudes towards genomic data sharing and genetic discrimination, newborn genomic sequencing, and the use of large language models in genomics.
• Given the expanding ELSI challenges of genomic data sharing in the context of novel technologies and research, REWS continues to grapple with and address systemic challenges of equitable access. This will require meaningful engagement with researchers globally about these developments.
• REWS will hold the following sessions at the September Connect 2024 meeting:

• REWS general meeting
• Public perspectives on genetic discrimination
• Generative AI for genomic data sharing

• REWS will also be hosting a joint satellite workshop with Monash’s Research Group on Health Law on 20 September, following GA4GH 12th Plenary. Registration is now available at this link.

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Forums

GA4GH Implementation Forum

The GA4GH Implementation Forum (GIF) drives GA4GH standards implementation within scientific, clinical, and industry domains. GIF aims to facilitate standards implementation, ensure interoperability, and promote best practices so that GA4GH solutions can solve real-world problems. By promoting the mission pillars of implementation, interoperability, and inclusivity, GIF brings the value and benefits of GA4GH standards to a wider audience. By considering diverse requirements and available resources, GIF aims to lower barriers to entry for implementing GA4GH standards in the spirit of “building networks of knowledge instead of silos of expertise.” Learn more.

Key achievements

• Based on feedback from April Connect around barriers to implementing GA4GH standards, the team developed the GIF charter. Additional feedback was collected on the approach and the document during an open for comment period.
• The team assessed the status of ongoing GIF projects and updated the GIF webpage to enhance transparency and provide clear information on how to get involved. Current GIF Project topics include Variant Level Matching (MME), Federated Imputation (H3Africa/eLwazi), and Standards Compliant Federated Insights (DNAStack).

Coming up next

• The team will review and update guidelines for GIF projects and develop infrastructure to enhance support and prepare for future outreach to potential project champions
• GIF showcase events will be planned in the upcoming year. These events focus on showcasing how a standard has been implemented. They will be highly interactive spaces for community members to share experiences implementing standards, discuss successes and challenges, and demonstrate how standards have enabled interoperability.
• At the September Connect 2024 meeting, current and prospective GIF projects will be discussed in the following sessions:

• Advancing Variant Level Matching (VLM) and phenotype data sharing: building a federated network will discuss the current VML GIF project.
• Towards GA4GH-powered SPEs/TREs will discuss the potential of forming a GIF project.

National Initiatives Forum (NIF)

The GA4GH National Initiatives Forum (NIF) supports uptake of GA4GH standards in the context of national- and other large-scale projects and provides real-world insights to the Work Streams as they develop new products to support data sharing. The group also enables collective learning by sharing best practices, challenges, and opportunities for implementing genomics in practice with a technical, regulatory, clinical, and educational focus. Learn more.

Key achievements

• NIF hosted a virtual workshop in May to gather feedback on the NIF strategy, using the newly drafted NIF charter as a foundation. A meeting summary can be found here.
• NIF recently welcomed the German Human Genome-Phenome Archive (GHGA) and the Pan-Canadian Genome Library (PCGL) as new members.

Coming up next

• The team will incorporate community feedback into the NIF charter and share the updated version widely to enhance understanding of NIF and its role within GA4GH.
• The annual NIF meeting will be held on 20 September in Melbourne, Australia. In-person registration is now closed. NIF members who wish to participate in-person may contact nif-coordinators@ga4gh.org. Virtual registration is open to anyone who’s interested .
  

Communities of Interest

Cancer Community of Interest
Meeting minutes
The GA4GH Cancer Community is a forum for cancer researchers, clinicians, and technical experts to: 1) foster the development of cancer-specific solutions by strengthening collaborations between cancer research tool users and developers; 2) boost opportunities for collaboration by prioritising interoperability and the sharing of cancer-related data; and 3) unite international cancer initiatives with common needs and shared goals.

Key achievements

• The Cancer Community welcomed three new Co-Leads to form a unique four-person leadership team. Benjamin Haibe-Kains, Bernie Pope, and Zinaida Perova join Salva Capella in steering the ship. Learn more about the new Co-Leads and the Cancer Community in the GA4GH press release.
• In the first week of August, GA4GH contributors convened for an unconference ahead of the Cancer Genome Consortium (CGC) 2024 meeting. Hosted by the GA4GH Driver Project Variant Interpretation for Cancer Consortium (VICC), in partnership with CGC, CIViC, and ClinGen, the meeting aimed to develop community consensus on data standards for the interpretation of cancer variants and to enhance interoperability resources. Learn more in a GA4GH guest blog post by VICC lead Alex Wagner, and view the event’s meeting minutes.
• On 12 August, the Cancer Community met, featuring a presentation from CSIRO on its work using large language models to make health APIs more accessible. They also shared a demonstration of their serverless Beacon implementation, which can be viewed in the Cancer Community meeting minutes.

Coming up next

• The Cancer Community will be hosting a Connect session at the 12th Plenary meeting focusing on Cancer Data Commons. The session will explore lessons learned from existing data commons, with a focus on the implementation of GA4GH standards. The session will then shift to exploring the critical components and unique features of data commons, including user requirements, data access, and minimal data models.
• Following this Connect session, the Cancer Co-Leads are looking to launch a Study Group dedicated to Cancer Data Commons, leveraging current work taking place across the broader GA4GH community in different geographical contexts.
• The community also has several topics for future investigation, such as automating the matching of patients to clinical trials. There are currently no standards to inform a protocol but several initiatives around the world are tackling this challenge in their specific contexts. The Cancer Community is looking at how it might serve as a convening body for these initiatives and support the development of standards in this topic area.

Rare Disease Community of Interest
Meeting minutes
The GA4GH Rare Disease Community (RD Community) is a forum for researchers, clinicians, and technical experts to define, discuss, and advance real-world rare disease use cases through the implementation of GA4GH interoperability standards. Bringing together rare disease genomics projects interested in data infrastructure, management, analysis, and sharing, the RD Community is uniquely positioned to bridge the gap between the clinical and technical rare disease communities.

Key achievements

• RD Community Co-Leads Tudor Groza and Nicole Vasilevsky published a GA4GH guest blog post about global organisations working to promote effective data sharing across the rare disease landscape.

Coming up next

• The Rare Disease Community will hold a session at the September Connect 2024 meeting. The group aims to discuss development of a rare disease portfolio showcasing how GA4GH standards can be applied to rare disease use cases. This resource will be helpful for outreach and engagement with other rare disease initiatives

Neuroscience Community of Interest
Meeting minutes
The Neuroscience Community aims to promote global cooperation, data sharing, and collaborative research in neuroscience. This is achieved through facilitating inter-institutional scientific collaborations, sharing best practices and governance models, and promoting adoption of standards for data sharing and federated analyses. The ultimate goal is to advance research and benefit patient communities worldwide.

Key achievements

• A collaboration between GA4GH, INCF, BRIDGE, and OBI, the Neuroscience Community held its inaugural meeting at GA4GH April Connect 2024 in Ascona, Switzerland, to introduce the community, outline its mission, and present planned initiatives.
• Three cross-initiative teams are currently developing projects in the areas of data harmonisation, data governance, and scientific partnerships and education. These focus areas were identified through initial exploratory meetings held at the end of 2023.

Coming up next

• The Neuroscience Community will host its second meeting at the BRIDGE Global Workshop in Austin, Texas, on September 23. This event will provide an opportunity for theme teams to present project updates, engage with the community, and outline future plans. If you are interested in joining virtually, email Melanie Collier for further details.

Other activities

Equity, Diversity, and Inclusion (EDI) Advisory Group
EDI meeting minutes
The Equity, Diversity, and Inclusion (EDI) Advisory Group aims to examine and address equity, diversity, and inclusion within the GA4GH community.

Key achievements

• The goals outlined in the EDI Strategic Plan have been finalised, reflecting valuable feedback received during the public comment period.
• The community has completed a voting exercise to prioritise the goals of the strategic plan. The results will help determine the timeline to address each goal.

Coming up next

• The next EDI meeting is scheduled for the end of the year — exact date to be determined.
• Publication of the strategic plan and its timeline is slated for the beginning of 2025. Staff are actively incorporating community priorities as they develop the implementation timelines.

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Technical Alignment Subcommittee (TASC)
TASC meeting minutes
The Technical Alignment Subcomittee’s (TASC) mission is to aid in the harmonisation of aspects of GA4GH's products to ensure that they can be used together effectively. TASC provides mechanisms and recommendations to create internal consistency and technical alignment across GA4GH Work Streams and products. While TASC functions as a central decision-making body, all of its decisions are informed by relevant stakeholders. The work of TASC, including all documentation and decisions, is regularly and openly communicated back to the GA4GH community.

Key achievements

• TASC recently voted on v4.0 of the Pagination guide, with no major objections. Some additional comments will be resolved before publishing. 
• TASC has made significant progress on developing supporting materials for citing GA4GH standards (GitHub issue #39). A DOI generator is now available from the GA4GH tech team!
• The Passports protocol is now registered in IANA.

Coming up next

• The team is continuing to work on the following GitHub issues:

• standardising API implementation optional capabilities;
• persistent url policy;
• IANA and media types registry.

• In collaboration with the GA4GH communications and web teams, TASC aims to develop a webpage on the GA4GH website to host TASC outputs.
• TASC will be hosting and supporting several Connect session at the September Connect meeting, including:

• Identifying challenges to interoperability and gaps in GA4GH standards;
• GA4GH product lifecycle.