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Learn how GA4GH helps expand responsible genomic data use to benefit human health.
The Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting was held from 22 to 23 September 2022 at the CosmoCaixa in Barcelona, Spain.
The 10th Plenary brought together organisations and stakeholders from the genomics and health community for two days of keynotes, talks, and workshops on genomic and clinical data sharing issues that pervade a diverse cross-section of industries, disciplines, and communities.
Attendees learned about GA4GH’s technical standards and policy frameworks, which aim to break down the many barriers to data sharing and advance genomic research. View the meeting report below and watch the videos on YouTube.
Table of Contents
Day 1 (22 September)
Opening remarks
Ewan Birney (EMBL-EBI) and Ester Morales (Generalitat de Catalunya)
Birney and Morales kicked off the 10th plenary meeting, welcoming over 200 attendees from more than 25 countries.
Updates from GA4GH
Peter Goodhand (GA4GH)
Goodhand provided an overview of GA4GH, from the organisation’s mission to how it works. Goodhand shared a few updates from GA4GH, including the announcement of the newly formed GA4GH Inc. Board of Directors, progress from the GA4GH Work Streams and products coming down the pipeline, and the GA4GH Starter Kit.
Spotlight on GA4GH technical standards and policies (Part 1)
Genomic knowledge standards advancements
Larry Babb (Broad Institute of MIT & Harvard)
Computable standards for sharing and evaluating genomic variation information can help evaluate the bottleneck caused by manual, time-intensive reviews. Babb discussed progress and future plans on the Variation Representation Specification (VRS), a GA4GH standard that aims to model genomic knowledge statements in a machine-readable way.
Discovering cases and variants: Beacon v2
Jordi Rambla (Center for Genomic Regulation)
Rambla provided an overview of the evolution of Beacon — a standard that helps the research community discover information on variants. In its initial concept, Beacon served as an easy entrypoint to securely share information about genomic data. The release of Beacon v2.0 expands upon this model, providing a more flexible and robust framework when querying a network and aligning with other standards.
REWS Consent Toolkit: A decade of consent harmonisation
Beatrice Kaiser (GA4GH)
Kaiser discussed the importance of streamlining and simplifying consent language when drafting consent forms — ultimately benefiting researchers, patients and participants, and review committees. The GA4GH Consent Toolkit aims to promote harmonisation and interoperability by providing a series of template clauses and standard language that the research and health community can reference when writing consent forms.
GA4GH and the Genetic Discrimination Observatory: developing tools to prevent genetic discrimination from impeding data sharing initiatives
Yann Joly (McGill University)
Joly emphasised the importance of developing tools and resources to address genetic discrimination. Doing so can promote clear and harmonised information for both researchers and patients, limit the risk of genetic discrimination for patients and participants, and foster international consensus on best approaches to prevent genetic discrimination. Joly outlined GA4GH’s future plans to address this topic.
Spotlight on GA4GH technical standards and policies (Part 2)
GA4GH Passport and AAI OIDC profile
Marin Kuba (ELIXIR Cloud & AAI for Human Data)
Kuba shared the latest updates on Passports v1.2, including changes to simplify terminology and redefine a passport as a token holding a researcher’s data access permissions. Future plans include adding a new type of token — Work Order Tokens — for Passports v2.0.
Aligning the NIH data use limitations to the GA4GH DUO standard
Elena Ghanaim (NIH NHGRI)
Ghanaim discussed the NIH’s project to conduct an empirical evaluation of the parity of data use limitations of NIH datasets with GA4GH’s Data Use Ontology (DUO) standard. Through this project, the team aims to develop policy recommendations for synergising the NIH data use limitations with DUO.
Security Task Force updates
Lucila Ohno-Machado (UC San Diego)
Ohno-Machado shared updates from the GA4GH Data Security Work Stream. One of their upcoming projects is Malfeasance rules, which aims to detect when a researcher is trying to inappropriately drill down on an individual’s information from a larger dataset. The team also aims to develop guides to better help groups audit how their data is being used.
Learning from CRAM
Geraldine van der Auwera (Broad Institute of MIT and Harvard)
Van der Auwera gave an overview of the GA4GH Large Scale Genomics Work Stream’s standards, before focusing in on the CRAM file format for genomic data compression. Van der Auwera used CRAM’s story as an example of engaging the community of developers, engineers, and data generators to ultimately drive community adoption and usage of the standard — a lesson that can be applied to building any standard, and getting people to use it.
Fireside chat
Heidi Rehm (Broad Institute of MIT and Harvard), Chris Wigley (Genomics England), Arcadi Navarro (Universitat Pompeu Fabra)
GA4GH Vice-Chair Heidi Rehm spoke with guests Mr. Chris Wrigley, CEO of Genomics England, and Dr. Arcadi Naarro, professor of genetics and lecturer at the Universitat Pompeu Fabra. The three discussed topics around the responsible sharing of genomic and health data and how best to link academia, industry, and healthcare.
Highlights from the expanding GA4GH network
Facilitating African data sharing and access
Nicola Mulder (University of Cape Town)
Mulder discussed the data ecosystem in Africa, and goals to make H3Africa’s data FAIR (findable, accessible, interoperable, and reusable), improve access to curated African data, and expand the African Open Data Science Platform, which runs on several GA4GH APIs.
Korea’s national genomics strategy: the National Project of Bio Big Data
Soo-Yong Shin (Kakao Health)
Bio big data is key to realising the promise of precision medicine. Shin discussed the goals and plans of Korea’s National Project of Bio Big Data, which includes the establishment of a national research cohort, recruiting one million Korean volunteers from hospitals and health exam centers, and collecting genomic, health, and real-world data about an individual.
Advancing genomics medicine sustainably and responsibly
Ariel Pradipta (Genomik Solidaritas Indonesia)
Pradipta discussed the genomics ecosystem in Indonesia, beginning with sequencing SARS-COV2 to expanding the genomics program to build a Biomedical and Genome Science Initiative that will include a biobank, registry, and bioinformatics platforms. Pradipta discussed plans to accelerate cross-platform genome sequencing and building capabilities, translating genomic data into health transformation, and building actionable genomic big data and bioinformatics.
New developments at European initiatives
Genomics: EU policy perspective
Szymon Bielecki (DG CNECT)
Bielecki provided an overview of the European Union’s goals and policy perspectives on genomics, sharing updates on projects such as the 1+Million Genomes EU initiative (1+MG), European Cancer Imaging Initiative, AI and medical imaging, Digital Twins for Health, AI for genomics and personalised medicine, and other pilot projects.
The IMPaCT program
Rosario Perona (Instituto de Salud Carlos III)
Perona discussed Spain’s strategy for personalised medicine, driven by IMPaCT: the Infrastructure for Personalised Precision Medicine based on Science & Technology. IMPaCT aims to carry out its mission by focusing on three programs — predictive medicine, genomic medicine, and data science.
The Federated EGA: global discovery and access for sensitive human data
Mallory Freeberg (EMBL-EBI)
The Federated European Genome-Phenome Archive (FEGA) project aims to support the discovery of and secure access to human data globally, while respecting national data protection regulations, with the goal of accelerating disease research and improving human health. Freeberg shared updates on the initiative, which now has over 24 countries engaging in the network, 5 collaboration agreements signed, and several GA4GH standards deployed.
The 1+MG initiative
Giovanni Tonon (University Vita-Salute San Raffaele)
Tonnon discussed the 1+Million Genomes (1+MG) and Beyond One Million Genomes (B1MG) projects, which together aim to realise the practice of personalised medicine in health. Tonon then dove into the projects’ aims: to establish a platform for cross-border access to genomic health datasets and develop a framework for sharing and linking phenotypic and clinical metadata with genomic information.
Day 2 (23 September)
GHIF: supporting uptake of GA4GH standards
Augusto Rendon (Genomics England)
Rendon shared updates from the Genomics in Health Implementation Forum (GHIF), which convenes global genomics in health initiatives from around the world to learn from each other, supports implementation of GA4GH standards, and develops pilot projects to address practical needs. GHIF recently held a Newborn Sequencing Workshop and developed pilot projects in sharing curation efforts and standardising quality control of whole genome sequencing,
Keynote address:
Challenges for implementing of genomics in Africa
Michèle Ramsay (University of the Witwatersrand)
In this keynote presentation, Ramsay addressed the barriers and opportunities to implementing genomics in Africa. These include pathways to data standardisation and harmonisation, building infrastructure to enable data sharing in genomics, and addressing the skills gap through training, retention of data scientists, and institutional support. Ramsay emphasised the importance of conducting research in the location where precision medicine will be implemented.
GA4GH in action: end-to-end and cross-platform implementations
A starter kit for interoperable genomic knowledge
Alex Wagner (Nationwide Children’s Hospital)
Wagner discussed how computable standards —such as the Variation Representation Specification — can help alleviate the bottleneck involved in accurately representing and sharing variation information. To lower barriers to adoption, Wagner shared a comprehensive roadmap on efforts to support the implementation of VRS.
Leveraging GA4GH standards for trans-continental federated analysis
Thomas Keane (EMBL-EBI)
Across the world, numerous longitudinal and disease-specific population cohorts have emerged. CINECA aims to enable interoperability and access to these datasets across borders, accelerating research and improving human health. Keane discussed key updates from CINECA, including developing infrastructure to enable an ecosystem for federated analysis.
GA4GH in action: Amazon Genomics CLI and GA4GH WES
Lee Pang (Amazon)
While huge challenges exist to leveraging genomics data, doing so can catalyze personalized health. Pang discussed how Amazon Web Services (AWS) can address certain challenges, from data transfer and storage to workflow automation. Pang shared a use case of how AWS can work together with the GA4GH Workflow Execution Standard (WES) to enable portable genomic analysis.
The NIH Cloud Platforms Interoperability (NCPI) Efforts
Valentina di Francesco (NIH NHGRI)
Di Francesco provided an update on the NIH Cloud Platform Interoperability (NCPI) effort, which aims to establish and implement guidelines and technical standards for a trans-NIH federated data ecosystem. Di Francesci shared the GA4GHs standards that will help realize this vision, along with a roadmap that will incorporate several scientific use cases.
Lessons learned from COVID and infectious disease data sharing
COVID-19 data sharing: a perspective from the Fiocruz genomic network
Gabriel Wallau (Fiocruz)
Wallau provided an overview of the Fiocruz genomic network based in Brazil, diving into the process of building trust with local partners, fostering accountability when sharing data, and having a communication strategy for the public and media.
Reproducible, transparent and customizable viral genomics with Galaxy
Wolfgang Maier (University of Freiburg)
Maier discussed how Galaxy — an open, web-based platform for reproducible, transparent, and accessible computational research — has been leveraged for genomic analysis of SARS-CoV-2 data. Maier walked through a sample use case, highlighting that workflows are easily customizable, shareable, and scalable.
Towards an internet for pandemic surveillance powered by GA4GH standards
Marc Fiume (DNAstack)
To address the COVID-19 pandemic, Fiume discussed the importance of building a global network for sharing genomics and related data on pathogens in real time. These efforts culminated in DNAstack’s Viral AI — four products, each powered by certain GA4GH standards, that together enable a federated network for infectious disease research.
Regulatory impacts on data sharing around the world
Developing a new culture: NIH data management & sharing (DMS) policy
Jaime Guidry Auvil (NIH NCI)
Guidry Auvil shared updates on the NIH’s policy for data management and sharing, to be implemented in 2023. Its vision, to share scientific data supported by the NIH broadly and immediately, will apply to all NIH-supported research that generates scientific data. Under the policy, investigators must share plans to manage and share data and agencies must make publications and supporting data from federally funded research free and publicly accessible.
Genomic data sharing in the EU: legal frameworks and interpretations in flux
Adrian Thorogood (University of Luxembourg)
Thorogood discussed the landscape of genomic data sharing in the European Union, in relation to the General Data Protection Regulation (GDPR). Thorogood dove into the competing interpretations of the GDPR and the complexities involved in data processing chains.
Global regulatory implications on data sharing: a perspective on the impact that the current and future regulatory landscape data sharing in Latin America
Fabiana Arzuaga (University of Buenos Aires)
Arzuaga discussed the global regulatory implications on data sharing, diving into different legal frameworks adopted by countries in Latin America and current practices in data sharing. Arzuaga concluded with challenges to data sharing, including the importance of understanding why researchers may not want to share their research data, finding ways to promote and incentivise data sharing, and developing a framework for secondary use of clinically-acquired data.
AI for genomics: successes, challenges, and future directions
Genomic medicine in the machine learning era
Gerardo Jiménez-Sánchez (Genomica Medica)
While Artificial intelligence (AI) can improve efficiency of decision making, save costs, and enable better resource allocation, it also raises serious questions, such as reinforcing existing biases or infringing on human rights and values. Jiménez-Sánchez discussed AI and deep learning applications in genomics, discussing its potential to assist in a variety of use cases, from accurately identifying genetic disorders to detecting cancer.
Exploring the societal implications of AI and genomics
Harry Farmer (Ada Lovelace Institute)
Farmer focused on the ethical and societal challenges posed by AI-powered genomics, ensuring that data and AI work for people and society. Farmer shared that with AI-powered genomics, certain challenges may still persist, such as problems with missing data and bias, and some challenges may become more profound, such as interpretability and accountability.
AI driven multi-modal target identification: from bedside to bench
Khalil Ouardini (Owkin)
A central question that patients, physicians, and drug developers are asking is: why do some patients respond well to drugs while others don’t? Ouardini discussed how the Owkin Platform aims to use federated learning and advanced AI to deliver on precision medicine. Ouardini emphasized the importance of leveraging multimodal approaches in developing predictive AI biomarkers and fusing clinical, pathology, and molecular data into a unified predictive framework.
Keynote address:
Accelerating access to genomics for global health
Soumya Swaminathan (World Health Organization)
In this keynote address, Swaminathan discussed the World Health Organization (WHO) Science Council’s aim to accelerate access to genomics for global health. This mandate rests on four key goals: 1) to promote the adoption or expanded use of genomics in all member states; 2) identify and overcome the practical issues that impede the implementation of genomics; 3) foster commitments to collaborative activities; and 4) promote ethical, legal, and equitable use.
Closing remarks
Peter Goodhand (GA4GH)
Goodhand closed the meeting with a few remarks, giving thanks to all speakers, the Programme Committee, and the Local Organising Committee. Goodhand also acknowledged our GA4GH funders and 10th Plenary Sponsors.
Acknowledgments
Core Funders
- Wellcome
- Genome Canada
- Medical Research Council
- Canadian Institutes of Health Research
- National Institute for Health Research
- National Institute of Health
Host Institutions
Supporting Funder
10th Plenary Diamond Sponsors
10th Plenary Gold Sponsors
10th Plenary Silver Sponsors
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