Australian Genomics

Australian Genomics is preparing Australia to embed genomic medicine into mainstream healthcare, by providing the evidence needed to transform the diagnostic process, inform the healthcare workforce, and to show how genomics is best delivered in the clinical setting. As a federated system, Australian Genomics unites 80 organizations, including clinical and diagnostic genetics services along with research and academic institutions. Four main infrastructural programs - diagnostic and research network, data federation and analysis, evaluation policy and ethics, and workforce and education - support clinical flagship projects in rare disease, cancers and reproductive carrier screening. Approximately 25,000 patients participate in these flagships.

Data Types: WGS, WES, RNAseq and panels

BIPMed

BIPMed aims to be the reference on the implementation of precision medicine in Brazil, and the catalytic element fostering collaboration between different stakeholders (scientists, physicians, health authorities, policy makers and the public). BIPMed is hosted at UNICAMP, but is an alliance of 5 research, innovation and dissemination centers - BRAINN, CCES, CTC, CRID and OCRC. To date, there are approximately 1000 Brazilians in BIPMed’s online genome databases for epilepsy, craniofacial abnormalities, beta thalassemia, hereditary hearing loss, neurofibromatosis and BRCA1/2. These databases are the first of their kind in Latin America. BIPMed is actively involved with government and non-government task forces working to regulate privacy issues related to health records and public data sharing. As technologies are implemented, BIPMed is looking for recommendations of tools for data sharing (ie. options for sharing information of variants).

Data Types: Whole Exome Sequencing (Illumina), SNP microarrays (Affymetrix)

Genome Canada’s Precision Health Strategy - Canadian Genomic Partnership for Rare Disease (CGP4-RD)

The goal of CGP4-RD is to ensure access to clinical genome-wide sequencing as a standard of care for Canadians at risk for a rare genetic condition and who would benefit from diagnosis and/or timely and effective intervention. This initiative lays the foundation for precision health in Canada, and emphasizes developing tools and policy that will improve clinical utility, cost efficiency and equitable access to genomic testing. CGP4-RD consists of a network of independent clinical sites at paediatric hospitals with a central policy and data coordinating functionality to promote harmonized data sharing. CGP4-RD is open to partnerships with other National Initiatives to share best practices and coordinate resources to achieve common objectives more effectively.

Data Types: Clinical, phenotypic, genomic and economic data. Data systems will be federated.

GA4GH Standards Implemented: While each of the clinical sites have already implemented GA4GH standards to varying levels, the broader initiative has not yet decided on general standards for harmonization.

Genome Medical Alliance Japan (GEM-Japan)

The GEM-J project aims at the harmonization of our established projects with the international standards for the genome based health system and the promotion of sharing our Japanese genomic and phenotypic information with global community. The projects include a nation-wide collection of disease associated variants (MGeND) and large-scale cohort-based biobanks - Biobank Japan and Tohoku Medical Megabank maintain 270,000 patients with ~50 adult common diseases and 157,000 healthy individuals, respectively.

Data Types: Genomic and phenotypic information, HLA genotype, pathogenic variants and allele frequencies

GA4GH Standards Implemented: Human Phenotype Ontology (HPO), Patient Archive (PA), Beacon, Common Workflow Language (CWL)

Swiss Personalized Health Network (SPHN)

SPHN is a national initiative designed to promote the development of personalized medicine, with the ultimate goal of preventing, diagnosing and treating unfavourable health conditions more precisely. It is a federated initiative linking existing projects and organizations aiming to create a national IT infrastructure for biomedical research and establish interoperability of health data by developing and implementing standards for responsible data sharing. The SPHN is active in ELIXIR, and is participating in implementation studies involving GA4GH standards in this context.

Data Types: Developing information management infrastructure at University hospitals and academic centres to allow for the exchange of patient and research data - ie. disease phenotypes, -omics data

GA4GH Standards Implemented: WES/TES where necessary, Beacon to be implemented in SPHN resources and driver projects (ie. SVIP), EGA implementations (Swiss EGA; evaluation of Federated EGA).

NIH All of Us Research Program

The mission of All of Us is to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment and care for all Americans. Data will be gathered from 1 million or more people living in the United States, without focusing on a specific disease or population. The All of Us program has partnered with the Mayo Clinic Biobank, technology centers, healthcare provider organizations and genomic centers across the nation to recruit, collect and analyze data.

Data Types: Lifestyle, environmental and biological (blood, urine, saliva samples), Physical Measurements, Electronic Health Record, WGS (forthcoming), and Genotyping (forthcoming)

Genomics England 

Genomics England was set up by the UK Department of Health and Social Care to deliver the UK’s 100,000 genomes project from NHS patients with a rare disease and their families, and patients with cancer. The sequencing milestone of 100,000 genomes was reached in December 2018; the return of results to patients will still be underway throughout 2019. In October 2018, it was announced that the 100,000 Genomes Project would be superseded with 500,000 whole genomes commissioned through routine clinical testing in the NHS as part of the newly created NHS Genomic Medicine Service. A centralized informatics and logistic infrastructure was established for the delivery of WGS diagnostic services. 13 regional NHS Genomic Medicine Centres representing 85 NHS trusts were established to acquire consent, enrol participants, collect samples and interpret findings. This infrastructure is being updated with a National Genomic Informatic Service to support the Genomic Medicine Service.

Genomics England makes the linked genetic and health record data available to both researchers and industry. Research access is coordinated via the Genomics England Clinical Interpretation Partnership (GeCIP), where more than 3000 researchers participate in either disease-facing or functional groups also called ‘domains’..

Data Types: WGS, primary and secondary clinical information. Samples for other omics-analyses in the bank but not yet produced.

CanDIG

ClinGen is building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. The main goals are to support the deposition of genomic and health data and curated knowledge into the public domain by all stakeholders, including patients, clinicians, laboratories and researchers, develop methods and infrastructure to answer critical questions of the data (curation), and create a genomic knowledge base that makes information available for improved patient care. ClinGen has over 850 Working Group and Expert Panel members from over 230 institutions from over 27 countries. It maintains a close partnership with NCBI’s publicly available ClinVar database for sharing variant classification and associated evidence. Numerous tools have been developed to support curation, including Gene and Variant Curation Interfaces as well as GenomeConnect, a patient registry for anyone who has had genetic testing, and consent resources consistent with the GA4GH Framework for Responsible Sharing of Genomic and Health-Related Data.

ClinGen

ClinGen is building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. The main goals are to support the deposition of genomic and health data and curated knowledge into the public domain by all stakeholders, including patients, clinicians, laboratories and researchers, develop methods and infrastructure to answer critical questions of the data (curation), and create a genomic knowledge base that makes information available for improved patient care. ClinGen has over 850 Working Group and Expert Panel members from over 230 institutions from over 27 countries. It maintains a close partnership with NCBI’s publicly available ClinVar database for sharing variant classification and associated evidence. Numerous tools have been developed to support curation, including Gene and Variant Curation Interfaces as well as GenomeConnect, a patient registry for anyone who has had genetic testing, and consent resources consistent with the GA4GH Framework for Responsible Sharing of Genomic and Health-Related Data.

Matchmaker Exchange (MME)

The main goal of MME is to facilitate the discovery of novel disease genes causing Mendelian conditions. MME is a federated platform that uses a standardized application programming interface and procedural conventions to match cases with the same candidate genes and enable evaluation of phenotype overlap to build evidence for candidate genes implicated in rare disease. To date, there has been data from over 130,000 rare disease patients submitted from 84 countries, with over half of the cases containing flagged candidate genes (>10,000 unique genes) available for matching on the MME platform. This platform has led to rapid advances in discovering the genetic causes of rare disease and other groups/countries are invited to participate, either through setting up their own node or depositing candidates in an existing node.

ELIXIR

ELIXIR is an intergovernmental federated organization that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and computing infrastructure. ELIXIR works by a hub and spoke model; the Hub is based in Cambridge at the Wellcome Genome Campus, and there are 23 connected Nodes that provide a range of bioinformatics services. Nodes range from a single institution (e.g. EMBL-EBI, or CSC in Finland), to many (e.g. the Italian Node contains 16 distinct institutions). In total there are over 250 institutions that are part of ELIXIR. The goal of ELIXIR is to coordinate these resources into a coherent ecosystem. The availability of a coordinated infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. In March 2019, an ELIXIR-GA4GH Strategic Partnership was announced as the next phase of collaboration. ELIXIR has implemented all approved GA4GH standards.

Human Heredity & Health in Africa (H3Africa)

The vision of H3Africa is to create and support a pan-continental network of laboratories that will be equipped to apply leading-edge research to the study of the complex interplay between environmental and genetic factors which determine disease susceptibility and drug responses in African populations. Data generated from this effort can inform strategies to address health inequity and ultimately lead to health benefits in Africa. To date, there are 51 projects taking place in 34 African countries, with a focus on cancer, rare disease, infectious disease, neurological disease, cardiovascular disease and other complex diseases. Collectively, up to 100,000 African individuals participate in these projects. H3Africa has developed a new African genotyping array, a standardized CRF for core phenotypes and a catalogue for searching samples and data from cohorts across multiple diseases and countries.

European Joint Programme on Rare Diseases (EJP-RD) 

EJP-RD aims to improve the integration, efficacy, production and social impact of research on rare disease through the development, demonstration and promotion of Europe-wide and even world-wide sharing of research and clinical data, materials, processes, knowledge and know-how. Additionally, EJP-RD aims to implement and further develop an efficient model of financial support for all types of research on rare disease (fundamental, clinical, epidemiological, social, and economic) coupled with accelerated exploitation of research results for the benefit of patients. The potential of already funded tools, projects, and programmes will be maximized by supporting them further, scaling them up, linking them together, and adapting them to the needs of end-users through implementation tests in real settings. There are 33 European and associated countries participating in EJP-RD and contributing to resources like Orphanet, DECIPHER, RD-Connect, Metabolights, Cellosaurus and Cafe Variome.

World Economic Forum

The World Economic Forum is the international organization for public-private cooperation. The Forum engages the foremost political, business and other leaders of society to shape global, regional and industry agenda. Two years ago, the Forum created the Centre for the Fourth Industrial Revolution (C4IR) in San Francisco, CA to act as a hub for global, multistakeholder cooperation to develop policy frameworks and advance collaborations that accelerate the benefits of science and technology. Precision medicine is one of the nine areas of focus at the C4IR, with a dedicated precision medicine policy team advancing new policy frameworks to accelerate the adoption of a precision medicine approach to the diagnosis and treatment of disease. Project areas being led by this team include: generating evidence of precision medicine’s effectiveness; data-sharing and related infrastructure; integrating a precision medicine approach into clinical practice; new approaches to regulation, pricing and reimbursement for diagnostics and treatment; and patient and public engagement.