CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis

Dursi, L. J.; Bozóky, Zoltán; Borja, Richard de; Li, Haoyuan; Bujold, David; Lipski, Adam; Rashid, Shaikh; Sethi, Amanjeev; Memon, Neelam; D, Naidoo; F, Coral-Sasso; Wong, Matthew L.; Quirion, P-O; Lu, Zhibin; S, Agarwal; Pavlov, Yu. V.; Ponomarev, Andrew; Husić, Mia; Pace, Krista; Palmer, Samantha; Grover, Stephanie A.; Hakgor, Sevan; Siu, Lillian L.; Malkin, David; Virtanen, Carl; Pugh, Trevor J.; Jacques, Pierre-Étienne; Joly, Yann; Jones, Steven J.M.; Bourque, Guillaume; Brudno, Michael

doi:10.1016/j.xgen.2021.100033

Cited by 13 publications

(7 citation statements)

References 13 publications

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“…The HostSeq Variant Search Portal ( https://hostseq.ca/dashboard/variants-search ) allows for queries of the HostSeq genetic data. The primary querying functionality is supported by the CanDIG-server [ 39 ], a platform enabling federated querying of genomics data. Beacon APIs [ 40 ] from the Global Alliance for Genomics and Health (GA4GH) are also built-in to allow HostSeq to join the federated Beacon network.…”

Section: Resultsmentioning

confidence: 99%

HostSeq: a Canadian whole genome sequencing and clinical data resource

Garg

Elliott

et al. 2023

BMC Genom Data

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HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

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Section: Resultsmentioning

confidence: 99%

HostSeq: a Canadian whole genome sequencing and clinical data resource

Garg

Elliott

et al. 2023

BMC Genom Data

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“…In Canada, each province has its own health data privacy legislation such that data generated in each province must follow provincial governance laws. The Canadian Distributed Infrastructure for Genomics (CanDIG) platform is tackling this with a fully distributed federated data model, enabling federated querying and analysis while making sure that local data governance laws are respected ( Dursi et al, 2021 ).…”

Section: Overcoming Secure Data Sharing Via Federa...mentioning

confidence: 99%

“…ELIXIR is further participating in the Beyond 1 Million genomes (B1MG) 2 , which aims to create a network of clinical and genomic data across Europe. At a global level, the Common Infrastructure for National Cohorts in Europe, Canada, and Africa (CINECA) project is working to federate data between cohorts and across continents ( Dursi et al, 2021 ). Through employing federated architectures, each of these initiatives allow organizations to store and manage their data locally while researchers worldwide can access the data securely.…”

Section: Overcoming Secure Data Sharing Via Federa...mentioning

confidence: 99%

Democratizing clinical-genomic data: How federated platforms can promote benefits sharing in genomics

Alvarellos¹,

Sheppard²,

Knarston³

et al. 2023

Front. Genet.

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Since the first sequencing of the human genome, associated sequencing costs have dramatically lowered, leading to an explosion of genomic data. This valuable data should in theory be of huge benefit to the global community, although unfortunately the benefits of these advances have not been widely distributed. Much of today’s clinical-genomic data is siloed and inaccessible in adherence with strict governance and privacy policies, with more than 97% of hospital data going unused, according to one reference. Despite these challenges, there are promising efforts to make clinical-genomic data accessible and useful without compromising security. Specifically, federated data platforms are emerging as key resources to facilitate secure data sharing without having to physically move the data from outside of its organizational or jurisdictional boundaries. In this perspective, we summarize the overarching progress in establishing federated data platforms, and highlight critical considerations on how they should be managed to ensure patient and public trust. These platforms are enabling global collaboration and improving representation of underrepresented groups, since sequencing efforts have not prioritized diverse population representation until recently. Federated data platforms, when combined with advances in no-code technology, can be accessible to the diverse end-users that make up the genomics workforce, and we discuss potential strategies to develop sustainable business models so that the platforms can continue to enable research long term. Although these platforms must be carefully managed to ensure appropriate and ethical use, they are democratizing access and insights to clinical-genomic data that will progress research and enable impactful therapeutic findings.

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“…The World Economic Forum has recently published a guideline document that focuses on sharing of sensitive health data in a federated consortium model considering the post-COVID-19 world [16]. Large-scale projects, such as the Global Alliance for Genomics and Health [17]; Canadian Distributed Infrastructure for Genomics [18]; Common Infrastructure for National Cohorts in Europe, Canada, and Africa [19]; and European Health Data and Evidence Network [20] projects, have laid out principles and frameworks supporting safe use of patient data [17,21]. While federated academic tooling (software that works on federated data sets) exists [22][23][24][25], the commercial sector appears to have more capability than the best in academia [26][27][28].…”

Section: Introductionmentioning

confidence: 99%

A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study

et al. 2022

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Background COVID-19 data have been generated across the United Kingdom as a by-product of clinical care and public health provision, as well as numerous bespoke and repurposed research endeavors. Analysis of these data has underpinned the United Kingdom’s response to the pandemic, and informed public health policies and clinical guidelines. However, these data are held by different organizations, and this fragmented landscape has presented challenges for public health agencies and researchers as they struggle to find relevant data to access and interrogate the data they need to inform the pandemic response at pace. Objective We aimed to transform UK COVID-19 diagnostic data sets to be findable, accessible, interoperable, and reusable (FAIR). Methods A federated infrastructure model (COVID - Curated and Open Analysis and Research Platform [CO-CONNECT]) was rapidly built to enable the automated and reproducible mapping of health data partners’ pseudonymized data to the Observational Medical Outcomes Partnership Common Data Model without the need for any data to leave the data controllers’ secure environments, and to support federated cohort discovery queries and meta-analysis. Results A total of 56 data sets from 19 organizations are being connected to the federated network. The data include research cohorts and COVID-19 data collected through routine health care provision linked to longitudinal health care records and demographics. The infrastructure is live, supporting aggregate-level querying of data across the United Kingdom. Conclusions CO-CONNECT was developed by a multidisciplinary team. It enables rapid COVID-19 data discovery and instantaneous meta-analysis across data sources, and it is researching streamlined data extraction for use in a Trusted Research Environment for research and public health analysis. CO-CONNECT has the potential to make UK health data more interconnected and better able to answer national-level research questions while maintaining patient confidentiality and local governance procedures.

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CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis

Cited by 13 publications

References 13 publications

HostSeq: a Canadian whole genome sequencing and clinical data resource

HostSeq: a Canadian whole genome sequencing and clinical data resource

Democratizing clinical-genomic data: How federated platforms can promote benefits sharing in genomics

A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study

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