Developing a Collaborative Virtual Biobank to Support Infectious Disease Research

doi:10.21203/rs.3.rs-4826447/v1

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Developing a Collaborative Virtual Biobank to Support Infectious Disease Research

https://doi.org/10.21203/rs.3.rs-4826447/v1

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The COVID-19 pandemic has highlighted the importance of biospecimens in driving new research, disease understanding and the development of diagnostic tests and treatments. Many infectious disease studies collect samples in an isolated manner, meaning that sample numbers may be modest and unused biospecimens remain after studies address their original questions. We assembled a multidisciplinary team to develop a robust and adaptable technical infrastructure for a collaborative virtual biobank. We describe the implementation of the project, including the ethical and governance considerations, technical solutions and challenges encountered, to provide a detailed understanding of the development of a valuable research platform, the APPRISE Virtual Biobank.

infectious disease

research

collaboration

specimen management

governance

virtual portal

Biological sampling underpins a wide range of medical research, including biomarker discovery and fundamental immunology through to the development and evaluation of therapeutics and vaccines in clinical trials. With advances in genomics, vaccine development and delivery, metabolomics, microbiome research and imaging technologies among other areas, access to high-quality biological samples is integral to scientific progress. There have been huge advances in biobanking sophistication and scope in recent decades, particularly for large population-based collections (e.g., UK Biobank (Collins, 2012), the Finnish Maternity Cohort (Lehtinen, Surcel, Natunen, Pukkala, & Dillner, 2017), and Biobank Graz (Sargsyan et al., 2015) which contain millions of specimens from hundreds of thousands of donors, often accompanied by clinical data. In infectious disease research, however, sample collections are often more limited in scope and number, with limited sharing mechanisms for collaborative research drawing from diverse cohorts and communities.

Infectious disease research can address questions about both the pathogen and the host. Pathogen investigations can include genomics, phylodynamics and susceptibility to treatments or vaccines. Host investigations can address clinical symptoms, immune responses, other biomarkers and the impact of treatments or vaccines. A variety of samples are therefore of interest to infectious disease researchers, ranging from swabs and bodily fluids collected for diagnostic purposes, through to larger quantities of blood, tissue and derivatives of these samples including cell lines and genetic materials. For detailed cellular and immunological studies, the cells of interest can be extracted from blood using time-consuming and specialised protocols to generate peripheral blood mononuclear cells (PBMC) (Betsou, Gaignaux, Ammerlaan, Norris, & Stone, 2019). PBMC preparation for research use and storage requires collection by a trained provider, rapid processing and liquid nitrogen storage.

Donor consent for the collection and use of biological samples for research purposes provides an incentive for researchers to ensure their use (Bledsoe & Sexton, 2019; Eikemo, Roten, & Vaaler, 2022; Warner et al., 2018). PBMC are expensive to collect, process and store, providing an additional incentive for them to be well used. Maximising the use of these valuable samples should therefore be a priority, particularly where residual specimens exist after the primary research question has been addressed. Even small collections demonstrate significant engagement and effort on behalf of donors, investigators, study and lab staff and can potentially be used to address additional research questions. This potential is maximised when samples can be pooled across multiple collections, either increasing the overall sample size, increasing the sample diversity, or both (Clapham et al., 2020; Combs et al., 2016; He & Han, 2021).

Typically, each research study or collection has its own sample and data custodianship arrangements, and consequently different arrangements enabling access by outside collaborators and researchers. Where samples are collected outside of a large-scale biobank, custodianship arrangements may be unclear (particularly once a study has officially ‘closed’), or when they are known, the requirements for additional access may be undefined or not widely accessible. Given the high value of biological specimens, study investigators are naturally protective of their collections and the willingness to share can be variable.

Internationally, there has been significant progress in the development of harmonisation strategies and guidance for biobanks and repositories. The International Society for Biological and Environmental Repositories (ISBER) have recently released the Fifth Edition of their Best Practices: Recommendations for Repositories (Snapes et al., 2023), and the Biobanking and BioMolecular resources Research Infrastructure European Research Infrastructure Consortium (BBMRI-ERIC) have developed the Minimum Information About Biobank data Sharing initiative (MIABIS), now in its third iteration (Eklund et al., 2024).

We saw an opportunity to address some of the challenges of infectious disease biobanking through the development of the Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (APPRISE) Virtual Biobank (Smith et al., 2023). This approach addresses the distributed nature of infectious disease collections, providing a central touchpoint for researchers to discover available samples from multiple sources. The Virtual Biobank enables collections to retain their existing governance arrangements, providing assurance that access will remain under their control. In this paper, we detail the development of the ethical and technical infrastructure to enable near real-time searching of multiple biospecimen collections via a single online portal.

Engagement with participating collections

Investigators with known biospecimen collections were approached, with additional collections identified through word-of-mouth. For each collection, the formal Data Custodian, Secondary Data Custodian (where applicable) and Collection Manager were identified. A signed Data Custodian Form provided formal permission from the Data Custodian(s) for involvement in the APPRISE Virtual Biobank.

Project Governance

The project was overseen by a working group involving representatives from BioGrid Australia and The University of Melbourne, with regular advisory meetings with the participating Data Custodians and Collection Managers. The Virtual Biobank protocol, listing each participating collection, was approved by the Royal Melbourne Hospital Human Research Ethics Committee, HREC/78249/MH-2021-292485. Site-specific approvals were sought at each collection site, involving formal study agreement/s (we used the Medicines Australia Clinical Trial Agreement for broad recognition, and some sites required an additional Data Transfer Agreement) plus any required IT approvals as determined by each participating site.

Technical approaches

Once permission was granted from the Data Custodian, contact was made with the relevant collection Database Manager. Discussions between BioGrid Australia and the Database Manager clarified the relevant technical solution. This included identifying the available (or required) IT infrastructure, ensuring contact points for back-end Database access and defining the Extract, Transform and Load (ETL) process for the establishment of an on-site Structured Data Model Database (SDMD). The APPRISE Virtual Biobank web portal was developed using the latest Microsoft technology stack and an Application Programming Interface (API) implemented to interface with those at participating sites.

An extensive testing phase was completed prior to data integration to ensure seamless portal functionality once data was available. The technical team developed a test dataset based on the fields in the SDMD. This test dataset was populated with dummy data about studies, samples and collection contact points. A small group of project members were selected for extensive testing and were provided with a written document containing detailed test scenarios. The technical team then collected and addressed end user feedback on the portal design, usability and cross-platform compatibility.

The APPRISE Virtual Biobank system architecture and security

We collaboratively developed a technical solution for a robust, expandable and adaptable virtual biobank as detailed in Fig. 1. This solution enables semantic interoperability, where data can be shared and unambiguously understood across different projects, systems and organisations. The establishment of a Structured Data Model Database (SDMD) within the home institution online environment ensures that all data transformation and aggregation occurs behind the institutional firewall and before any access by outside users. User registration is required for access to the APPRISE Virtual Biobank, and all data queries are conducted through secure pathways and Application Programming Interfaces (APIs). The requirement for user registration ensures that Data Custodians know who is accessing any information about their samples, when, and whether the query resulted in contact for further information.

The technical architecture of the APPRISE Virtual Biobank results in a secure information flow about currently available specimens from participating collections. Queries entered in the portal by authenticated users are compressed, encrypted and sent via the Virtual Biobank API to the site APIs with a token. At the site API, the query is decompressed, unencrypted and authenticated to the site SDMD. The SDMD is queried, and aggregated results then encrypted and sent with a token back to the Virtual Biobank API. The Virtual Biobank API then aggregates the data from all relevant sites and displays these results to the user via the online portal.

A key feature of the Virtual Biobank is that no data from participating biospecimen collections is stored centrally, not even temporarily. All aggregated data is destroyed once the user session is ended, with only the User ID, IP address, search terms and time of query stored in the central Virtual Biobank database. This collection-specific query information is made available to Data Custodians via the portal. This provides an audit trail on web portal access and enables reporting on the research community’s interest in different sample collections within the portal.

The APPRISE Virtual Biobank portal and database are hosted by BioGrid Australia Ltd, a not-for-profit charity company owned by the Australian medical research sector. Data and ICT security at BioGrid have been developed with reference to the ISO/IEC 27000 series and COBIT5 framework.

Application of the APPRISE Virtual Biobank data model

The data model for the APPRISE Virtual Biobank is based on the Minimum Information About Biobank data Sharing (MIABIS) (Eklund et al., 2020; Norlin et al., 2012), using the MIABIS core terminology to create a Minimum Information Model as outlined in Table 1. The Minimum Information Model includes data about the participating biobank, the specific study and high-level sample collection data. There is no requirement for access to any identifiable information for collection participants.

Participating collections provided a data dictionary to enable the relevant fields in their database to be identified for transformation to the SDMD. Data fields were mapped using a sample data export from the collection database. Additional study information was sourced separately from Data Custodians.

APPRISE Virtual Biobank portal design and features

The APPRISE Virtual Biobank portal was designed to provide a simple user experience. Users access the portal via a login/registration page requiring multi-factor authentication. Once portal access is obtained, the user is directed to the portal homepage. The homepage includes a user menu, a summary dashboard providing an overview of collection participation and available sample numbers and brief portal usage instructions.

The Search page (see Fig. 2) provides expandable search category menus enabling collections to be searched by Biobank name, Location, Sample type, Disease, Study name, Principal Investigator name and Age range (indicated as Query fields in Table 1). Results are returned on the same page and can be sorted by query field as required (except for Study and Principal Investigator name). Each search result has a checkbox for contacting the Data Custodian, enabling the User to send an automated email direct from the portal to the Data Custodian to note their interest and enable further information on sample access to be provided.

Ethical and governance issues

Seven specimen collections have been engaged in the development of the APPRISE Virtual Biobank. These collections are distributed across five institutions in three Australian states, with a variety of database setups and governance approval solutions as summarised in Table 2. As of the end of June 2024, four of these collections are accessible via the APPRISE Virtual Biobank, with ongoing negotiations and arrangements in process for a further two collections. Accessible sample types and numbers for the four integrated collections are also reflected in Table 2. One collection has not been integrated due to prohibitive IT infrastructure costs, although governance and ethical approval have been obtained.

The project workflow to obtain ethical, governance and technical solutions for the APPRISE Virtual Biobank is summarised in Fig. 3. The overall project concept was formalised in a study protocol which was then submitted for ethics approval at the Royal Melbourne Hospital, the host institution of the BioGrid Australia network infrastructure being utilised for this project. Each participating collection was individually listed within the study protocol. Integration into the APPRISE Virtual Biobank required governance and technical solutions tailored for each site, depending on institutional resources and requirements.

We have developed a user friendly, adaptable virtual biobank platform for infectious disease specimen collections in Australia. We provide detailed descriptions of the technical design and process for the development of the Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (APPRISE) Virtual Biobank. The APPRISE Virtual Biobank provides a tangible example of a value-adding, collaborative approach to improve biospecimen access for existing, distributed biospecimen collections.

With the launch of the Virtual Biobank, we demonstrate the potential for drawing together existing infectious disease biospecimen collections in a central platform without requiring changes to ethical and governance arrangements. The Virtual Biobank provides near real-time details of specimens that may be available for further research, which has been promoted to the infectious disease research and response community (Smith et al., 2023). The Virtual Biobank is also a platform which can be further developed and expanded in response to future needs.

A key consideration for the development of the Virtual Biobank was the need to engage with collections within scope of their existing ethics and governance arrangements. This ‘light touch’ ethics approach meant that no changes were required to the ethics approvals for participating collections, which was a motivating factor for some Data Custodians. Despite this, site specific governance approvals were still rigorously applied, with some sites requiring additional approvals. Now that the Virtual Biobank has been established, it is easily expandable to additional collections using the current engagement model. We also have commenced discussion with both existing and potential Data Custodians about an expansion of the data available through the portal which may require future ethics and governance changes. The ‘light touch’ approach also very clearly leaves the existing governance processes in place for specimen access, addressing one of the key concerns of Data Custodians (i.e. ensuring that they retain control over who can access their specimens).

The virtual biobank concept is not new. Virtual biobanks have been implemented to draw together multiple collections within a single institution (Zhang et al., 2015), and to connect resources across multiple organisations, either nationally (Saginur et al., 2023) or internationally (Ongarello, Fernandez Suarez, & Betsou, 2022). These have typically been large collaborations focussed on samples for commercial applications (Ongarello et al., 2022; Watson, Clark, & Williams, 2021) or to support large co-ordinated sample collection efforts (Saginur et al., 2023), (Asperger et al., 2021). Virtual biobanks have been noted for their benefits to transparency and sample metadata curation, particularly in the context of specimens for use in diagnostic test development where sample provenance and quality assurance is critical (Ongarello et al., 2022; Watson et al., 2021). The APPRISE Virtual Biobank is novel in three key aspects: 1) it enables the integration of specimen collections within the context of (and in parallel with) their existing governance arrangements, 2) it provides a (near) real-time snapshot of available specimens and not just a catalogue of specimens available at the time of integration and 3) it includes specimen collections across a diversity of institutions and database setups.

The current iteration of the APPRISE Virtual Biobank is a proof-of-concept that disparate studies can be drawn together in a harmonised way. The technical architecture is adaptable for easy integration of additional collections, as well as for expanding the data available on specimens within the portal. Through the development of the Virtual Biobank, we have fostered understanding of the infrastructure and data-related elements associated with infectious disease specimen collection in Australia. An expansion of the Virtual Biobank is already underway, and in future we can see potential to harmonise protocols for consent and specimen access and to provide quality assurance metrics, for example by noting collections that meet recognised quality standards e.g. ISO standards (National Association of Testing Authorities, 2024), or PBMC processing standards (Dyer et al., 2007). In the first instance, a pre-established Material Transfer Agreement could be considered for participating collections, as already exists for some distributed infectious disease collections (Saginur et al., 2023).

The Virtual Biobank project will enable further discussions around the purpose and process of specimen collection and use for infectious disease research. By improving the visibility and accessibility of existing collections, discussion of ongoing storage and access sustainability can be facilitated. This could include furthering the idea to link some collections together through a centralised governance mechanism, particularly when the study is no longer active. We can also focus collective attention on the desired outputs of biobanking efforts, including the distribution of samples for additional research and supporting new collaborations (Rush et al., 2020). The Virtual Biobank also addresses an almost universal concern among specimen donors and collection holders that valuable biospecimens are collected and stored, but not used (Cadigan et al., 2013). By making existing collections visible, they become more accessible, and we hope to enable a more streamlined access process in the next iteration where a harmonised application form could be considered by the separate governance bodies.

The process of establishing the APPRISE Virtual Biobank has not been without challenges. There was an initial cautiousness from some Data Custodians to engage in the project. In some cases, the Data Custodians and study leads were very keen to participate, but further discussion was required to ensure they received the institutional support to do so. The different institutional contexts for each participating collection presented a complex range of requirements, both formal and informal. This included the need to identify the relevant contact points for IT, security and database issues (often changing, or unknown to study investigators), navigating institutional governance approval processes and obtaining the necessary internal IT and security permissions. This all took time, and often required technical discussion. A further challenge was the need for flexibility to access or allocate IT resources – some institutions were able to do this without hesitation, whereas others required the project to purchase independent IT infrastructure.

The APPRISE Virtual Biobank brings together distributed infectious disease biospecimen collections. We have started with collections focussed on SARS-CoV-2, since these were active and recruiting during the development process. The platform, however, is easily extendable to collections in other disease areas, including pathogen collections. Now that we have established the process for integration of collections into the Virtual Biobank, it will be quicker and easier to bring new collections onboard. This is an important contribution to pandemic preparedness, with rapid access to high-quality specimens needed to progress infectious disease research including the development of diagnostics and treatments as well as investigation of disease pathogenesis and host impacts (Peeling, Boeras, Wilder-Smith, Sall, & Nkengasong, 2020).

The APPRISE Virtual Biobank represents an adaptable, scalable and sustainable approach to infectious disease specimen access. We have developed a technical solution which brings together specimen information across multiple institutional and technical contexts. This proof-of-concept stage forms an important platform for further collaboration and harmonisation in specimen management.

Acknowledgments

We thank the Executive of the Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (APPRISE) for endorsing the project from its inception. Further thanks go to the technical staff supporting each participating collection and enabling their integration into the portal. Finally, we acknowledge the ongoing generosity of all study participants whose samples form the basis of each biospecimen collection. This project is a collective effort to ensure the best use of these valuable resources in impactful infectious disease research.

Authorship contribution statement

Priyanka Nair-Turkich: Conceptualisation, Methodology, Validation, Data Curation, Writing – Review & Editing

Maureen Turner: Conceptualisation, Methodology, Resources, Writing – Review & Editing, Supervision, Project administration

Javier Haurat: Conceptualisation, Methodology, Software, Validation, Data Curation, Writing – Review & Editing, Supervision, Project administration

Wisam Abdelaziz: Conceptualisation, Methodology, Software, Validation, Data Curation, Writing – Review & Editing

Allison Bourne: Writing – Review & Editing, Project administration

Miranda Z. Smith: Conceptualisation, Validation, Resources, Writing – Original Draft, Visualisation, Supervision, Project administration, Funding acquisition

Competing Interests

The authors declare no financial or non-financial interests that are directly or indirectly related to the work submitted.

Funding statement

This work was funded by the National Health and Medical Research Council via the Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (NHMRC ID 1116530).

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Tables 1 to 2 are available in the Supplementary Files section

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Developing a Collaborative Virtual Biobank to Support Infectious Disease Research

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Abstract

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Introduction

Materials and Methods

Engagement with participating collections

Project Governance

Technical approaches

Results

The APPRISE Virtual Biobank system architecture and security

Application of the APPRISE Virtual Biobank data model

APPRISE Virtual Biobank portal design and features

Ethical and governance issues

Discussion

Conclusions

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References

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