A working BiBBox platform at a new Biobank that was established in a medical school in South Africa. The genetics laboratories that are part of the Southern African Human Genome Programme are collecting genetic material routinely and require the BiBBox functionality. The BiBBox platform will be tested in the laboratory of Professor Soraya Bardien-Kruger in Cape Town. Her laboratory collects biospecimens as part of a Parkinson Disease Project.
Biobank freezers will be monitored by their own independent management systems. The BIMS instrument management module will be used for freezer and tank maintenance and service events. The BIMS should interface with freezers where possible to upload temperature logs, and also allow for the manual capture of temperature logs.
The SOP for this module has been developed during the past 16 months at the NHLS-Stellenbosch Biobank in South Africa in collaboration with other h3Africa biobanks. A LIMS module will be developed using the refined SOP to managing sampling kits, their assembly, components, labels and suppliers
Integration and test of the LIMS in a Box integrated in the BiBBox and used in the proof of concept (Wp7)
A working BiBBox platform at research centers in Malawi, Kenya, Tanzania, Sudan, Kenya (M30) and cancer centres in Ghana, Egypt and Tunisia. Install and implement BiBBox at vector biology research sites in Africa to assess the establishment of new Biobanks. Four sites have been identified where no biobank exists but where biospecimens are processed regularly in the field. The sites are: • Zambia (Dr Lilly Sinyangwe: Central Veterinary Research Institute), • Nairobi, Kenya (Dr Dan Masiga: International Centre for Insect Physiology and Ecology), • Nakuru, Kenya (Dr Edwin Murungi: Egerton University), • Tanzania (Oliver Kijana: Tsetse and Trypnanosomiasis Research Institute), • Sudan (Dr Intisar Elrayah: Tropical Medicine Research Institute). Install BiBox at cancer centres in the BCNetwork, where biospecimens are being collected and processed but they do not have structured biobanks or LIMS systems. The sites are: Kumasi Ghana (Dr Beatrice Wiafe-Addai, Peace and love hospital): Cairo, Egypt (Dr Alaa EL HADDAD , National Cancer Institute); Tunis, Tunisia (Dr Sonia Abdelhak, Institute Pasteur de Tunis)
The purpose of this module is to manage samples in transit between source and destination, for both receiving samples and re-distributing them to authorized recipients. Shipping is integrated with the BIMS' sample chain of custody and storage inventory. The OpenSpecimen Project has a well-defined shipping module that was developed in JAVA for application at the National Cancer Institute. This module will be integrated in the Bika Health software. The data model for sample representation will be based on MIABIS and we will integrate ethics and regulations from WP1.
Setup and configuration of the LIMS in a Box from WP3 to be used in WP7
The primary purpose of the sample storage module is to assist users to find open shelf space in the freezers to store samples and to find the stored samples again when they need to retrieve them. The system will track sample volumes and link daughter aliquots and duplicate samples, and monitor freezing and thawing cycles, as well as disposal of them. The module will track samples from in and out of storage to the LIMS or Shipping module, with integrated chain of custody workflow.
Where samples are stored on a biobank client at a set fee, the BIMS should produce regular invoices for these services, say monthly, and export them to the BIMS accounts or ERP module.
Ethical approval is required before samples are released for use in new projects and the LIMS must capture these approvals. It will be based on WP1 ethics and regulation framework. Sample quality management An important function in sample storage is ensuring sample quality, e.g. validating the correct labelling of samples. Users working with personal patient information should not have access to test results in the BIMS. Other quality factors that should be captured are the sample's physical condition on arrival, e.g. possible contaminations, thawing, leaks, volume and temperature. Analytical quality factors, e.g. the purity and concentration of samples, are maintained in the LIMS function of the BIMS, but should be available in sample views as quality parameters.
Based on the previous specifications in D1.1 and D1.2, in advices from the ethics board and in the gained experiences during the project development specially the implementation of the use case (WP7), a final ethics and legal framework including data models for biobank data sharing, data disclosure filter and legal framework for collaboration with industry will be provided.
A formal definition of the data management policy based on D1.1 will be provided. A data model for biobank data sharing and integration will be designed based on MIABIS 2.0, the de facto standard for BBMRI-ERIC; and also based on the specified rules from D1.1. This model, together with the data management policy will be used by WP2 (development), WP3 (biobanking), WP4 (bioinformatics) to design the proof of concept of this project, WP7 (use case) to demonstrate biobanking interoperability, bioinformatics and education and training
Harmonization of data exchange standards for biobanking and registries (MIABIS): Requirements of the core implementation group (WP 7) and from associated partners will be harmonized with international and de-facto standard. The result of T2.3 will be directly applied in T 2.4
Install and implement BiBBox at the National Health Laboratory Services-Stellenbosch University Biobank (NSB). The bibbox platform will be tested in this medical biobank to assess performance and impact of biospecimen management and analysis tasks. Besides the application to biobank repositories, there is a need for routine labs to have access to biospecimen management software. The BiBBox will be tested at a research site linked to the H3Africa consortium.
Yearly consensus-targeting meetings of African stakeholders (e.g. programme coordinators, top-level biobank experts and medical researcher) together with their European counterparts
Definition of an informatics data model for analysis pipeline for the omics analysis defined in D4.1 incorporating ethics and regulations from WP1
Year Jamborees, i.e. work meetings where practice-level experts, appointed by the stakeholders, try out concepts
Report of available bioinformatics tools and public databases for omics data analysis taking into consideration the research conducted by participant partners. It will include a comparison of tools and definition of a final set of tools to be used in the proof of concept (WP7) to be integrated by WP2 [UWG month
Detailed learning and training needs assessment: target audiences will be specified, together with their learning needs. This will ensure that all key professionals involved in the implementation of the platform will be taken into account and that relevant courses and material will be produced. The assessment will be carried out towards the end of Phase 2.
Dissemination plan identifying activities to carry out to communicate to the Biobanking community and researchers the potential of B3Africa project. Information relating to regulatory framework, templates, protocols and software programs including information on harmonize practices will be made available in the project website
Definition of software components for biobanking (WP3), training and education and implementation of ethics and regulations. Definition of hardware for integration of the platform and bioinformatics tools based on the eBioKit from H3Africa project
Draft report of legal and ethical framework and an analysis of ethical viability: This deliverable will provide an early analysis of the ethical viability of the project, as well as a draft report about the legal and ethical framework for the project. A first draft of the data management policy in the platform will be provided. An independent Ethics Board with at least two members (-preferable one from each continent) will be created as part of this deliverable. The members of this board will not be directly or indirectly related to the beneficiaries. The Ethics board will address questions related to informed consent and data sharing policies and give inputs regarding the regulatory framework of the project
Definition of requirements for big data storage and analysis regarding conditions of participant partners and suggestion for integration with external e-infrastructures providing big data storage and analysis capabilities. An analysis of available e-infrastructures which are suitable for integration will be provided
A plan will be designed to continue the development of the B3Africa informatics platform as an open-source project to be adapted for use by the biobanking community worldwide.
Exploitation plan identifying opportunities and services for the B3Africa project. This will require linking with international biobanking organizational and societies e.g. ISBER, ESSBB and African research organizations such as AORTIC
Initial deliverable stating the management organization and planning for the entire project.
Production of generic learning and training material for WP6: the material produced during the project will be packaged as standalone learning and training material: e-tutorial to install and use the platform and its various tools, collection of training material to organize face-to-face training sessions to support the implementation of such a platform. The material will be produced in English. Key material will also be translated into French. The activities will be carried out under the coordination of IARC and with the contribution of relevant partners.
Training of key target audiences: a blended approach will be developed in order to train the relevant players engaged in the implementation of the platform in selected institutions: Face-to-face training: a first course will be organized at the beginning of Phase 4 to train relevant players for the implementation of WP7, at one of the African institute chosen for implementation. A second course will be organized towards the end of the project at another institute chosen for implementation, as a side event to one of the dissemination workshops (WP6), in order to train future users of the platform. Online live sessions will be run for follow-up and further training. This will imply that recipient locations will be equipped with the appropriate facilities and reliable internet access.
Face to face course 2 held to train future users of the platform
Key target audiences of WP7 trained (face-to-face and online)
Searching for OpenAIRE data...
Author(s): Hocine Bendou, Lunga Sizani, Tim Reid, Carmen Swanepoel, Toluwaleke Ademuyiwa, Roxana Merino-Martinez, Heimo Meuller, Akin Abayomi, Alan Christoffels
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Published in: Briefings in Functional Genomics, 2017, ISSN 2041-2649
Author(s): Tomas Klingstrom, Maimuna Mendy, Dominique Meunier, Anouk Berger, Jane Reichel, Alan Christoffels, Hocine Bendou, Carmen Swanepoel, Lemoene Smit, Campbell Mckellar-Basset, Erik Bongcam-Rudloff, Jonas Soderberg, Roxana Merino-Martinez, Suyesh Amatya, Absolomon Kihara, Steve Kemp, Robert Reihs, Heimo Muller
Published in: 2016 IST-Africa Week Conference, 2016, Page(s) 1-10