RESEARCH PROJECTS AND COLLABORATIONS

1. Multimorbidity in the Western Cape

The focus of this project is the management, integration and analysis of routine health data from health care clients attending government health facilities in the Western Cape. Establishing a virtual population cohort using routine health data for epidemiological analyses.

1.1  Establishing a virtual population cohort using routine health data for epidemiological analyses

Nature and purpose:

We are analysing anonymised and perturbed routine health data from a virtual cohort of all health care clients who attended any government health facility in the Khayelitsha sub-district in Cape Town during 2016 and 2017. Analysis of this data provides insights into multimorbidity in this population group that suffers from a high burden of both infectious and non-communicable diseases. In addition, we have continued to work in collaboration with the Provincial Health Data Centre (PHDC) at the Western Cape Department of Health in epidemiological and service-delivery projects working with routine health data from the Western Cape.

Researchers:

Tsaone Tamuhla, Sohail Simon, Florence Phelanyane. 

Outputs in the past 12 months:

Dixon J, Morton B, Nkhata MJ, Silman A, Simiyu IG, Spencer SA, et al. including Tiffin N. (2024) Interdisciplinary perspectives on multimorbidity in Africa: Developing an expanded conceptual model. PLoS Glob Public Health 4(7): e0003434. https://doi.org/10.1371/journal.pgph.0003434

Osei-Yeboah R, Ngwenya O, Tiffin N. Kidney function in healthcare clients in Khayelitsha, South Africa: Routine laboratory testing and results reflect distinct healthcare experiences by age for healthcare clients with and without HIV (2024). PLoS Global Public Health, 2024 May, 4(5): e0002526.
https://doi.org/10.1371/journal.pgph.0002526

Future Directions:

In this project, we will continue to build on appropriate methodologies for analysis of complex routine health data in order to inform evidence-based care. Sohail Simon will continue working within this project to further explore analysis using latent factor analysis as well as machine learning approaches to analyse risk factors for kidney disease in this population group. In addition, we will be using this dataset in our preliminary data modelling and epidemiological analyses for our new programme investigating drivers of gestational diabetes and pre-eclampsia in African populations.

1.2 Piloting a virtual genotyped population cohort linking genotype and routine health data: 

Nature and purpose:

With informed consent from health care clients, it is possible to link individuals’ genotype data with their routine health data in order to establish a genotyped virtual cohort with complex clinical phenotype data that can be updated into the future using routine health records. We have piloted this approach by establishing the informed consent process, sample and data workflows to create, in the first instance, a virtual genotyped cohort for patients with diabetes in Cape Town. UKRI/MRC has funded a pilot study for proof-of-principle establishment of a virtual genotyped population cohort using this approach, as well as establishment of the infrastructure to return actionable findings from the analysis to clinicians at the Western Cape Department of Health. In addition to myself and Tsaone, Ms Irene Muchada has been working as a genetic counsellor on this programme throughout 2024, successfully establishing excellent working relationships with our collaborators at the Nephrology Unit at Groote Schuur Hospital, our ongoing collaborators at the Diabetes Clinic at Groote Schuur Hospital, and our new collaborators at the UWC Dentistry Faculty clinics. We successfully completed the pilot project in December 2024 and will continue to work with collaborators across a variety of projects as new approaches to genomic data analyses are applied to genomic data from African populations. Ms Tiffany Fredericks is also joining this project to work with the VCAMM data for her MSc (Bioinformatics) which will start in January 2025.

Researchers:

Tsaone Tamuhla, Nicki Tiffin, Irene Muchada, Tiffany Fredericks.

Outputs in the past 12 months:

Tamuhla T, Coussens AK, Abrahams M, Blumenthal MJ, Lakay F, Wilkinson RJ, Riou C, Raubenheimer P, Dave JA, Tiffin N (2024) Implementation of a genotyped African population cohort, with virtual follow-up: A feasibility study in the Western Cape Province, South Africa. https://wellcomeopenresearch.org/articles/9-620/v1. 

Future Directions:

A proof-of-concept pilot project has now been completed, with development of the analysis pipeline with an appropriate informed consent process, collection of buccal swabs and preparation of high-quality DNA sample, generation and analysis of genotype data, and linkage to routine health data for phenotype definition. We are currently completing the building of our data infrastructure to ensure that actionable genetic findings from these studies are appropriately returned to the Western Cape Department of Health to inform evidence-based care.  We have a stakeholder meeting taking place in early 2025 and are actively seeking new funding resources to take this work forward. 

1.3 Optimising data linkage of African health client data

Nature and Purpose:

When integrating individualised data from a variety of sources, different linkage algorithms can be used to ensure the most accurate linkage and de-duplication of records that originate from the same individual. Most of these algorithms, however, have been developed using Euro-centric datasets and do not necessarily perform as well in African contexts, and we are working on a systematic approach to improve data linkage for routine health data. Themba Mutemaringa has continued to take this work forward by successfully developing a curated test dataset, and ongoing benchmarking of existing linkage algorithms using African data.

Researcher: Themba Mutemaringa

Collaborators: Andrew Boulle, Alexa Heekes, Western Cape Department of Health.

Outputs in the past 12 months:
Mutemaringa T, Boulle A and Tiffin N. (2024) Data governance for ethical usage of linked routine health data in South Africa: balancing privacy and data sharing. Conference Proceedings: International Journal of Population Data Science, 9(5). doi:10.23889/ijpds.v9i5.2721.

Future Direction: In this project, Themba Mutemaringa will continue to lead the validation and benchmarking of existing linkage and de-duplication algorithms, and will develop and test new methodologies and algorithms to best achieve de-duplication and data linkage.

2. Facilitating ethical and equitable sharing of African data and biospecimens: the African Data and Biospecimen Exchange – ADBEx

Nature and purpose:

Towards the end of 2021 I established a programme, funded by the Calestous Juma fellowship from the Bill & Melinda Gates Foundation, to build an online platform to facilitate ethical and equitable secondary sharing of African data and biospecimen resources. The query-able platform will store meta-data about sample and data collections, submitted by researchers who hold those resources, and will enable direct sharing partnerships to be established between resource providers and resource consumers without centralisation of samples or data. It will also provide online infrastructure for drawing up and recording data-sharing, benefit-sharing and collaborative agreements as well as building a repository of data and biospecimen guidelines and governance resources.

The development of the ADBEx platform has reached completion at the end of 2024, thanks to the highly competent and professional work of our partners in User Interface – Hominum (https://www.hominum.digital/) and software developers MethodLab.

We have developed two related projects that are linked to ADBEx: Tsaone created a stand-alone, browser-based application that can be used to build fit-for-purpose data- and biospecimen-sharing agreements. Whilst this functionality will be incorporated into the ADBEx platform we were keen to also test this concept and introduce it to a wider audience. The app can be found here https://adbex-template-mou-builder.streamlit.app/ (just wake up the app if it is sleeping!).

We completed and published a collaborative project with PHA4GE to create a Data Sharing Accord – a document that outlines the basic “common sense” principles for sharing microbial data, that end users can adopt as a common ground for general accepted principles for sharing data for secondary use. We presented this Accord to various stakeholders, at the PHA4GE Conference in Cape Town and also at the Wellcome AMR Workshop in Johannesburg, and were able to incorporate feedback from the community in the version of the Accord that we published.

We are still in the process of building a Data Sharing license. Drawing inspiration from the Creative Commons licensing structure, we have developed a prototype for a similar type of license that can be used to effectively and unambiguously communicate the nuanced sharing requirements for individual datasets. In 2025, this will be operationalised as an online browser-based license generator.

Researchers: Nicki Tiffin, Eddie Lulamba, Tsaone Tamuhla.

Collaborators: Hominum Global, www.hominum.global – User Interface and Software Specification and Development; MethodLab, https://methodlab.io/ – Software development.

PHA4GE collaborators: Peter van Heusden, Emma Griffiths, Michelle Nichols, Anja Bedeker.

Outputs in the past 12 months:
Story of the UI Development by Hominum: https://www.hominum.digital/blog/adbex

MOU Builder for data- and biospecimen-sharing agreements: https://adbex-template-mou-builder.streamlit.app/

Griffiths EJ, van Heusden P, Tamuhla T, Lulamba ET, Bedeker A, Nichols M, Christoffels A, Tiffin N (2024). The PHA4GE Microbial Data-Sharing Accord: establishing baseline consensus microbial data-sharing norms to facilitate cross-sectoral collaboration. BMJ Glob Health. 2024 Oct 30;9(10): e016474.
doi: 10.1136/bmjgh-2024-016474. 

Future Direction: We are excited to test and launch the ADBEx platform in 2025 and will be undertaking a series of roadshows to introduce the platform to African researchers across the Continent, and to help individuals to start uploading the metadata for their sample collections and datasets.

We will also be building an online tool for creating data-sharing licenses for end-users wishing to stipulate what kinds of data use are acceptable for the datasets that they are sharing.

3. Ethics and governance to promote ethical and equitable health research in Africa 

Nature and purpose:  In order to undertake ethical research in Africa and other regions of the global South, there are multiple considerations around risks, benefits, informed consent and equitable research. We explore different ways to better do research and to ensure that health research in Africa is ethical and equitable through the development of tools and frameworks. I also participate in multiple ethics and governance working groups of international consortia including PHA4GE (Chair: Ethics and Data Sharing Working Group), G2MC/IHCC (Co-chair: Policy and Advocacy working group). We have also some exciting outputs from the PHA4GE Ethics and Data Sharing sub-grant awardees who were previously funded to conduct research projects in ethics and data sharing.

Outputs in the past 12 months:
Tiruneh G, Yilma M, Wakuma B, Abdisa E, Bayisa L, Nichols M, Bedeker A, Tiffin N. Compliance with research ethics in epidemiological studies targeted to conflict-affected areas in Western Ethiopia: validity of informed consent (VIC) by information comprehension and voluntariness (ICV). BMC Med Ethics. 2024 Jan 18;25(1):9.
doi:10.1186/s12910-024-01003-5.

Pillay N, Ncube N, Moopelo K, Mothoagae G, Welte O, Shogole M, Gwiji N, Scott L, Moshani N, Tiffin N, Boulle A, Griffiths F, Fairlie L, Mehta U, LeFevre A, Scott K. Translating the consent form is the tip of the iceberg: using cognitive interviews to assess the barriers to informed consent in South African health facilities. Sex Reprod Health Matters. 2023 Dec;31(4):2302553.
doi: 10.1080/26410397.2024.2302553. Epub 2024 Jan 26.

Griffiths EJ, van Heusden P, Tamuhla T, Lulamba ET, Bedeker A, Nichols M, Christoffels A, Tiffin N (2024). The PHA4GE Microbial Data-Sharing Accord: establishing baseline consensus microbial data-sharing norms to facilitate cross-sectoral collaboration. BMJ Glob Health. 2024 Oct 30;9(10): e016474.
doi: 10.1136/bmjgh-2024-016474.

Future Direction: We are currently developing a data sharing license to capture and communicate nuances of data sharing permissions, and to facilitate data sharing that respects conditions of sharing.