## Background
The journey to establish a collaborative African Population Cohorts Consortium (APCC) started with a meeting in Uganda (March 2020) attended by African scientists and funders where the need, vision, and ambition for a research population data platform to address the Continent’s most pressing health and socioeconomic needs was agreed to. This was followed by a consultative process to write a scoping paper, involving African scientists doing cohort-based research, research funders, and led by Dr Nicki Tiffin. The result of the scoping phase was an agreement on the need for, a vision and broad structure of APCC, and clear areas identified for further exploration in the formative phase as set out in the scoping phase [report](https://cms.wellcome.org/sites/default/files/2021-03/APCC%20Scoping%20paper_%20FINAL_EN_0.pdf).
In March 2021 the Wellcome Trust published a Request for Proposals (RFP) for African Population Cohort Consortium (APCC) Formative phase Delivery Team. A team co-lead by JP Ochieng'-Odero and Kobus Herbst submitted a proposal under the auspices of the African Population Health Research Center (APHRC) with Evelyn Gitau as the institutional lead. This proposal was successful and in October 2022 the Collaboration for the Establishment of the African Population Cohorts Consortium (CE-APCC) commenced work funded by the Wellcome Trust, Bill & Melinda Gates Foundation, and UKRI Medical Research Council.
The lead institution was the African Population and Health Research Center (APHRC), collaborating with the Africa Health Research Institute (AHRI), Africa Research and Impact Network (ARIN), Malawi Epidemiology and Intervention Research Unit (MEIRU), and African Institute for Development Policy (AFIDEP).
The CE-APCC co-leads **Kobus Herbst** and **Evelyn Gitau** are supported by the co-applicants of the different workstreams and their team members which are as follows:
**Stakeholder & Community Engagement:** Maame Peterson & Joanes Atela, assisted by Leah Aoko
**Ethics**: Dorcas Kamuya is assisted by Alex Hinga, Michael Ogutu, and Jane Kahindi
**Existing cohorts:** Mia Crampin & Jim Todd are assisted by Edith Chikumbu & Jethro Banda
**Research Vision & Objectives:** Anjali Sharma, Mercy Wanjala & Jacques Emina are assisted by Samuel Ugbaja (postdoc). Shabir Moosa was an early member of this workstream.
**Data & Methodology:** Agnes Kiragga & Sikhulile Moyo are assisted by Samuel Ugbaja & Verrah Akinyi (postdocs)
**Governance:** Umberto D’allesandro, Stephen Tollman & Jude Igumbor
**Omics:** Michele Ramsay, Gerald Mboowa, and Emily Wong and assisted by a postdoc Samuel Ugbaja.
**Capacity Building:** Evelyn Gitau, assisted at various points by Damazo Kadengye and Marylene Wamukoya. The original convenors were Ayaga Bawah and Samson Kiware.
The following individuals were involved in the earlier parts of the CE-APCC work:
JP Ochieng'-Odero. Co-lead until March 2023.
Shabir Moosa. Co-applicant until Oct 2022.
Samson Kiware. Co-applicant until May 2023
Ayaga Bawah. Co-applicant until July 2023
The CE-APCC adopted the CSCCE Community Participation Model to structure its approach to stakeholder engagement (see Figure x). This approach enabled us to build an intensive stakeholder engagement effort to provide the basis for APCC blueprint development.
Figure 1: Stakeholder Engagement Approach
![[Engagement.png]]
## First Phase: Scoping Review & Stakeholders Identification (January-July 2023)
In the lead-up to the first phase of this process, co-leads of the CE-APCC, Kobus Herbst and Evelyn Gitau, made presentations on the formation of the APCC across various conferences and meetings including at the International HundredK+ Cohorts Consortium (IHCC) conference in December 2022, H3Africa 20th Consortium Meeting, International Conference on Human Genomics (ICHG) in February 2023, where Kobus Herbst gave an overview of the APCC, Michele Ramsay presented the ‘Omics workstream and objectives, and Jude Igumbor introduced approaches to governance.
**Existing cohorts workstream:** The main activities during this phase include preliminary criteria consultation, listing of existing cohorts, and cohort survey designing. The report is briefly summarised in the attached diagrams below.
Figure 2a: Surveyed Population Cohorts in Africa
![[Map.png]]
Figure 2b: Breakdown of cohort locations
![[Location.png]]
Figure 2c: Breakdown of Cohort Type
![[Cohort type.png]]
**Ethics workstream:** The activities in this phase include mapping countries with and without data protection legislation (Figure 3) and the implications for data sharing in APCC; mapping ethical issues for data and sample sharing in African cohort studies including a review of frameworks in use; reviewing consent processes and nature of consent and propose a template for APCC work; and reviewing of ethics approval of current multi-site studies.
Figure 3: Status of Protection of Personal Information legislation in Africa.
![[Laws.png]]
**Governance workstream:** The activities in this phase involve reviewing the governance principles which include strategic vision, participation & consensus orientation, transparency, equity and inclusion, accountability, risk management, decision-making, data protection, training & capacity development, reporting & feedback mechanisms, and rules of law. Case studies were done on the Human Heredity and Health in Africa (H3Africa) Consortium, the European Open Science Cloud (EOSC), the Innovative Medicines Initiative (IMI), and the eMERGE (electronic medical records genomics) network.
**Findings:** Based on an extensive scoping review, it was found that traditional academic partnerships are the most common model, where two or more organizations collaborate to share expertise, resources, and intellectual capital to benefit both individuals and their respective organizations. Therefore, an APCC will foster research collaborations and partnerships that provide numerous benefits, including cost savings from resource sharing, access to talent and expertise, speed of discovery, enhanced credibility, increased visibility and recognition, and improved coordination amongst multiple entities (cohorts).
**Omics & Data and Methodology Workstreams:** The data and methodology group, in collaboration with the Omics working group, was tasked to document current standards for phenotypic, genomic, and other omics data generated in African cohorts and to assess which international standards were applied. The aim is to provide guidelines for standards to cohort producers and users to enable uniform datasets for collaborative and comparative analyses and interventions for improving population health in Africa.
**Findings:** The two workstreams identified a need for the development of recommendations for cohorts in terms of international best-practice standards and approaches to data collection, storage, access, sharing and biobanking, and omics. This involves establishing a consensus set of guidelines for data collection, data management, and data sharing, enabling efficient and reliable collaboration among participating cohorts, as well as promoting data harmonisation, and enabling large-scale investigations into African population health and disease patterns.
**Research, Vision, and Objective:** Summarised research aims, objectives, countries of affiliations, and research focus areas for select cohorts included in longitudinal population studies and their networks. They identified gaps in research domains/areas in existing cohorts and their core indicators vis-à-vis primary health care (PHC) and universal health coverage (UHC).
**Findings:** While the vision and objectives inherent in the consortium and population studies have applications for primary health care (PHC), they do not explicitly meet its requirements on aspects such as social determinants of health, intersectionality, primary healthcare service delivery, integrated care, and interprofessional collaboration, comprehensive and preventive services, quality of care, precision medicine, precision public health, health systems strengthening, health workforce development, health information systems, building resilience/mitigating climate change, financial protection and health financing, intersectoral collaboration, policy & programme impact evaluation. Therefore, a strong PHC system is a prerequisite for universal health coverage (UHC) that aims to increase access to quality care without financial hardship for the most underserved and marginalised populations.
During this phase, an Independent Advisory Group (IAG) was constituted (table 1).
Table 1: Independent Advisory Group (IAG)
| **Member** | **Country** | **Designation** |
| ---------------------------- | ------------ | ------------------------------------------- |
| Alash'le Abimiku (Chair) | Nigeria | Virology, biobanking |
| Charles Mwansambo (Co-chair) | Malawi | Chief of Health Services |
| Andrew Haines | UK | Environmental Change & Public Health, LSHTM |
| Ronald Sinkala | Zambia | Legal and Governance |
| Paulina Tindana | Ghana | Bioethics |
| Alex Ezeh | Nigeria/US | Global and population health |
| Nicki Tiffin | South Africa | Computational biology, Bioinformatics |
| Sonia Abdelhak | Tunisia | Genetics |
| Oumar Gaye | Senegal | Parasitology (malaria) |
| Daniel Mwai | Kenya | Health Economics, UHC, PHC |
| Simisola Akintola | Nigeria | Legal and Governance |
Second Phase: Thematic Workshops and Nairobi in-person meeting (August-December 2023)
Following the **Scoping Review & stakeholder identification**, the CE-APCC engaged a range of stakeholders through a series of thematic workshops (Table 2). These virtual workshops engaged a range of stakeholders to explore and focus on the findings of the scoping review. Stakeholders were drawn from the existing cohorts survey, a stakeholder landscape review done by the stakeholder engagement workstream, the network of co-applicant researcher contacts, and contacts made at scientific meetings where the CE-APCC co-leads and others presented the initiative.
The objectives of this phase were:
1. Explore themes identified during the scoping phase with a range of stakeholders.
1. Identify aspects of establishing the APCC that were not elucidated during the scoping phase.
1. Identify and encourage individuals and institutions to engage with the CE-APCC during the blueprint development phase.
Table 2: Thematic Workshops
| **Date** | **Thematic Workshop** | **Workstream** | **# Participants** |
| ---------------- | ------------------------------------------------------------------------------------------------------------------------------ | ------------------------------ | ------------------ |
| 2 Jun 23 | Existing Cohorts Workshop | Existing Cohorts | 18 |
| 9 Jun 23 | Existing Cohorts Workshop (repeat) | Existing Cohorts | 18 |
| 16 Jun 23 | Existing Cohorts Synthesis Workshop | Existing Cohorts | 23 |
| 26 Oct 23 | Existing Cohorts Workshop | Existing Cohorts | 8 |
| 27 Jul 23 | Data Standards & ‘Omics Virtual Stakeholder Engagement Workshop | Data Standards & ‘Omics | 76 |
| 19 Oct 23 | ‘Omics and Data Methodology follow-up workshop | Data Standards & ‘Omics | 17 |
| 28 Sept 23 | Data Sharing in African Population Cohorts | Ethics | 78 |
| 12 Oct 23 | Ethics review, consent, and governance structures | Ethics & Governance | 40 |
| 11 Oct 23 | Understanding opportunities and barriers towards inclusive population research and action in Africa: Towards an APCC Blueprint | Stakeholder Engagement | 24 |
| 21 Nov<br><br>23 | Building Consensus for Research Vision and Objectives for Population Studies in Africa | Research Vision and Objectives | 24 |
**Note: A total of 194 different individuals attended the 10 thematic workshops from 21 different African countries.**
### Findings/Outcomes from the Thematic Workshops
#### Existing Cohorts Workstream
**Data harmonisation and sharing**: Stakeholders emphasised the need for APCC to develop harmonised & standardised data collection instruments and surveillance methodologies.
**Capacity strengthening**: Participants saw capacity building as a key role for the APCC, especially in supporting the unique challenges related to the sustainability and impact of longitudinal cohorts.
**Governance**: There is a strong sense that cohorts should play an active role in the governance of the consortium with involvement both in the running of the organization and the development and implementation of research projects.
**Stakeholders**: It is important to understand who the key stakeholders in cohorts are, ranging from regional entities such as Africa CDC and WHO AFRO to in-country policymakers, hosting academic institutions, local government, and communities.
**Cohort sustainability**: Maintaining cohorts beyond relatively short-term study-specific research funding is a long-term challenge. Consideration needs to be given to bottom-up (cohorts to consortium) development of research priorities. National governments can play a role in supporting cohorts' sustainability with the South African Population Research Infrastructure Network (SAPRIN) as a prime example.
#### Stakeholder Engagement Workstream
**Community Engagement**: The importance of ethical, transparent, and accountable community engagement in the APCC process to document community needs, and build long-term trust was highlighted.
**Research Questions and Evidence Needs**: Stakeholders, particularly academia and research policy influencers, are keenly interested in identifying priority research questions and evidence needs.
**Communication and Engagement Strategy**: Stakeholders are keen to shape the communication and engagement strategy of the APCC: This involves developing effective channels and platforms for collaboration, interaction, and knowledge sharing among stakeholders.
**Effective Channels/Platforms for Engagement**: Leverage virtual platforms, such as webinars, online forums, and in-person workshops and conferences as collaborative tools, to facilitate real-time interactions and knowledge sharing among stakeholders.
#### Governance Workstream
This workstream identified the following approaches:
- Prioritise maximising efficiency to attract funding and identify and approach relevant funders.
- Establish a framework for identifying and resolving disputes before collaboration starts and allocate responsibilities and leadership roles.
- Provide skills development and capacity-building opportunities, such as grant writing training and access to funding sources.
- Ensure adequate funding, impartial leadership, equitable distribution of resources, and address perceptions of dominance within the collaboration.
- Focus on effective governance, resource allocation, accountability, and inclusivity in the organisational structure.
#### Ethics Workstream
This workstream reached the following conclusions:
- Explicitly acknowledge the legal, socio-economic, and ethical differences across cohorts in terms of data sharing, consent, and ethics review.
- Given that most participants felt that they wouldn’t trust reviews conducted in other countries, it seems multiple ethics reviews in cohorts might be inevitable.
- There is a need for a careful process of harmonizing and standardizing data sharing, consent, and ethics review processes in the APCC.
- The APCC is likely to adopt collaborations of entities with varying levels of capacities and powers, including the capacities and powers to give valid informed consent, review protocols obtain approvals, and share or use data.
#### Research Vision and Objectives Workstream
This workstream developed the following recommendations:
- Explore the relationships between megatrends and the incidence of chronic and infectious diseases across geographies (Megatrends include technological advancements, demographic shifts, socio-economic changes, climate change, pollution, and urbanisation).
- Identify best practices for integrating health considerations into policies and actions across various sectors and their impact on public health.
- Identify effective policies, programs, and interventions through population-level research and evaluation.
- Investigate strategies to enhance the resilience and adaptability of health systems to cope with emerging challenges and disruptions, and how they can be redesigned to be more responsive to the changing needs of populations.
- Develop skills and frameworks for effective cross-sectoral collaboration to address the multifaceted determinants of health such as education, environment, and urban planning
- Develop communication strategies that encourage clear, transparent, and culturally sensitive engagement with stakeholders and communities through various communication channels, including social media, community meetings, and public forums, to reach a wider audience.
- Develop strategies for sustaining engagement and participation beyond the lifecycle of individual projects or initiatives.
#### Data and Methodology Workstream
**Mismatched Data Standards**: The workstream is creating a data standards blueprint that will be used to adapt and modify data standards to better meet the particular characteristics of LPC datasets in the African setting. This modification can enable smoother interoperability and improve data compliance with worldwide research standards.
**Data Standards Awareness Gap**: The workstream plays a critical role in creating awareness and providing training on the significance of data standards in the African research setting. This includes conducting seminars, and training sessions, and collaborating with research institutes to encourage data standard adoption.
**Interoperability with ‘Omics Data**: To enable the smooth integration of these different data types into research endeavours, it is critical to create standards that can efficiently manage them through collaboration with specialists in genomes and ‘Omics research to develop a unified data architecture that incorporates all essential data types.
#### Omics Workstream
**Skills Gap and Capacity Development**: Comprehensive training programs were proposed to bring all stakeholders to a level of confidence in dealing with mixed data to create successful partnerships among subject matter experts and data scientists.
**High Cost of Generating ’Omics Data**: Stakeholders suggested looking into cooperation with industry players to secure funds for massive ’Omics data initiatives. Local knowledge development was also emphasized as a requirement for effective ’Omics research within specific cohorts.
**APCC Futureproofing for ’Omics Research**: Participants proposed the establishment of accessible hubs around the continent to assist institutions and academics with data gathering storage, analysis, and usage. These centres would boost involvement in phenotypic and mixed data gathering for further ’Omics research.
**Infrastructure and Sample Collection**: A key concern was the disparity in infrastructure between cohorts for sample collection before data gathering, DNA analysis, and data processing. Some locations lacked the adequate infrastructure to do these duties, and addressing this shortcoming was deemed crucial before moving on to analyse the data and capacity building.
#### Capacity Strengthening Workstream
The workstream identified capacity-building gaps in cohorts that include data harmonisation to enhance data access and data sharing, cohort management (stakeholder engagement, funding, developing, and implementing research strategy and agenda, among others) to ensure the sustainability of cohorts, and ensure that the capacity-building exercises are geared towards filling gaps identified through the existing cohorts survey.
Capacity-building models should be leverage through collaborations/partnerships to avoid duplication of efforts. Where it is not possible to leverage existing models, establishing new programs and specialized short courses to deliver identified skills is recommended.
Capacity building should be at both the pre-and post-doctoral levels including embedding higher degrees in the cohorts, while including partnerships with universities.
Exchange programs between cohorts would be important for building capacity in best practices in cohort management.
### Nairobi in-person meeting
The Nairobi in-person meeting of the CE-APCC team members took place on 10-12 December 2023. The meeting which was hosted by the African Population Health Research Centre (APHRC) was attended by the afore-mentioned Co-Chairs, Co-Applicants, and their teams. Discussions were had on the different workstreams’ activities and this culminated in a discussion document which formed the basis for what is now the APCC Blueprint document.
## Third Phase: APCC Blueprint Discussion document, Collaborative Workshops & Draft Blueprint (January-April 2024).
To get the thoughts of the cohort leads on the CE-APCC blueprint document, the existing cohorts’ workstream coordinated three 3-hour collaborative workshops on March 11th, 13th, and 14th. Several concerns were raised during the workshops which will be included in this document. Apart from CE-APCC team members, the three workshops were attended by 40 cohort representatives. In line with the APCC Blueprint discussion document, CE-APCC representatives presented several sections which were followed by the responses outlined in Table 3.
**Table 3: Summary of the** **existing cohorts’ workstream coordinated three 3-hour collaborative workshops on 11th, 13th, and 14th March 2024.**
|**Category**|**Cohort’s Queries**|**CE-APCC Response**|
|---|---|---|
|APCC|Similarities/differences to INSPIRE? Is it replacing INSPIRE?|INSPIRE will advise APCC, ensure FAIR data, and train data managers. APCC is not replacing INSPIRE.|
||Who funds APCC and its functions?|The current funders are Wellcome Trust, BMGF, and UKRI MRC. The intention is to increase the funding base in the future.|
|Membership|Differences between candidate/full members? Legacy cohorts' status?|Candidate members work towards full membership; legacy cohorts need not resume data collection.|
|APCC Membership|Can embedded/nested cohorts be members? Criteria for membership?|Embedded cohorts can join if not shared with parent cohort in APCC. Networks of cohorts membership criteria outlined in Blueprint document.|
|Governance|Who can be on the steering committee? Role of rural/urban groups?|Secretariat members cannot be investigators. Urban/rural considerations depend on membership.|
|Capacity Strengthening|How will capacity strengthening be provided? Stabilization fund details?|Based on Capability Readiness Matric with funding prioritization based on need.|
|Scientific Networking|How will stakeholder engagement be handled? Strategic programs' design and funding?|Collaboration with regional organizations. Funding support via Secretariat. Strategic programs will evolve.|
|Ethics|AVAREF model and multi-country ethics reviews? Broad consent forms?|AVAREF facilitates multi-country ethics reviews. Broad consent forms and ethics guidelines are evolving.|
|Cohort Methodology (Data/Samples)|Data standardization challenges? TRE use and data access? Authorship guidelines?|APCC to ensure data standardization and TRE use. Authorship guidelines in place.|
|Cohort Methodology (Biosamples)|Biosample ethics and sharing considerations? Handling of pre-consortium bio-specimens?|Ethics guidelines and consent crucial for biosample sharing. Pre-consortium samples considered based on consent.|