RFA: South African 110,000 Human Genome Pilot Programme: Submission of Longitudinal Patient Cohorts for Whole Genome Sequencing
Overview
The SAMRC, in collaboration with the DSTI, invites applications for the submission of existing longitudinal patient cohort samples to be considered for inclusion in the pilot phase of the South African 110,000 Human Genome Programme (SA110K-HGP).
This pilot phase will aim to sequence 10,000 human genomes over a two-year period using Next Generation Sequencing (NGS) technologies. The initiative forms part of a broader national strategy to build sustainable infrastructure for precision medicine, genomics research, and healthcare innovation. Therefore, this pilot Programme does not just aim to build sequencing capacity but rather to develop a clinical genomics ecosystem. This can be achieved by embedding WGS into trials, the programme will test how genomic data can be used to improve care and research in African populations, with real health needs within the region. The selected samples will be foundational in validating protocols, establishing cost structures, optimising workflows, and demonstrating feasibility for nationwide scale-up toward a national population genome programme.
Applications are welcome from research institutions, hospitals, and clinical trial networks for the submission of existing longitudinal patient cohorts to conduct Whole Genome Sequencing (WGS) at 30x coverage. This pilot initiative aims to sequence 10,000 samples using Next Generation Sequencing (NGS) technology to establish a coordinated federated ecosystem within South Africa capable of supporting precision medicine, improving clinical outcomes, and advancing understanding of disease mechanisms and therapeutic responses. Applicants should clearly demonstrate how genomic insights from the proposed cohorts will support improved diagnostics, therapeutic stratification, or elucidation of disease etiology in existing or planned clinical studies.
We are not simply looking for patient samples; rather, we aim to build a national system for precision medicine. Your cohort must add scientific value, help test infrastructure, contribute data to a national archive, and show how it can improve patient outcomes. Successful applicants must be ready to explain how data generated on their patient samples will be used!
This RFA aims to address the following scope and objectives:
- To identify diverse patient cohorts for WGS at 30x coverage.
- To utilize genomic data to address critical gaps in disease understanding and therapeutic response.
- To integrate genomic insights into clinical trial studies for improved patient outcomes.
- To build national genomic resources that inform the scalable workflow of a larger scale National Genome Programme.
- To contribute data to a National Archive for enhanced analytics and broader population-based impact.
- To promote tertiary analyses that extract actionable insights from genomic data and strengthen the scientific contributions of this pilot phase of the SA-110K-HGP.
Scope of Required Samples
Applicants must propose a minimum of 500 samples per cohort for submission. Each sample must meet the following:
- Be blood-derived, with sufficient volume for DNA extraction and sequencing.
- Accompanied by a minimum set of de-identified phenotype/clinical metadata linked to each sample. Pertinent aspects such as (age, sex, ethnicity and main disease aspect), this type of information is necessary to provide some level of sample differentiation within a genome Archive.
- Have traceability and documentation from the point of collection to current storage.
- Be of high integrity and stored under appropriate conditions for genomic analysis.
Eligibility Criteria
The following eligibility criteria sets the minimum requirement for participation:
- Be a recognised academic institution, clinical research centre, hospital, or clinical trial institute or network based in South Africa.
- Submit an existing or planned cohort that is part of an ethically approved clinical or research study, with valid participant consent for genetic studies such as Whole Genome Sequencing (WGS) and data sharing.
- Ethical approval must be from a registered South African Human Research Ethics Committee.
- Applicants must agree to deposit resulting genomic and associated metadata into the National Genomics Archive for integration, analysis, and future reuse, subject to appropriate governance and access controls.
- Commitment to comply with standardized sample preparation and DNA extraction protocols.
Funding & Support
- The programme will centrally procure sequencing services to ensure competitive pricing on Illumina and MGI platforms, within South Africa.
- Therefore, funding allocations will support sample transport, minimum personnel, and tertiary bioinformatics analysis.
- Proposals must include a plan for genotype-phenotype association studies with clearly defined scientific objectives.
- Funding amounts will be determined based on cohort size, disease relevance, and scientific merit.
- Sequencing will take place at local sequencing centres; data processing will follow a centralised pipeline within the central programme workflow and data will be processed and stored within a National Archive.
Therefore, successful applicants will work with the programme infrastructure team to refine budgets and finalise their applications.
How to Apply
Applications must be submitted via the SAMRC Application Portal: Application Registration
Review the complete RFA scope and guideline to submit Longitudinal Patient Cohorts for Whole Genome Sequencing
Standard terms and conditions for SAMRC funding apply
Required Documents:
Please use the templates below:
Additional documents required to be submitted with your application:
- Ethics approval
- Informed Consent forms
- List of deidentified Samples with participant demographics such as Age, sex and ethnicity
- Supporting information for Sample Traceability and QC
- Data sharing plan and consent framework
- Clinical and genomic data management plan (if available)
- CVs of all investigators
Only applications submitted through the official portal with completed documentation will be considered. Late submissions will not be accepted.
Contact information
For inquiries regarding this funding call, please contact:
Rizwana Mia (Senior Programme Manager – South African 110K Human Genome Programme)
Email: 10K-Genome_Pilot@mrc.ac.za
