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Pilot Project

GenCoE PAGRA African WGS Moonshot Project

A groundbreaking initiative to generate a foundational dataset of whole genome sequences representing African genomic diversity.

Project at a Glance

25,000

African genomes

2

Sequencing sites in Africa

100%

Consented, anonymized samples

15+

African countries providing samples

Project Workflow

Samples

Collected with informed consent from African participants

Sequencing in Africa

IGH in Nigeria, CERI in South Africa

Data Processing

Advanced bioinformatics analysis by UCT and IGH

Secure Storage

Hosted on UCT's Ilifu cluster with controlled access

Controlled Access

Governed by H3Africa DBAC and data sharing agreements

Scientific & Health Impact

Precision medicine and diagnostics for Africa

Project Overview

The GenCoE-PAGRA African WGS Moonshot Project aims to generate a foundational dataset of at least 25,000 whole genome sequences representing African genomic diversity. This ambitious initiative represents a major step forward in advancing genomic research tailored to African populations.

Advance Genomic Research

Build comprehensive understanding of African genetic diversity through large-scale sequencing

Enable Translational Medicine

Bridge the gap between genomic discoveries and clinical applications

Support Pharmaceutical Development

Inform drug development and precision medicine tailored to African populations

Sample Collection & Ethical Standards

The project maintains the highest ethical and legal standards throughout the research process:

Ethical Compliance

All samples are secured with informed consent and in full compliance with local laws and international best practices. The project ensures participant rights are protected at every stage.

Sequencing Infrastructure

Sequencing is conducted entirely within Africa, utilizing state-of-the-art facilities:

  • Institute of Genomic Health (IGH) in Nigeria
  • Centre for Epidemic Response and Innovation (CERI) in South Africa

Data processing is performed by expert bioinformatics teams at the University of Cape Town (UCT) and IGH, ensuring African ownership and capacity building throughout the pipeline.

Data Flow & Management

Sample Collection

Samples obtained with informed consent from H3Africa Biorepositories and African investigators. All activities governed by Material Transfer Agreements (MTAs) and Data Access Agreements (DAAs).

De-identification

All data is de-identified by Sample Providers prior to processing to ensure participant privacy and confidentiality.

Sequencing & QC

Whole genome sequencing (WGS) data generated using Dragen pipelines with comprehensive quality control metrics (CRAM, BAM, gVCF, joint VCF). Performed at CERI and IGH sequencing facilities.

Data Hosting & Sharing

UCT hosts and shares data via the Ilifu cluster, Globus transfers, and the Illumina Connected Analytics (ICA) platform.

Quality Control & Integration

UCT performs comprehensive data quality control, joint calling, and integration into the African Reference Panel and African Genome Variation Database.

Data Distribution

Data shared with Sample Providers and PAGRA (Pharmaceutical) partners via Data Sharing Agreements. Controlled public release through the European Genome-phenome Archive (EGA) under H3Africa DBAC governance.

Reporting & Oversight

Quarterly reporting to the Joint Steering Committee (JSC) ensures transparency and accountability.

Key Stakeholders

The project brings together diverse stakeholders committed to advancing African genomics:

GenCoE Leadership

UCT & IGH providing strategic direction and technical expertise

Sample Providers

African investigators and biorepositories

PAGRA Consortium

Roche, AstraZeneca, Boehringer Ingelheim, and future pharma partners

Research Community

African researchers and global scientific community

H3Africa DBAC

Data access governance and ethical oversight

Impact & Vision

The GenCoE-PAGRA African WGS Moonshot Project represents a transformative investment in Africa's genomic future. By generating a comprehensive dataset of African genomic diversity, the project will:

  • Enable more accurate disease risk prediction for African populations
  • Support development of therapeutics tailored to African genetic profiles
  • Build sustainable genomic research capacity across the continent
  • Establish Africa as a leader in genomic medicine and research
  • Create a valuable resource for global health research

A Foundation for the Future

This pilot project establishes the infrastructure, partnerships, and protocols that will enable GenCoE to expand its impact across Africa, ensuring that African populations benefit equitably from advances in genomic medicine.