Page 138 - SAMRC AnnualReport 2025-26

AI-enabled tools and large language models were Through initiatives such as DDD-Africa and
further used to optimise bioinformatics pipelines, the ITP programme, the Platform is addressing
improving efficiency and reproducibility. In gaps in access to genomic diagnostics and
addition, the DeepFASTQ framework enhanced specialist expertise. These programmes integrate
sequencing quality control through genomic sequencing, deep phenotyping, AI tools, and
language modelling, reducing error rates and capacity development to improve diagnostic
shortening analytical turnaround times. yield, support clinical care, and enable sustainable
implementation of genomic medicine in resource-
The Platform also contributed to antimicrobial limited settings.
resistance research through the AMRoots project,
deploying a field-based laboratory in 2025 to Building Capacity Through
enable real-time DNA extraction and portable
sequencing in livestock communities. In biodiversity Training, Mentorship, and Support
genomics, the Platform led the Southern African Capacity development remained a strategic priority
Node of the Africa BioGenome Project, including for the Genomics Platform in 2025/2026, with a
the sequencing of Helichrysum odoratissimum – strong focus on strengthening technical expertise,
the first chromosome-level genome assembly of a supporting postgraduate training, and enhancing
plant species generated in Africa. workforce readiness in genomics and precision
medicine.
A benchmarking RNA-Seq study provided
independent validation of the Platform’s automated, In partnership with DIPLOMICS, the platform
high-throughput workflows, confirming that they continued to deliver a structured internship
generate robust and reproducible data suitable for programme designed to develop practical skills
tuberculosis biomarker research. This strengthens in next-generation sequencing (NGS) and Good
confidence in the Platform’s technical capabilities Laboratory Practice (GLP). The programme offers
and positions it as a trusted partner for large-scale graduates hands-on experience in essential
translational studies. molecular biology techniques, including sample
quality control, nucleic acid extraction, and
sequencing library preparation. Interns are integrated
into active laboratory workflows, gaining exposure
to high-throughput sequencing processes and
enhancing both technical skills and employability.

The Platform also maintains an open-access training
model for postgraduate students and postdoctoral
fellows. While outsourcing sequencing services may
offer efficiency advantages, it limits direct technical
exposure. To address this, students whose samples
are processed through the Platform are encouraged
to observe and, where appropriate, participate
in relevant workflows. This approach enhances
experiential learning while maintaining access to
advanced technologies, interdisciplinary research
environments, and structured mentorship.

Staff development is reinforced through ongoing
ISO-aligned training programmes, ensuring
adherence to international quality standards and
best practices in laboratory operations, data
management, and quality assurance. In addition, the
Platform hosted an Oxford Nanopore Technologies
sequencing “Safari,” training 13 students in DNA
preparation and real-time sequencing using ONT
The ONT Training SAFARI initiative.
platforms, providing exposure to portable and
emerging sequencing technologies.

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