Page 128 - SAMRC Annual Report 2024-2025

Genomics Platform
Advancing Research Priorities:
Strategic Objectives and Impact
One of the key focus areas of the Genomics
Platform has been to break down the barriers to
entry for Next Generation Sequencing. We have
optimised DNA and RNA extractions from diverse
samples, including plant material, vitreous fluid for
ocular diseases, saliva for non-invasive diagnostics,
and animal samples for One Health initiatives.
These optimisations enhance the accessibility and
applicability of NGS across different fields.
In environmental and clinical contexts, we have NGS
being applied through wastewater sequencing for
public health surveillance and exome sequencing
for diagnosing genetic conditions. Our work has
also focused on onboarding novel technologies. For
example, we have developed an Oxford Nanopore
Technologies (ONT)-based methylation testing assay
to replace older methods like MS-MLPA, improving
diagnostic efficiency and accuracy.
Additionally, we have optimised RNA sequencing
from formalin-fixed, paraffin-embedded (FFPE)
samples to enhance diagnostics for B-cell
lymphoma by providing high-quality genetic data
from archived tissue samples. These developments
not only improve NGS accessibility but also expand
its applications in agriculture, medicine, and
environmental science. Overall, these efforts aim
at leveraging NGS for better disease diagnosis,
environmental monitoring, and agricultural
advancements, ultimately contributing to improved
public health and sustainable practices.
126 SAMRC ANNUAL REPOR T 2024-25
Platform director:
Prof. Craig Kinnear
craig.kinnear2@mrc.ac.za
Key Milestones and Achievements
The Genomics Platform is a key partner in the
AMRoots project, which was awarded £500,000 for
its innovative approach to addressing Anti-Microbial
Resistance (AMR) through the Trinity Challenge.
The team is led by Prof Helen Mcilleron from UCT
and includes two non-profit organisations and five
co-leads. AMRoots focuses on generating new
data to holistically understand the development
and transmission of AMR in livestock farming
communities, which are critical for the future food
security of sub-Saharan Africa. The project integrates
scalable and community-led approaches to mitigate
AMR in these regions. Prof Craig Kinnear will lead
the Genomics Arm of this study.
In 2024, the Africa BioGenome project (AfricaBP),
which is a pan-African initiative aimed at sequencing
the genomes of Africa's biodiversity to support
conservation, agriculture, and biotechnology,
In May 2024, the Genomics Platform held
a stakeholder event to commemorate the
sequencing of the 10,000th sample at the
Genomics Platform.