Page 167 - SAMRC AnnualReport 2025-26

P E R FOR M A NC E I N FOR M A T I ON

Precision Medicine is a key priority within the is to use the BRCA point-of-care assay as a first-
SHIP programme, advancing through a portfolio tier test, coupled with genetic counselling. This
of funded projects focused on pharmacogenomics successful initiative marks a significant step
and large-scale human genome sequencing. towards incorporating germline whole-genome
Pharmacogenomics offers hope that prescribed sequencing and tumour genetics via next-
drug treatments can move away from the so-called generation sequencing to advance precision
"one-dose-fits-all" approach. The SAMRC and oncology.
DSTI, through SHIP, launched a Precision Medicine › Julia Goedeke and team underwent a peer
programme in 2020 with investments in projects review evaluation in a review meeting hosted by
aimed at understanding the pharmacogenomics the ERA-PerMed call secretariat in Paris for their
behind treatment failures with essential drugs (or drug OPTIMA study, which was highlighted as a success
classes) for non-communicable diseases, specifically story in the EU Africa Research Collaboration in
hypertension, cardiovascular disease, diabetes, and Personalised Medicine (https://www.euafrica-
cancer, in the South African population. Following permed.eu/optima-2/ and also placed on the EU-
the 2024 expert review of the initial portfolio of 9 AFRICA Innovation strategy dashboard).
pharmacogenomics projects selected through the
MRC-RFA-SHIP 01-2019, two projects were chosen for The South African 110K Human
follow-on funding, led by Prof Kotze (GKnowmix) and Genome Programme
Prof Peter (UCT). The third project in this portfolio The South African 110K Human Genome programme
was selected via the ERA PerMed Joint Transnational aims to support a cohesive omics ecosystem and
Call 2020, led by Prof J Goedecke (SAMRC/Wits). invest in a national genome-phenome archive
Key developments on these during the current through the establishment of the 10K pilot phase.
reporting period include: This approach will help South Africa establish the
workflows and ultimately deliver 110,000 human
› Prof Kotze’s team has created the genome sequences. This level of data generation and
Pharmacogenomics Information Technology storage will bolster the health innovation ecosystem
(PGx-I) platform, developed since 2020, along with in scaled genomics research, big data analytics, and
a rapid Nextflow pipeline for variant prioritisation a population registry that will be used to develop
– Variant Calling Format (VCF)-prioritise – that can relevant biomarkers and innovative digital health
convert variant data into an actionable spreadsheet tools for diagnosis, to inform better treatments, and
of results in just 20-40 minutes using laptop-grade to understand the pharmacogenomics profiles of
hardware, thereby reducing turnaround times. The South Africa's diverse population. This rich database
pipeline replicated previously obtained results will aid in developing relevant drugs and vaccines for
across all studied patients while also uncovering our patient populations and uncover African human
new findings (e.g., EXO1 variant in a patient with genomic diversity, creating new opportunities for
triple-negative breast cancer). Additionally, the the country's overall bioeconomy.
ParaDNA system accurately identified all nine The SHIP Steering Committee and the SAMRC
variants, achieving sensitivity and specificity above EMC approved the initiation of the 10K pilot phase
95%, with full concordance to reference results. of the 110K Genome Programme, with an initial
With the streamlined workflow, results were investment of R30,9 million that has now increased
delivered in under two hours, facilitating same-visit to a total commitment of R56 million from the DSTI
clinical decisions. These outcomes demonstrate SHIP Programme. An RFA process was run in the
that the ParaDNA system is a dependable and last financial year to select cohorts, resulting in 10
efficient tool for detecting South African BRCA1/2 feasible projects. The available budget will be used
founder and recurrent variants. Its integration into to sequence approximately 4400 samples from the
primary healthcare could support the national first 4 selected longitudinal cohorts. Additional
objective of decentralised breast cancer risk fundraising is required to complete the full 10,000
management, increasing access to early genetic sequences.
assessment in primary care. Discovery Health
has approved the team’s application for a health Strategic partnerships in this programme also
technology assessment to reimburse tumour- included global industry leaders MGI Tech Co and
based next-generation sequencing. The goal Illumina Pty Ltd. During the reporting period, the

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