Page 114 - SAMRC Annual Report 2023-24

Genomics Platform

Platform director:
Prof. Craig Kinnear

Prioritising responsive research the South African context. This initiative is expected
through impactful interventions to advance precision medicine in South Africa by
addressing knowledge and infrastructure gaps,
The SAMRC Genomics Platform (SGP) was advocating for the integration of precision medicine
established to offer affordable, high-quality next- into routine care for genetic disorders. Additionally,
generation sequencing (NGS) services to African it will bolster next-generation sequencing capacity
scientists. While primarily focused on delivering and provide bioinformatics and variant interpretation
NGS services, SGP is engaged in precision medicine training for young scientists, enhancing the country's
research, utilising whole exome sequencing (WES) genomics capabilities. Ultimately, EDDI aims to
to identify disease-causing variants in patients improve patient outcomes by facilitating timely
with immune disorders and developmental issues. and accurate diagnoses through WES within the
The aim is to enhance patient treatment and South African healthcare system.
management through precise diagnoses.

In developed countries, WES is a primary diagnostic Equitable capacity development
tool for genetic disorders, significantly reducing for empowering communities
diagnostic timelines. However, in South Africa, In response to the COVID-19 pandemic, the SAMRC
patients face barriers accessing WES due to limited initiated the Wastewater Surveillance and Research
clinical genetics units, insufficient integration of Programme to predict infection waves and track
genetic testing in standard care, and the high cost SARS-CoV-2 variants. To broaden surveillance,
of WES testing, which isn't covered by the state SAMRC partnered with six local institutions. These
healthcare system.
institutions unfortunately lacked sequencing
To address these challenges, SGP launched the capacity. To address this, the SAMRC partnered with
Exome Sequencing Diagnostic Initiative (EDDI) to DIPLOMICS to establish the Broadening Access to
integrate WES into the South African healthcare Sequencing in South Africa (BASSA) programme.
system. A pilot study aims to develop practical BASSA aimed to empower these institutions with
clinical WES workflows and assess its feasibility portable sequencing equipment and training.
as a first-tier diagnostic tool. Phase one involves
optimising WES sequencing strategies to lower In August 2023, a workshop at the DIPLOMICS
costs while maintaining quality. training laboratory provided training for one
participant from each partner institution, supplying
The next phase will sequence 200 patients' exomes them with portable ONT MinION sequencers
from the State Healthcare System to evaluate WES's and necessary peripheral equipment for sample
diagnostic utility, considering factors like positive preparation and sequencing. This initiative aimed to
diagnoses, time to diagnosis, and cost per test. decentralise sequencing capabilities, enabling local
Tailored clinical WES workflows will be developed for monitoring of SARS-CoV-2 variants.

112 SAMRC ANNUAL REPOR T 2023-24