The recently concluded Intermediate to Advanced Bioinformatics Workshop hosted by the Next Generation Sequencing (UFS-NGS) Unit at the University of Free State (UFS), was aimed to equip participants with the necessary skills to enable them to effectively perform analysis of sequenced data at an intermediate-advanced level.

There is a need for data analysis training in Africa and the UFS-NGS workshop, funded by DIPLOMICS, is essential to bridge this gap and equip a targeted group of emerging and established researchers and students/interns with the necessary skills based on their prospects.

The workshop, which took place from 1 to 5 July, combined both theoretical and practical sessions on advanced Linux command lines, 16S/ITS metagenomics data analysis aspects, whole genome data analysis, whole genome and advanced molecular phylogenetics, and viral metagenomics/Virome data analysis.

Guest Speakers at the workshop included Dr Francis Chikuse from Africa CDC, Prof Arox Kamng’ona, Kamuzu University of Health Sciences, Malawi, Dr Khuzwayo Jere, University of Liverpool, and Dr Francis Dennis, Noguchi Memorial Institute for Medical Research, Ghana.

Specialist Bioinformatics trainers at the occasion included Dr Kwe Claude Yinda from the US, Dr Celeste Donato from Australia, Prof Benjamin Kumwenda from Malawi, Prof Errol Cason from the UFS, Dr Mhlekazi Molatoli from DIPLOMICS SA, and Stephanus Riekert from the UFS. Additional assistant trainers included Chimwemwe Mhango from Malawi, Dr Morne du Plessis, Dr Mathabatha Maleka, Precious Letebele, and Lurgasho Minnie all from South Africa.

Advancing scientific research and discovery

Welcoming the and introducing the guests on Day 1 of the workshop, Prof Nicholas Pearce, Acting Dean for the Faculty of Health Sciences, said the commencement of this workshop marks a significant milestone in the journey towards advancing scientific research and discovery.

“Bioinformatics at its core represents the convergence of biology, computer science and information technology. It empowers researchers and scientists with tools and methodologies to unravel the complexities of biological systems decoding derive meaningful insights that can revolutionise health care, agriculture, environmental sciences and beyond,” said Prof Pearce.

The establishment of the UFS-NGS unit, he continued, is a testament to the UFS’s commitment to excellence and research and innovation. It serves as dedicated hub where experts from diverse fields come together to harness the power of next-generation sequencing technologies. These technologies have not only accelerated the pace of genomic research, but paved the way for personalised medicine, precision agriculture and understanding of ecological dynamics.

NGS applications in Africa are growing but remain constrained by resource limitations. Researchers are increasingly utilising NGS to study genetic diversity, infectious diseases prevalent in our region such malaria, TB, HIV/Aids, and agriculture genomics to try and improve crop production.

The UFS-NGS Unit embodies the UFS’s commitment to education and capacity-building by nurturing the next generation of bioinformatics and computational biologists. We cultivate a talent pool that is not only proficient in technical skills but is also equipped with a critical thinking and problem-solving ability necessary to tackle complex biological questions.

The workshop audience included individuals from a Molecular Biology background, interested in bioinformatics, and who work (or are planning to work) on genomic datasets.

Genomics to clinical forum

The UFS-NGS Unit also hosted a Genomics to Clinical Forum on 9 July the Genomics to Clinical Forum which were intended for clinicians, health practitioners, doctors, nurses and public health officials. This is an effort to provide evidence-based information for health care practitioners (HCPS’s) on the efficiency of new advanced high throughput genomic testing using NGS in patients’ diagnoses and management including therapeutic interventions.

According to Prof Martin Nyaga, Associate Professor and Head of the UFS-NGS Unit, research has shown that many HCPs are less familiar with the clinical applicability and benefits of genomic testing and have little confidence in providing genomics informed care and discussing genomics topics with their patients.

“Limited physician knowledge of genomics testing is repeatedly cited as a barrier for the implementation of genomics in clinical practice. Furthermore, lack of HCP knowledge of technological advances in genomics has the potential to exacerbate health disparities in access to genomic testing among traditionally underserved populations.

“Besides, development of genomic-clinical based research by scientists, which is centred on patient disease diagnosis and care, will largely benefit from having practitioners with ample knowledge of patients’ diagnostics and choice of treatment,” says Prof Nyaga.

Prof Corlia Janse van Vuuren, Acting Dean for the Faculty of Health Sciences, welcomed and introduced the guests and re-emphasised the role the UFS-NGS Unit plays in supporting the World Health Organisation’s (WHO) mandate to promote health, prevent disease, and improve health equity worldwide. This is being done through the development of evidence-based policies, guidelines, and strategies in areas such as disease control, health promotion, and emergency response, shaping global health agendas and priorities.

The UFS-NGS Unit is the designated WHO Collaborating Center for Vaccine Preventable Diseases Surveillance and Pathogen Genomics.

Distinguished keynote guest speakers were Prof Dominique Goedhals from South Africa. Other distinguished speakers included Prof Lucy Gitonga from Kenya, Dr Kwe Claude Yinda from the US, Prof Champion Nyoni, Dr Kimesh Naidoo, Prof Veron Ramsuran, Dr Milton Mogotsi, Dr Fredy Simo Nemg and Prof Saheed Sabiu from South Africa.