What led you to transition from academia to the private sector?

After completing my master’s degree in Germany, I moved to South Africa for my PhD and eventually spent 14 years in academia. I enjoyed teaching and working with young minds, primarily at the University of Cape Town (UCT) and Wits University. However, academia moves at a slower pace due to administrative and funding processes, which didn’t align with my dynamic aspirations. When I learned about Inqaba Biotec and its introduction of next-generation sequencing (NGS) in Africa back in 2007, I knew I wanted to be part of this transformative journey. The private sector’s ability to act swiftly on good ideas and customer needs was the perfect fit for me.  

What unique challenges have you encountered in implementing NGS/WGS technologies across South Africa? 

When NGS began, sequencing was costly and limited to simpler projects like bacterial genomes. Now, the technology has evolved exponentially, allowing us to sequence an entire human genome in just 24 hours—compared to the 13 years it took for the first one. We’ve consistently upgraded our platforms to provide the best and most cost-effective solutions for our customers, which brought us to Geneyx Analysis.  

The efficiency of sequencing projects has improved with advances in technology, especially as larger systems produce data more cost-effectively. Despite challenges like shipping samples under cold temperatures to the tip of Africa, we prioritize maintaining quality and affordability.  

Can you share success stories where your NGS/WGS services have directly impacted molecular diagnostics or disease research in African populations?  

We’ve made significant contributions to landmark projects, such as the Southern African Human Genome Project, which studies genetic diversity across African populations. We’re also partners in the African BioGenome Project, sequencing genomes of plants, animals, and pathogens to understand and conserve Africa’s biodiversity.  

A noteworthy example involves hearing loss research in African populations. Unlike Europe or Asia, the genetic mutations responsible for hearing loss in Africa differ, and we supported this research by providing human genome sequences free of charge. It’s extremely rewarding to be a part of this change to people’s lives. Similarly, we’re collaborating with Rare Diseases South Africa to showcase the advantages of long-read sequencing for rare disease diagnostics, which we hope will become the gold standard. 

What role does African genetic diversity play in the global genomics landscape?  

African populations hold the most genetic diversity of any group worldwide, offering critical insights into human evolution, disease susceptibility, and drug response. This diversity is an invaluable resource for global genomics research, particularly for developing treatments and interventions that are inclusive of all populations. By studying African genomes, we contribute to a better understanding of complex traits and diseases, benefiting global healthcare initiatives.  

What’s the difference between short-read and long-read sequencing, and why is it important?  

Short-read sequencing involves chopping DNA into small fragments and sequencing them in parallel. While efficient, it lacks context when mutations on the same DNA strand need to be analyzed. Long-read sequencing, on the other hand, sequences larger DNA fragments, offering greater clarity and context for complex genomic variations.  

This distinction is crucial for identifying structural variations, alternative splicing in RNA, and epigenetic modifications, which are often missed in short-read methods. Long-read technology provides more informative data, making it a game-changer for genomics.  

How are you working to make NGS/WGS technologies more accessible to researchers and healthcare providers in resource-limited regions across Africa?  

Accessibility is key to the success of genomics in Africa. We are actively involved in providing cost-effective sequencing solutions, developing modular training programs, and promoting remote support to empower researchers in resource-limited areas. Collaborating with governments and NGOs to subsidize technology costs and create awareness has also been instrumental. These efforts aim to ensure that even researchers in the most remote locations can leverage the power of genomic technologies.  

What kind of collaborations or partnerships have been established to enhance academic, clinical, or industrial research across the continent?  

Collaborations are a cornerstone of progress. We’ve established partnerships with universities, healthcare institutions, and research consortia to drive innovation and share knowledge. For example, collaborations with academic researchers have resulted in studies addressing the genetic basis of diseases prevalent in Africa. Partnerships with industry have facilitated the development of applications in agriculture, such as sequencing crop genomes to improve yields and disease resistance.  

How has your work contributed to improving public health or addressing key healthcare challenges in African communities?  

Our initiatives have contributed to tackling some of Africa’s most pressing health challenges. For instance, genomic data has been used to better understand diseases like malaria and tuberculosis, leading to more targeted treatments and interventions. Also, the integration of WGS (whole genome sequencing) into routine diagnostics is enhancing the precision of medical care. These contributions ultimately aim to reduce the burden of disease and improve health outcomes across the continent. 

We also address logistical challenges like sample transportation by offering tailored solutions for handling delicate materials like RNA in extreme climates, which Africa does have. This ensures high-quality samples for sequencing, even in remote areas.  

The work my team and I do extends beyond research to crisis response.  

During the COVID-19 pandemic, we helped analyze the virus, contributing to vaccine development. In agriculture, we sequenced the bird flu and bluetongue viruses, enabling vaccine production to mitigate devastating outbreaks that threatened food security.  

We’ve also assisted in controlling bacterial outbreaks, such as Listeria, by sequencing the pathogen to identify contamination sources in food production.   

How is the future of genomics in Africa looking?  

Africa’s genetic diversity is unparalleled, offering immense potential for breakthroughs in drug development and precision medicine. While human genome sequencing is still costly, advancements are making it more accessible. In the future, genomic screening at birth could become a norm, guiding personalized healthcare from an early age.  

Through initiatives like multiomics and epigenetics research, we’re unlocking complex biological insights, paving the way for innovative treatments. With continued investment in technology and training, we’re optimistic about a future where African communities fully benefit from genomics. Inqaba is a Geneyx Distributor on Geneyx Analysis in Africa

Read about Prof. Beggs insights on the Integration of Genomic Data Analysis in Clinical Practice