SANBI in the Media During 2014, research at SANBI was featured on the cover of two prestigious scientific journals.
Two commentaries were also placed in European media: PROFILE
COMMUNICABLE DISEASES
A UNIQUELY AFRICAN FOCUS Bioinformatics is a field that has grown exponentially in the past few years, and it is becoming increasingly important to collaborate as the field continues to gather momentum
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oday, bioinformatics and computational biology is an animated field of research and development in Africa, particularly South Africa. Historically, researchers in bioinformatics conduct research in a space where biology, computer science and statistics converge. This understanding of bioinformatics has evolved into something more sophisticated, particularly as it pertains to genomic research. The quantity and type of genomic data that comprise this informatics has increased exponentially on an annual basis. This growth is naturally a reason for excitement, yet also for concern as bioinformatics is subject to the same ethical constraints that monitor all other wet lab biomedical research. The biomedical ethics that governs this kind of research is similar to that which controls clinically-based research. As bioinformatics grows as a field, a singular concern stands out as an impediment to maintaining the momentum of this burgeoning area: the consistent presence of internationally recognised protocols for storing data, and for transporting genetic material across the continent. In a field that thrives on collaborative research, and which also indirectly supports economies, bio-computing in Africa is in need of critical engagement with and support for the logistics of creating a super-structural network across the African continent. The South African National Bioinformatics Institute, (SANBI), founded in 1996 and an affiliate of the University of the Western Cape in South Africa, has grown exponentially in the last 18 years. Professor Alan Christoffels is both the incumbent director as well the recipient of the South African Research Chair (SARCHi) in Bioinformatics and Public Health Genomics. Though not the only site of bioinformatics research in Africa, SANBI is the only institute in Africa dedicated solely to bioinformatics research and is funded to this end. It is internationally regarded as the ideal place on the continent for graduate and postdoctoral training in bioinformatics. SANBI generally concentrates on genomics research that spans both communicable and non-communicable diseases that is ultimately driven by the quest for biomarker discovery. While human health is clearly the focus of SANBI-based research, SANBI staff are making forays into agricultural research as well.
The Tsetse genome paper was published in Science on 25 April 2014 (Volume 344) and a collection of satellite papers including an editorial in PLoS Neglected Tropical Diseases followed.
2011 marked a milestone in genomics research in Africa. Both the Wellcome Trust and the NIH, made strong scientific, political, and economic statements by investing substantial funds to the genomics research community. In particular, these research organisations invested in what is known as the H3Africa programme: the Human, Heredity, and Health programme.
Coincidently, 2011 was the same year in which the Southern African Human Genome Programme (sahgp.org) was established, which is specifically tailored to enhance South Africa’s capacity for genomics research. More recently, the US-South Africa Program for Collaborative Biomedical Research provided yet another strong investment into biomedical research that provides the impetus for African scientists to drive genomics research. Training researchers in an environment underpinned by collaborative bio-computing projects has been enormously successful through partnerships between African, North America, and European scientists. Horizon 2020 is an ideal framework within which to continue these partnerships. Specifically, Horizon 2020 presents us with the ideal opportunity to develop biobank standards. This in turn provides the platform to devise, with international partners, ways to transport and transfer genetic material and its associated (meta) data, and house and maintain it. So, Horizon 2020 is not only a research opportunity on the African continent, it is also potentially a place for political and financial investment into high-performance computing and biomedical logistics. The question of intellectual property impacts bio-computing research as is commonly experienced in all collaboration-based research. Peculiar to Africa-based research is the question of what informatics remains on the continent and is archived in Africa once the research project has concluded. The end of a bio-computing project in Africa is often the beginning of a discussion on African scientific history, cultural history, ethics, and identity, so this field is constantly growing in influence in both the science and the humanities. Bioinfomatics, under the umbrella of Horizon 2020, is not then only a space for biocomputing research, but it is potentially the genesis of new scholarly intersections of intellectual inquiry with a uniquely African focus.
Alan Christoffels Director, and DST/NRF Research Chair in Bioinformatics and Public Health Genomics South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape tel: +27 2195 93645 alan@sanbi.ac.za www.sanbi.ac.za Reproduced by kind permission of Pan European Networks Ltd, www.paneuropeannetworks.com © Pan European Networks 2014
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DR ALAN CHRISTOFFELS
Responding to a parasitic invasion Research Chair in Bioinformatics and Health Genomics, Dr Alan Christoffels, shares some of the details of his laboratory’s work on genomics and the role that he plays as an educator of future scientists specifically, its application to communicable diseases? My career started out in the medical sciences, and as time went on, I found myself having to engage with data more and more. A natural affinity for computers made the transition to formal computational biology training an easy career shift for me. The first bioinformatics institute was established at the time when I was considering my PhD options. My choice of research topic is linked to the prevailing disease burden on the African continent and specifically in South Africa.
You lead the South African National Bioinformatics Institute (SANBI) lab’s research on host-pathogen interaction. Could you provide a brief overview of your work in the field? Different host immune responses are invoked during parasitic invasion. These immune responses can represent evolutionary adaptations specific to certain organisms, and they are clearly illustrated in the three model systems that are used in my laboratory. The three relationships we focus on are between Anopheles and Plasmodium, humans and Mycobacterium, and Glossina and Trypanosoma. My lab uses a combination of computational and experimental approaches to unravel the molecular interactions at the hostpathogen interface. We also aim to develop high throughput genomics methods, including next generation sequencing data analysis approaches, in order to study communicable diseases such as tuberculosis, malaria and sleeping sickness. As part of an international tsetse genome consortium, my group has been analysing the tsetse genome with a view to understanding the evolution of the immune system and its response to invading parasites. Why did you decide to pursue a career in computational biology research and,
The Journal of Experimental Zoology featured the coelacanth research in the September 2014 Volume 322B, Number 6 edition.
By what means is SANBI developing throughput genomics methods such as next generation sequencing data analysis for the study of diseases like tuberculosis, malaria and sleeping sickness? Across all these disease model systems, the issue of data integration is key. We have access to large sequencing datasets, and we often find ourselves having to either alter existing computational approaches such as genome annotation pipelines or detect genetic variation. On the other hand, we are using machine-learning techniques to identify protein interaction networks between humans and mycobacteria. How is the biomedical research conducted at SANBI relevant in both African and international contexts? The research portfolio at SANBI spans both communicable and non-communicable diseases. Each project focuses on a disease that is pertinent to South Africa, the African region and the international community; for example, our work on developing a cost effective assay for HIV drug resistance testing has a global impact. Multidrug resistance and extreme drug resistance is also a global problem. We are using a combination of metabolic networks and drug design to look at new drug targets. Alongside pioneering biomedical research, SANBI aims to foster the highest levels of
excellence in education. Could you outline the undergraduate and postgraduate programmes and training courses offered by the Institute? Currently, we do not offer any complete undergraduate programmes, although we do teach a term module to third year BSc students as part of the biotechnology degree at the University of the Western Cape. At SANBI, we offer an MSc and PhD degree programme. These postgraduate degrees are researchbased and supplemented with short courses. Among these short courses is a compulsory seven-week course hosted at SANBI for all South African universities. What can students expect from SANBI with regard to mentoring, research opportunities and teaching environments? We have five research laboratories and their research themes cover HIV dynamics, noncommunicable diseases, plant viruses, clinical biomarker discovery and host-pathogen interactions. Each of these labs is embedded in multinational collaborative projects, and students will have an opportunity to engage with an international network of researchers. Participation in this global collaboration will also allow students to enjoy overseas visits as part of their graduate experience. On a personal level, what do you believe to be SANBI’s greatest accomplishment to date? I will not single out any specific research project, but the institute as a whole has achieved a number of important accomplishments. We have delivered on our mandate to develop computational biology in South Africa and the African region, for example, and our graduate students have taken up prominent academic positions at local universities – or have gone abroad, and are contributing significantly on an international stage.
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