Mar 11

Researchers at SANBI facilitate low-cost HIV drug resistance testing

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Members of the Travers group involved in the development of Seq2Res

The introduction of HIV antiretroviral (ARV) therapy programmes in Southern Africa has substantially reduced the burden of infection in HIV-positive individuals. In fact, the 2012 UNAIDS report estimates that as many as 14 million lives have been saved as a result of the rollout of such programmes throughout the world. There is, however, a problem facing the continued success of ARV therapy programmes: the emergence of viral resistance to ARVs. To date, no cost-effective HIV drug resistance test has been available for routine use in South Africa and other countries suffering from a high burden of HIV infections.

Recent advances in DNA sequencing have made it possible to offer a more sensitive HIV drug resistance test at a fraction of the cost (as much as a fivefold decrease). The downside of this approach, however, is that these technologies generate a vast amount of data that needs to be analysed and interpreted in a specialised and expensive manner, and are thus not easy to incorporate into routine testing procedures within South African hospitals and clinics, especially in remote and resource-limited settings.

The South African National Bioinformatics Institute (SANBI) at the University of the Western Cape has a solution. A team led by Prof Simon Travers has developed an easy-to-use computational tool called Seq2ResTM that can effectively process this data, meaning that the realisation of a cost-effective HIV drug resistance test is now a reality.

While Seq2ResTM is being used routinely within SANBI by bioinformatics specialists, the team has recently received significant funding from the South African Department of Science and Technology to deliver Seq2ResTM as a web-based application. This application will enable researchers and clinicians to routinely and easily process their drug resistance testing data without needing expert bioinformatics assistance. This development is being undertaken in collaboration with partners at the National Health Laboratory Service (NHLS) genotyping units in Tygerberg (Cape Town), the NHLS/University of the Witwatersrand Medical School (Johannesburg) and the National Institute for Communicable Diseases (NICD) in Johannesburg.

According to Prof Travers: “The real value of this approach is that it has been developed in a research environment in conjunction with all of the prospective end users in the South African public sector.”

When completed, SANBI will present Seq2ResTM for clinical, research and surveillance use, enabling the establishment of routine HIV drug resistance testing in Southern Africa.

For more information about SANBI’s involvement in the projects mentioned above, please visit the Travers’ Group site.

Nov 12

SANBI-UWC helps investigate health and heredity in Africa

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Genomics for Africa: Attendees at the inaugural H3Africa meeting in Addis Ababa on 6-10 October.

The first-ever pan-African research programme into disease and DNA was launched last month in Ethiopia, and scientists from the universities of the Western Cape, Cape Town, Witwatersrand, Pretoria, Limpopo, Rhodes and Stellenbosch are playing a starring role.

The Human Heredity and Health in Africa (H3Africa) project will unravel how Africans’ genes deal with illnesses such as tuberculosis, heart disease and sleeping sickness. Read more at the City Press.

Pictured below are some of the South African collaborators of this exciting initiative.

From the H3A bioinformatics network: Dr Oyekanmi Nash (National Biotechnology Development Agency, Nigeria), Dr Judith Kumuthini (CPGR, South Africa), Dr Nicky Mulder (UCT), Dr Nicki Tiffin (SANBI-UWC)

From the H3Africa kidney disease research network: from left to right, Professor Dwomoa Adu (University of Ghana Medical School), Dr Charlotte Osafo (Korle-Bu Teaching Hospital, Ghana), and Dr Nicki Tiffin (SANBI, UWC)

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Nov 09

SANBI takes top honours at ROD2012

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Imogen Wright(l) and UWC Dean of Science, Prof Davies-Coleman(r)

Alecia Naidu(l) and UWC Dean of Science, Prof Davies-Coleman(r)

Two of SANBI’s students received top honours at the recent 2012 UWC Science Faculty Post-Graduate Research Open Day (ROD2012). PhD student Imogen Wright from the HIV Evolution group at SANBI received the first prize for her oral presentation on the use of graphical processing units (GPUs) for the generation of biologically relevant multiple sequence alignments. Her implementation of the Hirchberg algorithm speeds up the process by several factors, decreasing the process from hours or days to mere minutes, and in some instances, seconds.

Another of SANBI’s PhD students, Alecia Naidu, a member of the TB Genomics Group, received the first prize for her poster presentation on the development of a computational framework for the management of next-generation sequencing (NGS) data. Her specific implementation of this framework manages mycobacterium tuberculosis NGS data.