Recipient organisationGenome Research Limited operating as the Wellcome Trust Sanger Institute
Funding£2.0M
PeriodApr 2018 — Sept 2022
In plain English
AI plain-English summary
Malaria researchers are shifting genome sequencing out of a single UK super-lab and into labs across West Africa, where the disease kills hundreds of thousands of children each year. For over a decade, the Wellcome Sanger Institute has sequenced malaria parasites and mosquito genomes from field samples at its central facility in Cambridge. That made sense when the equipment was expensive and the science was fundamental. But sequencing technology has become cheaper and more portable, and the need is now practical: national malaria control programmes need real-time genetic data to track drug-resistant parasites or insecticide-resistant mosquitoes as they emerge and spread. If this decentralisation succeeds, local teams in West Africa will run their own sequencing machines and feed data into a global surveillance network. That means a malaria control officer in Ghana could learn within weeks—not years—that a new resistant strain has arrived from another continent, and adjust treatment guidelines accordingly. The project also builds local leadership in genomic epidemiology, so that the analytical tools and data-sharing policies are shaped by the people who use them, not dictated from abroad.
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BACKGROUND OF STRATEGIC INVESTMENT The Sanger Institute has played a pioneering role in genome research on infectious pathogens. One of the first genomes to be sequenced at Sanger was the malaria parasite Plasmodium falciparum, and in 2006 the Institute committed to a major programme of basic research on malaria, with the long term goal of translating this into new tools to control and eliminate the disease. Our 2016-21 quinquennial plan comprises five major scientific programmes in Cancer, Malaria, Infection Genomics, Human Genetics and Cellular Genetics. Sanger researchers have made seminal discoveries about how parasites invade human red blood cells, genetic resistance to malaria in African children, Plasmodium drug resistance, Anopheles insecticide resistance and other fundamental parasite biology. Sanger has also made an impact on malaria research worldwide through the large data resources and novel technologies that it has developed and made openly available to the research community. From its inception, the Sanger Malaria Programme has worked in close collaboration with research groups in developing countries. Together with the MRC Centre for Genomics and Global Health at Oxford University, it serves as the resource centre for MalariaGEN, a data-sharing network of malaria researchers in more than 35 malaria-endemic countries (www.malariagen.net). Over the past 12 years, MalariaGEN has established an international reputation for generating large open access datasets, which have become the benchmark for Plasmodium and Anopheles population genomics; for promoting equitable data sharing between researchers in rich and poor countries; and for research capacity building in malaria endemic countries. STRATEGIC CASE FOR DECENTRALISATION This proposal represents a major shift in the way that we work with our collaborators in malaria endemic countries. When we started out on genome sequencing of Plasmodium parasites and Anopheles mosquitoes from field samples, there were massive technical and computational challenges to overcome, and both we and our collaborators saw it primarily as basic rather than applied research. It also required expensive capital equipment and infrastructure, and it made practical sense for the genome sequencing to be done at Sanger. There has been remarkable progress in all of these areas over the past few years, and it now makes both the economic and the technical for the genome sequencing done to be locally. The case for decentralisation is in large measure a successful consequence of our past strategic investment. Having put in place the scientific foundations and developed much of the underlying technology required for genomic surveillance of malaria, we are now in a good position to translate this into practical tools and procedures that will help national malaria control programmes (NMCPs) to achieve their objectives. Making the transition from centralised to local genome sequencing is not just a matter of installing the equipment and training local staff, because genomic surveillance is one of the most rapidly growing areas of 'Big Data', i.e. the data generated by a local sequencing machine is greatly amplified in information content and practical value if it is part of a global data sharing network. For example, if a new form of parasite drug resistance or mosquito insecticide resistance emerges elsewhere in the world, it will greatly help an NMCP to monitor and manage the problem if the genomic analysis software is continually updated to incorporate the most useful genetic markers, which are likely to have been discovered elsewhere. Therefore, as well as installing the equipment and providing training, it is crucial to build local leadership in the new science of genomic epidemiology, combined with mechanisms of sharing data across different sequencing labs. It requires the development of informatic systems to share data, and also the development policies
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