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Targeted next generation sequencing for malaria molecular epidemiology in Africa

New Content ItemThe last decade has seen a revolution in sequencing technology. The advent of parallelized high-throughput sequencing methods has supported an explosion in the amount of data that can be generated with dramatic reductions in the per base cost of the sequencing. Laboratory and bioinformatic processes have been rapidly developing to allow these innovations to assess a variety of biologic questions, ranging from questions best answered by whole genome sequencing to those best understood by evaluating more samples at one or a few specific loci in the genome (i.e. targeted sequencing). For the most part, this sequencing work has been conducted in Europe, North America and Asia.

Timely and annotated targeted sequencing data can provide essential information directly usable by National Malaria Control Programmes (NMCP), as well as answer basic questions in malaria epidemiology and biology. Surveillance of drug resistance, assessing parasite migration, and understanding transmission routes are all areas where targeted sequencing can provide valuable biologic insights and inform malaria control. These approaches allow higher-throughput, sensitivity and quantification of mixed samples compared to previously used targeted Sanger sequencing methods. At the same time, the development of more inexpensive benchtop sequencers has the potential to change the penetration of next generation sequencing into African research institutions. However, there remain significant technical and computational challenges for such analyses and highlight a need for additional bioinformatics expertise given the wide applicability.

This Thematic Series of Malaria Journal aims to highlight the potential uses of parallelized high-throughput sequencing methods in a way that is accessible to malaria control programmes to fulfil the potential for understanding the molecular epidemiology of malaria in Africa. It highlights some of the questions that are important to programmes and the potential approaches to answer these questions. The hurdles for implementing these methods at African institutions will be partially addressed, as well as potential approaches for making these methodologies achievable and sustainable in Africa.

Guest Editor: Jonathan Juliano
Series published:  2019

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