Journal Article

PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation

Mark D. Preston, Samuel A. Assefa, Harold Ocholla, Colin J. Sutherland, Steffen Borrmann, Alexis Nzila, Pascal Michon, Tran Tinh Hien, Teun Bousema, Christopher J. Drakeley, Issaka Zongo, Jean-Bosco Ouédraogo, Abdoulaye A. Djimde, Ogobara K. Doumbo, Francois Nosten, Rick M. Fairhurst, David J. Conway, Cally Roper and Taane G. Clark

in The Journal of Infectious Diseases

Published on behalf of Infectious Diseases Society of America

Volume 209, issue 11, pages 1808-1815
Published in print June 2014 | ISSN: 0022-1899
Published online December 2013 | e-ISSN: 1537-6613 | DOI: https://dx.doi.org/10.1093/infdis/jit812

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Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).

Keywords: Plasmodium falciparum; malaria; genomics; drug resistance; vaccine targets; visualization

Journal Article.  3315 words.  Illustrated.

Subjects: Infectious Diseases ; Immunology ; Public Health and Epidemiology ; Microbiology

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