PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.


Preston, MD; Assefa, SA; Ocholla, H; Sutherland, CJ; Borrmann, S; Nzila, A; Michon, P; Hien, TT; Bousema, T; Drakeley, CJ; Zongo, I; Ouédraogo, JB; Djimde, AA; Doumbo, OK; Nosten, F; Fairhurst, RM; Conway, DJ; Roper, C; Clark, TG; (2014) PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. The Journal of infectious diseases, 209 (11). pp. 1808-15. ISSN 0022-1899 DOI: 10.1093/infdis/jit812

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Abstract

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).

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Faculty of Infectious and Tropical Diseases > Dept of Immunology and Infection
Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Research Centre: Malaria Centre
Centre for Statistical Methodology
PubMed ID: 24338354
Web of Science ID: 336485900018
URI: http://researchonline.lshtm.ac.uk/id/eprint/2131872

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