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).
Highlights
High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations
Using PlasmoView to analyze more than double the number of samples and 5 additional populations, we identify 22 nonsynonymous single-nucleotide polymorphisms (SNPs) and confirm the locus has low diversity (Figure 4) with only 5 SNPs exhibiting a frequency greater than 10%
The continued public health burden of malaria and emergence of drug resistance requires the development of new treatments, vaccines and control measures
Summary
High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. Whilst the plasmodDB [12] and genedb [13] web-browsers provide genomic annotation and support the investigation of SNPs in individual parasite strains, there is a need for additional information (eg, allele frequencies and population statistics) across the growing collection of publicly available sequences and genotypes from clinical Pf isolates.
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