Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research

Abstract

The study of the three protagonists in malaria-the Plasmodium parasite, the Anopheles mosquito, and the human host-is key to developing methods to control and eventually eliminate the disease. Genomic technologies, including the recent development of next-generation sequencing, enable interrogation of this triangle to an unprecedented level of scrutiny, and promise exciting progress toward real-time epidemiology studies and the study of evolutionary adaptation. We discuss the use of genomics by the International Centers of Excellence for Malaria Research, a network of field sites and laboratories in malaria-endemic countries that undertake cutting-edge research, training, and technology transfer in malarious countries of the world.

Figure 1.

Quantification of multiclonal Plasmodium chabaudi mixtures using Ion Torrent amplicon sequencing and quantitative polymerase chain reaction (qPCR). Stacked plots representing proportion of P. chabaudi clones ER (black), BC (gray), and AT (white) obtained for two sets of parasite mixtures, shown in panels (A) and (B), containing low concentrations of the ER and AT clones, respectively. qPCR replicates are represented as qPCR_1 and qPCR_2, whereas sequencing replicates are grouped as Run1 and Run2 (biological replicates) and Lane1 and Lane2 (technical replicates).

Figure 2.

A simple and efficient filtering procedure to remove leukocytes from small volumes of Plasmodium-infected venous blood. The left panel (A) shows how to prepare commercially available leukocyte depletion filters (Fresenius Kabi BioR 01 Plus) for removing leukocytes. Note that the tubing must be cut with a scissor as indicated, to remove the storage bag and the adaptor from the filtering device. The right panel (B) shows how the adapted filters are used, in a laminar flow safety hood. A 10-mL syringe is used to apply acid citrate dextrose (ACD) treated blood samples, whereas a second 10-mL syringe is adapted to the end of the tubing to recover the filtered (leukocyte-depleted) material. After the filtering procedure, the leukocyte depletion filter is washed extensively with RPMI 1640 medium to recover red blood cells that have been retained in the tubing.

Figure 3.

Screen shots from PlasmoDB illustrating methods to access single-nucleotide polymorphism (SNP) data from International Centers of Excellence for Malaria Research (ICEMR) projects. (A) PlasmoDB home page showing where SNP data can be accessed (red rectangles). (B) Map of the geographic distribution of sequenced Plasmodium isolates from ICEMR locations. (C) Sequenced isolates can be compared in PlasmoDB using the search “Identify SNPs based on differences between groups of isolates.” (D) Metadata characteristics such as geographical location can be leveraged to identify SNPs that differentiate isolates from Peru and Colombia. (E) Results are returned in a table containing the location of the SNP and various SNP statistics. (F) The sequence alignment around any SNP can be visualized in the PlasmoDB genome browser.

Figure 4.

Screen shots from PlasmoDB depicting a search for genes containing at least 20 non-synonymous SNPs based on data from ICEMR isolates. (A) The search for genes based on SNP characteristics allows filtering of isolates based on metadata, such as geographic location, and defining the type of SNPs of interest. (B) Results are returned in a table that shows which genes contain the SNPs of interest.