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Background  Genome and transcriptome studies of  Plasmodium  nucleic acids obtained from parasitized whole blood are greatly improved by depletion of human DNA or enrichment of parasite DNA prior to next-generation sequencing and microarray hybridization. The most effective method currently used is a two-step procedure to deplete leukocytes: centrifugation using density gradient media followed by filtration through expensive, commercially available columns. This method is not easily implemented in field studies that collect hundreds of samples and simultaneously process samples for multiple laboratory analyses. Inexpensive syringes, hand-packed with CF11 cellulose powder, were recently shown to improve  ex vivo  cultivation of  Plasmodium vivax  obtained from parasitized whole blood. This study was undertaken to determine whether CF11 columns could be adapted to isolate  Plasmodium falciparum  DNA from parasitized whole blood and achieve current quantity and purity requirements for Illumina sequencing.    Methods  The CF11 procedure was compared with the current two-step standard of leukocyte depletion using parasitized red blood cells cultured  in vitro  and parasitized blood obtained  ex vivo  from Cambodian patients with malaria. Procedural variations in centrifugation and column size were tested, along with a range of blood volumes and parasite densities.    Results  CF11 filtration reliably produces 500 nanograms of DNA with less than 50% human DNA contamination, which is comparable to that obtained by the two-step method and falls within the current quality control requirements for Illumina sequencing. In addition, a centrifuge-free version of the CF11 filtration method to isolate  P. falciparum  DNA at remote and minimally equipped field sites in malaria-endemic areas was validated.    Conclusions  CF11 filtration is a cost-effective, scalable, one-step approach to remove human DNA from  P. falciparum -infected whole blood samples.

Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples