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

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.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.CF11 filtration is a cost-effective, scalable, one-step approach to remove human DNA from P. falciparum-infected whole blood samples.Recent technological advances have enabled next-generation genomic and transcriptomic analysis of Plasmodium falciparum from parasitized whole blood samples without the need for culturing. High-density genotyping of parasites obtained directly from patients with malaria has improved our understanding of population structure and genomic and transcriptional variation [1,2]. Highly parallel sequencing is currently being used to identify the genetic determinants of clinically relevant phenotypes including drug resistance, vaccine escape and disease severity. Importantly, genomic characterization of parasite populations in patients captures intra-host diversity and prevents the potential loss of sequence data from phenotype-conferring parasite isolates during their culture adaptation.The performance of highly parallel sequencing platforms, such as Illumina, is greatly enhanced in sample preparations with a high parasite-to-human nucleic acid ratio [3]. Such high ratios can be achieved by either selectively capturing parasite nucleic acids or by removing human material from the sample.