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Open Access Highly Accessed Methodology

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

Meera Venkatesan12, Chanaki Amaratunga3, Susana Campino4, Sarah Auburn45, Oliver Koch6, Pharath Lim37, Sambunny Uk7, Duong Socheat7, Dominic P Kwiatkowski46, Rick M Fairhurst3 and Christopher V Plowe128*

Author Affiliations

1 Howard Hughes Medical Institute, University of Maryland School of Medicine, Baltimore, MD, USA

2 WorldWide Antimalarial Resistance Network Molecular Module, University of Maryland School of Medicine, Baltimore, MD, USA

3 National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA

4 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

5 Global Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia

6 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

7 National Centre for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia

8 Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA

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Malaria Journal 2012, 11:41  doi:10.1186/1475-2875-11-41

Published: 10 February 2012

Abstract

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.

Keywords:
CF11; Cellulose powder; Leukocyte depletion; Plasmodium falciparum; Malaria; Next-generation sequencing