Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples
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 us...
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ftdoajarticles:oai:doaj.org/article:0c6918187f5440e09ba58cd1df5a4860 2023-05-15T15:14:10+02:00 Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples Venkatesan Meera Amaratunga Chanaki Campino Susana Auburn Sarah Koch Oliver Lim Pharath Uk Sambunny Socheat Duong Kwiatkowski Dominic P Fairhurst Rick M Plowe Christopher V 2012-02-01T00:00:00Z https://doi.org/10.1186/1475-2875-11-41 https://doaj.org/article/0c6918187f5440e09ba58cd1df5a4860 EN eng BMC http://www.malariajournal.com/content/11/1/41 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-11-41 1475-2875 https://doaj.org/article/0c6918187f5440e09ba58cd1df5a4860 Malaria Journal, Vol 11, Iss 1, p 41 (2012) CF11 Cellulose powder Leukocyte depletion Plasmodium falciparum Malaria Next-generation sequencing Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2012 ftdoajarticles https://doi.org/10.1186/1475-2875-11-41 2022-12-31T09:09:26Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 11 1 41 |
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ftdoajarticles |
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English |
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CF11 Cellulose powder Leukocyte depletion Plasmodium falciparum Malaria Next-generation sequencing Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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CF11 Cellulose powder Leukocyte depletion Plasmodium falciparum Malaria Next-generation sequencing Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Venkatesan Meera Amaratunga Chanaki Campino Susana Auburn Sarah Koch Oliver Lim Pharath Uk Sambunny Socheat Duong Kwiatkowski Dominic P Fairhurst Rick M Plowe Christopher V Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
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CF11 Cellulose powder Leukocyte depletion Plasmodium falciparum Malaria Next-generation sequencing Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Venkatesan Meera Amaratunga Chanaki Campino Susana Auburn Sarah Koch Oliver Lim Pharath Uk Sambunny Socheat Duong Kwiatkowski Dominic P Fairhurst Rick M Plowe Christopher V |
author_facet |
Venkatesan Meera Amaratunga Chanaki Campino Susana Auburn Sarah Koch Oliver Lim Pharath Uk Sambunny Socheat Duong Kwiatkowski Dominic P Fairhurst Rick M Plowe Christopher V |
author_sort |
Venkatesan Meera |
title |
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
title_short |
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
title_full |
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
title_fullStr |
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
title_full_unstemmed |
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum -infected whole blood samples |
title_sort |
using cf11 cellulose columns to inexpensively and effectively remove human dna from plasmodium falciparum -infected whole blood samples |
publisher |
BMC |
publishDate |
2012 |
url |
https://doi.org/10.1186/1475-2875-11-41 https://doaj.org/article/0c6918187f5440e09ba58cd1df5a4860 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 11, Iss 1, p 41 (2012) |
op_relation |
http://www.malariajournal.com/content/11/1/41 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-11-41 1475-2875 https://doaj.org/article/0c6918187f5440e09ba58cd1df5a4860 |
op_doi |
https://doi.org/10.1186/1475-2875-11-41 |
container_title |
Malaria Journal |
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11 |
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1 |
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41 |
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1766344659849707520 |