Efficient depletion of host DNA contamination in malaria clinical sequencing.

Oyola, S. O. et al. (2013) Efficient depletion of host DNA contamination in malaria clinical sequencing. Journal of Clinical Microbiology, 51(3), pp. 745-751. (doi: 10.1128/JCM.02507-12) (PMID:23224084) (PMCID:PMC3592063)

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Abstract

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Oyola, S. O., Gu, Y., Manske, M., Otto, T. D., O'Brien, J., Alcock, D., Macinnis, B., Berriman, M., Newbold, C. I., Kwiatkowski, D. P., Swerdlow, H. P., and Quail, M. A.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Journal of Clinical Microbiology
ISSN:0095-1137
ISSN (Online):1098-660X
Published Online:05 December 2012
Copyright Holders:Copyright ©2013 American Society for Microbiology
First Published:First published in Journal of Clinical Microbiology 51(3):745-751:
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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