Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

Overview

Journal J Clin Microbiol

Specialty Microbiology

Date 2012 Dec 11

PMID 23224084

Citations 36

Authors

Samuel O Oyola

Yong Gu

Magnus Manske

Thomas D Otto

John OBrien

Daniel Alcock

Bronwyn MacInnis

Matthew Berriman

Chris I Newbold

Dominic P Kwiatkowski

Harold P Swerdlow

Michael A Quail

Affiliations

Soon will be listed here.

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.

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