title: Efficient depletion of host DNA contamination in malaria clinical sequencing.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom. Samuel.oyola@sanger.ac.uk
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Oyola
authors.forename: Yong
authors.initials: Y
authors.lastname: Gu
authors.forename: Magnus
authors.initials: M
authors.lastname: Manske
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.forename: John
authors.initials: J
authors.lastname: O'Brien
authors.forename: Daniel
authors.initials: D
authors.lastname: Alcock
authors.forename: Bronwyn
authors.initials: B
authors.lastname: Macinnis
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Chris I
authors.initials: CI
authors.lastname: Newbold
authors.forename: Dominic P
authors.initials: DP
authors.lastname: Kwiatkowski
authors.forename: Harold P
authors.initials: HP
authors.lastname: Swerdlow
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
mesh_terms: D059018:DNA Contamination; D019175:DNA Methylation; D016054:DNA, Protozoan / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D006868:Hydrolysis; D016778:Malaria, Falciparum / Q000469:parasitology*; D008967:Molecular Biology / Q000379:methods*; D017720:Molecular Epidemiology / Q000379:methods; D010274:Parasitology / Q000379:methods*; D010963:Plasmodium falciparum / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D016054:DNA, Protozoan