title: Hybrid selection for sequencing pathogen genomes from clinical samples.
abstract: We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.
authors.affiliation: Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Melnikov
authors.forename: Kevin
authors.initials: K
authors.lastname: Galinsky
authors.forename: Peter
authors.initials: P
authors.lastname: Rogov
authors.forename: Timothy
authors.initials: T
authors.lastname: Fennell
authors.forename: Daria
authors.initials: D
authors.lastname: Van Tyne
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Rachel
authors.initials: R
authors.lastname: Daniels
authors.forename: Kayla G
authors.initials: KG
authors.lastname: Barnes
authors.forename: James
authors.initials: J
authors.lastname: Bochicchio
authors.forename: Daouda
authors.initials: D
authors.lastname: Ndiaye
authors.forename: Papa D
authors.initials: PD
authors.lastname: Sene
authors.forename: Dyann F
authors.initials: DF
authors.lastname: Wirth
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Volkman
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Neafsey
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D016054:DNA, Protozoan / Q000235:genetics*; D018503:Genome, Protozoan; D006801:Humans; D016778:Malaria, Falciparum / Q000469:parasitology*; D009693:Nucleic Acid Hybridization / Q000379:methods; D010963:Plasmodium falciparum / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D016054:DNA, Protozoan