Hybrid selection for sequencing pathogen genomes from clinical samples

• Published in: Genome biology Vol. 12; no. 8; pp. R73 - 2655
• Main Authors: Melnikov, Alexandre, Galinsky, Kevin, Rogov, Peter, Fennell, Timothy, Van Tyne, Daria, Russ, Carsten, Daniels, Rachel, Barnes, Kayla G, Bochicchio, James, Ndiaye, Daouda, Sene, Papa D, Wirth, Dyann F, Nusbaum, Chad, Volkman, Sarah K, Birren, Bruce W, Gnirke, Andreas, Neafsey, Daniel E
• Format: Journal Article
• Language: English
• Published: London BioMed Central 11.08.2011
• Subjects: Animal Genetics and Genomics; Animalia; Bioinformatics; Biomedical and Life Sciences; Chromosome Mapping - methods; DNA; DNA, Protozoan - genetics; Evolutionary Biology; genome; Genome, Protozoan; Human Genetics; Humans; Life Sciences; malaria; Malaria, Falciparum - parasitology; Method; Microbial Genetics and Genomics; Nucleic Acid Hybridization - methods; parasites; pathogens; patients; Plant Genetics and Genomics; Plasmodium falciparum; Plasmodium falciparum - genetics; sequence analysis; Sequence Analysis, DNA - methods; Wolbachia; Sequencing Coverage; Malaria; Whole Genome Amplification; Falciparum Genome; Hybrid Selection
• ISSN: 1474-760X; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/gb-2011-12-8-r73

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.