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Báo cáo y học: "Hybrid selection for sequencing pathogen genomes from clinical samples"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Hybrid selection for sequencing pathogen genomes from clinical samples. | Melnikov et al. Genome Biology 2011 12 R73 http genomebiology.eom 2011 12 8 R73 Genome Biology METHOD Open Access Hybrid selection for sequencing pathogen genomes from clinical samples 1 11 1 2 1 Alexandre Melnikov Kevin Galinsky Peter Rogov Timothy Fennell Daria Van Tyne Carsten Russ 12 1 3 3 2 Rachel Daniels Kayla G Barnes James Bochicchio Daouda Ndiaye Papa D Sene Dyann F Wirth Chad Nusbaum1 Sarah K Volkman2 Bruce W Birren1 Andreas Gnirke1 and Daniel E Neafsey1 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. Background The falling cost of DNA sequencing means that sample quality rather than expense is now the blocking issue for many infectious disease genome sequencing projects. Pathogen genomes are generally very small relative to that of their human host and are typically haploid in nature. Therefore even a modest number of nucleated human cells present in infectious disease samples may result in the pathogen DNA representation being dwarfed relative to the host human DNA. This difference in representation poses a significant challenge to achieving adequate sequence coverage of the pathogen genome in a cost-effective manner. Separation of host and pathogen cells prior to DNA extraction can be difficult or inconvenient particularly in field settings common to clinics in developing countries. This barrier to the efficient sequencing of pathogen genomes comes at a time when the potential motivations and rewards for large-scale sequencing of pathogens .