High-throughput automated microfluidic sample preparation for accurate microbial genomics
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Nature Communications, Volume 8, pp. 1-10
Abstract
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼ 10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.Description
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Kim, S, De Jonghe, J, Kulesa, A B, Feldman, D, Vatanen, T, Bhattacharyya, R P, Berdy, B, Gomez, J, Nolan, J, Epstein, S & Blainey, P C 2017, 'High-throughput automated microfluidic sample preparation for accurate microbial genomics', Nature Communications, vol. 8, 13919, pp. 1-10. https://doi.org/10.1038/ncomms13919