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High-throughput automated microfluidic sample preparation for accurate microbial genomics

Author(s)
De Jonghe, Joachim; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Kim, Soohong; Kulesa, Anthony Benjamin; Feldman, David; Blainey, Paul C; ... Show more Show less
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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.
Date issued
2017-01
URI
http://hdl.handle.net/1721.1/108270
Department
Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Physics
Journal
Nature Communications
Publisher
Nature Publishing Group
Citation
Kim, Soohong et al. “High-Throughput Automated Microfluidic Sample Preparation for Accurate Microbial Genomics.” Nature Communications 8 (2017): 13919. © 2017 Macmillan Publishers Limited
Version: Final published version
ISSN
2041-1723

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