High-throughput automated microfluidic sample preparation for accurate microbial genomics
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High-throughput automated.pdf
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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
Date Issued
January 2017
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
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.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Physics
Terms of Use
Creative Commons Attribution 4.0 International License
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DOI of Published Version
https://doi.org/10.1038/ncomms13919
