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High-throughput automated microfluidic sample preparation for accurate microbial genomics

Author

Listed:
  • Soohong Kim

    (The Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

  • Joachim De Jonghe

    (The Broad Institute of MIT and Harvard
    University of Cambridge)

  • Anthony B. Kulesa

    (The Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

  • David Feldman

    (The Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

  • Tommi Vatanen

    (The Broad Institute of MIT and Harvard
    Aalto University School of Science)

  • Roby P. Bhattacharyya

    (The Broad Institute of MIT and Harvard
    Massachusetts General Hospital)

  • Brittany Berdy

    (Northeastern University)

  • James Gomez

    (The Broad Institute of MIT and Harvard)

  • Jill Nolan

    (The Broad Institute of MIT and Harvard)

  • Slava Epstein

    (Northeastern University)

  • Paul C. Blainey

    (The Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

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.

Suggested Citation

  • Soohong Kim & Joachim De Jonghe & Anthony B. Kulesa & David Feldman & Tommi Vatanen & Roby P. Bhattacharyya & Brittany Berdy & James Gomez & Jill Nolan & Slava Epstein & Paul C. Blainey, 2017. "High-throughput automated microfluidic sample preparation for accurate microbial genomics," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms13919
    DOI: 10.1038/ncomms13919
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