The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Nat Commun. 2017 Jan 27;8:13919. doi: 10.1038/ncomms13919.
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.
低成本的 shotgun 基因测序正在改变微生物科学。测序仪器非常有效，以至于样品制备现在是关键的限制因素。在这里，我们引入了一种微流控样品制备平台，它集成了细胞中的关键步骤，用于多达 96 个样品的测序文库样品制备，同时将 DNA 输入要求降低 100 倍，而保持或提高数据质量。我们展示的通用微架构支持具有任意数量的反应、清洗或捕获步骤的工作流程。通过减少样品数量要求，我们实现了低输入（∼10,000 个细胞）结核分枝杆菌和土壤微生物群落的全基因组 shotgun（WGS）测序，结果更优。我们还利用增强的通量对约 400 个临床铜绿假单胞菌文库进行了测序，并展示了出色的单核苷酸多态性检测性能，该性能解释了表型观察到的抗生素耐药性。完全集成的芯片实验室样品制备克服了技术障碍，使基因组学在许多基础研究和转化应用中得到更广泛的应用。
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