title: A microfluidic DNA library preparation platform for next-generation sequencing.
abstract: Next-generation sequencing (NGS) is emerging as a powerful tool for elucidating genetic information for a wide range of applications. Unfortunately, the surging popularity of NGS has not yet been accompanied by an improvement in automated techniques for preparing formatted sequencing libraries. To address this challenge, we have developed a prototype microfluidic system for preparing sequencer-ready DNA libraries for analysis by Illumina sequencing. Our system combines droplet-based digital microfluidic (DMF) sample handling with peripheral modules to create a fully-integrated, sample-in library-out platform. In this report, we use our automated system to prepare NGS libraries from samples of human and bacterial genomic DNA. E. coli libraries prepared on-device from 5 ng of total DNA yielded excellent sequence coverage over the entire bacterial genome, with >99% alignment to the reference genome, even genome coverage, and good quality scores. Furthermore, we produced a de novo assembly on a previously unsequenced multi-drug resistant Klebsiella pneumoniae strain BAA-2146 (KpnNDM). The new method described here is fast, robust, scalable, and automated. Our device for library preparation will assist in the integration of NGS technology into a wide variety of laboratories, including small research laboratories and clinical laboratories.
authors.affiliation: Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, California, USA.
authors.forename: Hanyoup
authors.initials: H
authors.lastname: Kim
authors.forename: Mais J
authors.initials: MJ
authors.lastname: Jebrail
authors.forename: Anupama
authors.initials: A
authors.lastname: Sinha
authors.forename: Zachary W
authors.initials: ZW
authors.lastname: Bent
authors.forename: Owen D
authors.initials: OD
authors.lastname: Solberg
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Williams
authors.forename: Stanley A
authors.initials: SA
authors.lastname: Langevin
authors.forename: Ronald F
authors.initials: RF
authors.lastname: Renzi
authors.forename: James L
authors.initials: JL
authors.lastname: Van De Vreugde
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Meagher
authors.forename: Joseph S
authors.initials: JS
authors.lastname: Schoeniger
authors.forename: Todd W
authors.initials: TW
authors.lastname: Lane
authors.forename: Steven S
authors.initials: SS
authors.lastname: Branda
authors.forename: Michael S
authors.initials: MS
authors.lastname: Bartsch
authors.forename: Kamlesh D
authors.initials: KD
authors.lastname: Patel
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D015723:Gene Library; D016680:Genome, Bacterial / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation*; D006801:Humans; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation*; D017422:Sequence Analysis, DNA / Q000295:instrumentation*; D018511:Systems Integration
chemical_list: D004269:DNA, Bacterial
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