A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

被引:55
作者
Kim, Hanyoup [1 ]
Jebrail, Mais J. [1 ]
Sinha, Anupama [2 ]
Bent, Zachary W. [2 ]
Solberg, Owen D. [2 ]
Williams, Kelly P. [2 ]
Langevin, Stanley A. [2 ]
Renzi, Ronald F. [3 ]
Van De Vreugde, James L. [3 ]
Meagher, Robert J. [1 ]
Schoeniger, Joseph S. [2 ]
Lane, Todd W. [2 ]
Branda, Steven S. [1 ]
Bartsch, Michael S. [3 ]
Patel, Kamlesh D. [3 ]
机构
[1] Sandia Natl Labs, Dept Biotechnol & Bioengn, Livermore, CA USA
[2] Sandia Natl Labs, Dept Syst Biol, Livermore, CA USA
[3] Sandia Natl Labs, Livermore, CA USA
来源
PLOS ONE | 2013年 / 8卷 / 07期
关键词
PLURONIC ADDITIVES; SAMPLE PREPARATION; READ ALIGNMENT; CHEMISTRY; DROPLETS;
D O I
10.1371/journal.pone.0068988
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
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页数:9
相关论文
共 45 条
[31]   Deep sequencing reveals 50 novel genes for recessive cognitive disorders [J].
Najmabadi, Hossein ;
Hu, Hao ;
Garshasbi, Masoud ;
Zemojtel, Tomasz ;
Abedini, Seyedeh Sedigheh ;
Chen, Wei ;
Hosseini, Masoumeh ;
Behjati, Farkhondeh ;
Haas, Stefan ;
Jamali, Payman ;
Zecha, Agnes ;
Mohseni, Marzieh ;
Puettmann, Lucia ;
Vahid, Leyla Nouri ;
Jensen, Corinna ;
Moheb, Lia Abbasi ;
Bienek, Melanie ;
Larti, Farzaneh ;
Mueller, Ines ;
Weissmann, Robert ;
Darvish, Hossein ;
Wrogemann, Klaus ;
Hadavi, Valeh ;
Lipkowitz, Bettina ;
Esmaeeli-Nieh, Sahar ;
Wieczorek, Dagmar ;
Kariminejad, Roxana ;
Firouzabadi, Saghar Ghasemi ;
Cohen, Monika ;
Fattahi, Zohreh ;
Rost, Imma ;
Mojahedi, Faezeh ;
Hertzberg, Christoph ;
Dehghan, Atefeh ;
Rajab, Anna ;
Banavandi, Mohammad Javad Soltani ;
Hoffer, Julia ;
Falah, Masoumeh ;
Musante, Luciana ;
Kalscheuer, Vera ;
Ullmann, Reinhard ;
Kuss, Andreas Walter ;
Tzschach, Andreas ;
Kahrizi, Kimia ;
Ropers, H. Hilger .
NATURE, 2011, 478 (7367) :57-63
[32]   Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach [J].
Nakamura, Shota ;
Yang, Cheng-Song ;
Sakon, Naomi ;
Ueda, Mayo ;
Tougan, Takahiro ;
Yamashita, Akifumi ;
Goto, Naohisa ;
Takahashi, Kazuo ;
Yasunaga, Teruo ;
Ikuta, Kazuyoshi ;
Mizutani, Tetsuya ;
Okamoto, Yoshiko ;
Tagami, Michihira ;
Morita, Ryoji ;
Maeda, Norihiro ;
Kawai, Jun ;
Hayashizaki, Yoshihide ;
Nagai, Yoshiyuki ;
Horii, Toshihiro ;
Iida, Tetsuya ;
Nakaya, Takaaki .
PLOS ONE, 2009, 4 (01)
[33]  
Nextera&REG, 2012, NEXTERA SAMPLE PREP
[34]  
Nextera&TRADE, 2011, NEXTERA DNA SAMPLE P
[35]   Digital Microfluidic Magnetic Separation for Particle-Based Immunoassays [J].
Ng, Alphonsus H. C. ;
Choi, Kihwan ;
Luoma, Robert P. ;
Robinson, John M. ;
Wheeler, Aaron R. .
ANALYTICAL CHEMISTRY, 2012, 84 (20) :8805-8812
[36]   Electrowetting-based actuation of liquid droplets for microfluidic applications [J].
Pollack, MG ;
Fair, RB ;
Shenderov, AD .
APPLIED PHYSICS LETTERS, 2000, 77 (11) :1725-1726
[37]   Unlocking Short Read Sequencing for Metagenomics [J].
Rodrigue, Sebastien ;
Materna, Arne C. ;
Timberlake, Sonia C. ;
Blackburn, Matthew C. ;
Malmstrom, Rex R. ;
Alm, Eric J. ;
Chisholm, Sallie W. .
PLOS ONE, 2010, 5 (07)
[38]   Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis [J].
Scholz, Matthew B. ;
Lo, Chien-Chi ;
Chain, Patrick S. G. .
CURRENT OPINION IN BIOTECHNOLOGY, 2012, 23 (01) :9-15
[39]   A feedback control system for high-fidelity digital microfluidics [J].
Shih, Steve C. C. ;
Fobel, Ryan ;
Kumar, Paresh ;
Wheeler, Aaron R. .
LAB ON A CHIP, 2011, 11 (03) :535-540
[40]   Development of a digital microfluidic platform for point of care testing [J].
Sista, Ramakrishna ;
Hua, Zhishan ;
Thwar, Prasanna ;
Sudarsan, Arjun ;
Srinivasan, Vijay ;
Eckhardt, Allen ;
Pollack, Michael ;
Pamula, Vamsee .
LAB ON A CHIP, 2008, 8 (12) :2091-2104