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Ott O, Tolppi S, Figueroa-Cruz J, Myagmar K, Unurbuyan K, Tripathi A. Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation. Sci Rep 2024; 14:12564. [PMID: 38822053 DOI: 10.1038/s41598-024-63014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Next-generation sequencing (NGS) is emerging as a powerful tool for molecular diagnostics but remains limited by cumbersome and inefficient sample preparation. We present an innovative automated NGS library preparation system with a simplified mechanical design that exploits both macro- and microfluidic properties for optimizing heat transfer, reaction kinetics, mass transfer, fluid mechanics, adsorption-desorption rates, and molecular thermodynamics. Our approach introduces a unique two-cannula cylindrical capillary system connected to a programmable syringe pump and a Peltier heating element able to execute all steps with high efficiency. Automatic reagent movement, mixing, and magnetic bead-based washing with capillary-based thermal cycling (capillary-PCR) are completely integrated into a single platform. The manual 3-h library preparation process is reduced to less than 15 min of hands-on time via optimally pre-plated reagent plates, followed by less than 6 h of instrument run time during which no user interaction is required. We applied this method to two library preparation assays with different DNA fragmentation requirements (mechanical vs. enzymatic fragmentation), sufficiently limiting consumable use to one cartridge and one 384 well-plate per run. Our platform successfully prepared eight libraries in parallel, generating sequencing data for both human and Escherichia coli DNA libraries with negligible coverage bias compared to positive controls. All sequencing data from our libraries attained Phred (Q) scores > 30, mapping to reference genomes at 99% confidence. The method achieved final library concentrations and size distributions comparable with the conventional manual approach, demonstrating compatibility with downstream sequencing and subsequent data analysis. Our engineering design offers repeatability and consistency in the quality of sequence-able libraries, asserting the importance of mechanical design considerations that employ and optimize fundamental fluid mechanics and heat transfer properties. Furthermore in this work, we provide unique insights into the mechanisms of sample loss within NGS library preparation assays compared with automated adaptations and pinpoint areas in which the principles of thermodynamics, fluid mechanics, and heat transfer can improve future mechanical design iterations.
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Affiliation(s)
- Olivia Ott
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Sabrina Tolppi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Jennifer Figueroa-Cruz
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khaliun Myagmar
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khulan Unurbuyan
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
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Guo J, Brassard D, Adam N, Verster AJ, Shay JA, Miville-Godin C, Janta-Polczynski M, Ferreira J, Mounier M, Pilar AV, Tapp K, Classen A, Shiu M, Charlebois D, Petronella N, Weedmark K, Corneau N, Veres T. Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries. LAB ON A CHIP 2024; 24:182-196. [PMID: 38044704 DOI: 10.1039/d3lc00781b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.
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Affiliation(s)
- Jimin Guo
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Daniel Brassard
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Nadine Adam
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Julie A Shay
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Caroline Miville-Godin
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Mojra Janta-Polczynski
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Jason Ferreira
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Maxence Mounier
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Ana V Pilar
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Kyle Tapp
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adam Classen
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew Shiu
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Denis Charlebois
- Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Nathalie Corneau
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Teodor Veres
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
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Ma C, Sun Y, Huang Y, Gao Z, Huang Y, Pandey I, Jia C, Feng S, Zhao J. On-Chip Nucleic Acid Purification Followed by ddPCR for SARS-CoV-2 Detection. BIOSENSORS 2023; 13:bios13050517. [PMID: 37232879 DOI: 10.3390/bios13050517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
We developed a microfluidic chip integrated with nucleic acid purification and droplet-based digital polymerase chain reaction (ddPCR) modules to realize a 'sample-in, result-out' infectious virus diagnosis. The whole process involved pulling magnetic beads through drops in an oil-enclosed environment. The purified nucleic acids were dispensed into microdroplets by a concentric-ring, oil-water-mixing, flow-focusing droplets generator driven under negative pressure conditions. Microdroplets were generated with good uniformity (CV = 5.8%), adjustable diameters (50-200 μm), and controllable flow rates (0-0.3 μL/s). Further verification was provided by quantitative detection of plasmids. We observed a linear correlation of R2 = 0.9998 in the concentration range from 10 to 105 copies/μL. Finally, this chip was applied to quantify the nucleic acid concentrations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The measured nucleic acid recovery rate of 75 ± 8.8% and detection limit of 10 copies/μL proved its on-chip purification and accurate detection abilities. This chip can potentially be a valuable tool in point-of-care testing.
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Affiliation(s)
- Cong Ma
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimeng Sun
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhang Huang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- School of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Zehang Gao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yaru Huang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- School of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Ikshu Pandey
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Xiangfu Laboratory, Jiaxing 314102, China
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Lee K, Tripathi A. An investigation into simplifying total RNA extraction with minimal equipment using a low volume, electrokinetically driven microfluidic protocol. BIOMICROFLUIDICS 2022; 16:044107. [PMID: 35992642 PMCID: PMC9385220 DOI: 10.1063/5.0096684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Current methods for total RNA extraction are time-consuming and require several hands-on steps and specialized equipment. Microfluidic devices can offer the opportunity to reduce the number of hands-on steps, decrease the volumes of reagents required for purification, and make extraction high throughput. Here, we investigated the translation of a high volume magnetic bead-based total RNA extraction method (from human whole blood) onto a low input volume microfluidic device. Our results first show that RNA integrity is maintained when the reagent volumes are scaled down by a factor of 22 and the wash buffers are combined 1:1. With our microfluidic method, the number of wash steps can be reduced from four to one. Thus, the time to complete RNA extraction can be reduced from 2 h to 40 min. These manipulations to the conventional protocol yielded RNA amplifiable within 40 cycles of reverse transcription quantitative PCR (RT-qPCR) when using the microfluidic device to simplify the wash steps. To improve the purification of the RNA during the bead transport through the microchannel, we also investigated the effect of a synergetic application of the electrokinetic flow. Our results show that DNase I and other contaminants surrounding the beads get washed away more effectively via electrophoretic transport. Most notably, RNA adsorption on the beads is strong enough to counter electrophoretically-driven desorption. In all, our work opens new ways to extract high-quality total RNA rapidly and simply from a small quantity of blood, making the process of RNA extraction more accessible.
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Affiliation(s)
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, USA
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