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Bet B, Georgiev R, Uspal W, Eral HB, van Roij R, Samin S. Calculating the motion of highly confined, arbitrary-shaped particles in Hele-Shaw channels. MICROFLUIDICS AND NANOFLUIDICS 2018; 22:77. [PMID: 30881266 PMCID: PMC6394751 DOI: 10.1007/s10404-018-2092-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/18/2018] [Indexed: 06/09/2023]
Abstract
We combine theory and numerical calculations to accurately predict the motion of anisotropic particles in shallow microfluidic channels, in which the particles are strongly confined in the vertical direction. We formulate an effective quasi-two-dimensional description of the Stokes flow around the particle via the Brinkman equation, which can be solved in a time that is two orders of magnitude faster than the three-dimensional problem. The computational speedup enables us to calculate the full trajectories of particles in the channel. To validate our scheme, we study the motion of dumbbell-shaped particles that are produced in a microfluidic channel using 'continuous-flow lithography'. Contrary to what was reported in earlier work (Uspal et al. in Nat Commun 4:2666, 2013), we find that the reorientation time of a dumbbell particle in an external flow exhibits a minimum as a function of its disk size ratio. This finding is in excellent agreement with new experiments, thus confirming the predictive power of our scheme.
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Affiliation(s)
- Bram Bet
- Center for Extreme Matter and Emergent Phenomena, Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Rumen Georgiev
- Process and Energy Department, Delft University of Technology, 2628 CD Delft, The Netherlands
- Van’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - William Uspal
- Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universitt Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Huseyin Burak Eral
- Process and Energy Department, Delft University of Technology, 2628 CD Delft, The Netherlands
- Van’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - René van Roij
- Center for Extreme Matter and Emergent Phenomena, Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Sela Samin
- Center for Extreme Matter and Emergent Phenomena, Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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52
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Guo S, Lin WN, Hu Y, Sun G, Phan DT, Chen CH. Ultrahigh-throughput droplet microfluidic device for single-cell miRNA detection with isothermal amplification. LAB ON A CHIP 2018; 18:1914-1920. [PMID: 29877542 DOI: 10.1039/c8lc00390d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Analysis of microRNA (miRNA), a pivotal primary regulator of fundamental cellular processes, at the single-cell level is essential to elucidate regulated gene expression precisely. Most single-cell gene sequencing methods use the polymerase chain reaction (PCR) to increase the concentration of the target gene for detection, thus requiring a barcoding process for cell identification and creating a challenge for real-time, large-scale screening of sequences in cells to rapidly profile physiological samples. In this study, a rapid, PCR-free, single-cell miRNA assay is developed from a continuous-flow microfluidic process employing a DNA hybridization chain reaction to amplify the target miRNA signal. Individual cells are encapsulated with DNA amplifiers in water-in-oil droplets and then lysed. The released target miRNA interacts with the DNA amplifiers to trigger hybridization reactions, producing fluorescence signals. Afterward, the target sequences are recycled to trigger a cyclic cascade reaction and significantly amplify the fluorescence signals without using PCR thermal cycling. Multiple DNA amplifiers with distinct fluorescence signals can be encapsulated simultaneously in a droplet to measure multiple miRNAs from a single cell simultaneously. Moreover, this process converts the lab bench PCR assay to a real-time droplet assay with the post-reaction fluorescence signal as a readout to allow flow cytometry-like continuous-flow measurement of sequences in a single cell with an ultrahigh throughput (300-500 cells per minute) for rapid biomedical identification.
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Affiliation(s)
- Song Guo
- Department of Biomedical Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore.
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53
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Bet B, Samin S, Georgiev R, Eral HB, van Roij R. Steering particles by breaking symmetries. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:224002. [PMID: 29664011 DOI: 10.1088/1361-648x/aabea9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We derive general equations of motions for highly-confined particles that perform quasi-two-dimensional motion in Hele-Shaw channels, which we solve analytically, aiming to derive design principles for self-steering particles. Based on symmetry properties of a particle, its equations of motion can be simplified, where we retrieve an earlier-known equation of motion for the orientation of dimer particles consisting of disks (Uspal et al 2013 Nat. Commun. 4), but now in full generality. Subsequently, these solutions are compared with particle trajectories that are obtained numerically. For mirror-symmetric particles, excellent agreement between the analytical and numerical solutions is found. For particles lacking mirror symmetry, the analytic solutions provide means to classify the motion based on particle geometry, while we find that taking the side-wall interactions into account is important to accurately describe the trajectories.
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Affiliation(s)
- Bram Bet
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
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54
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Scanga R, Chrastecka L, Mohammad R, Meadows A, Quan PL, Brouzes E. Click Chemistry Approaches to Expand the Repertoire of PEG-based Fluorinated Surfactants for Droplet Microfluidics. RSC Adv 2018; 8:12960-12974. [PMID: 31592185 PMCID: PMC6779154 DOI: 10.1039/c8ra01254g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report the novel and simplified synthesis of fluorinated surfactants for droplet microfluidics. The range of applications of droplet microfluidics has greatly expanded during the last decade thanks to its ability to manipulate and process tiny amount of sample and reagents at high throughput in independent reactors. A critical component of the technology is the formulation of the immiscible oil phase that contains surfactants to stabilize droplets. The success of droplet microfluidics relies mostly on a single fluorinated formulation that uses a PFPE–PEG triblock surfactant. The synthesis of this surfactant is laborious and requires skills in synthetic chemistry preventing the wider community to explore the synthesis of surfactants with alternate structures. We sought to provide a simplified synthesis for novel PFPE–PEG surfactants based on click chemistry approaches such as copper-catalyzed azide-alkyne cycloaddition (CuAAC) and UV-activated thiol–yne reactions. Our strategy is based on converting a moisture sensitive intermediate typically used in the synthesis of the triblock PFPE–PEG surfactant into a stable and click ready molecule. We successfully combined that fluorinated tail with differently functionalized PEG and glycerol ethoxylate molecules to generate surfactants with diverse structures via CuACC and thiol–yne reactions. We report the characterization, biocompatibility and ability to stabilize emulsions of those surfactants, as well as the unique advantages and challenges of the strategy. Click-synthesis of fluorinated surfactants for droplet microfluidics.![]()
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Affiliation(s)
- Randall Scanga
- Department of chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lucie Chrastecka
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Ridhwan Mohammad
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Austin Meadows
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
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55
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Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP. Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases. J Neuromuscul Dis 2018; 3:209-225. [PMID: 27854218 DOI: 10.3233/jnd-160151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. OBJECTIVE To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. METHODS We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. RESULTS We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. CONCLUSIONS Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.
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Affiliation(s)
- Jaya Punetha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Akanchha Kesari
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Prech Uapinyoying
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mamta Giri
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Nigel F Clarke
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Leigh B Waddell
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Kathryn N North
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, University of Melbourne, Melbourne, Australia
| | - Roula Ghaoui
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gina L O'Grady
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Emily C Oates
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Sarah A Sandaradura
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Paul H Plotz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward C Smith
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC, USA
| | - Carolina Tesi-Rocha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Tulio E Bertorini
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mark A Tarnopolsky
- Departments of Pediatrics and Medicine, McMaster University, Neuromuscular Disease Clinic, Health Sciences Centre, ON, Canada
| | - Bernd Reitter
- Children's Hospital, Johannes Gutenberg University, Mainz, Germany
| | | | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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56
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Damiati S, Mhanna R, Kodzius R, Ehmoser EK. Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics. Genes (Basel) 2018; 9:E144. [PMID: 29509709 PMCID: PMC5867865 DOI: 10.3390/genes9030144] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rami Mhanna
- Biomedical Engineering Program, The American University of Beirut (AUB), Beirut 1107-2020, Lebanon.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Eva-Kathrin Ehmoser
- Department of Nanobiotechnology, Institute for Synthetic Bioarchitecture, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
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57
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Porter TM, Hajibabaei M. Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol 2018; 27:313-338. [PMID: 29292539 DOI: 10.1111/mec.14478] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/19/2022]
Abstract
The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.
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Affiliation(s)
- Teresita M Porter
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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58
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Li X, Zhang D, Zhang H, Guan Z, Song Y, Liu R, Zhu Z, Yang C. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis. Anal Chem 2018; 90:2570-2577. [PMID: 29350029 DOI: 10.1021/acs.analchem.7b04040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.
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Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China.,The MOE Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, People's Republic of China
| | - Ruochen Liu
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey United States
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
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Komori HK, LaMere SA, Hart T, Head SR, Torkamani A, Salomon DR. Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing. Methods Mol Biol 2018; 1708:333-348. [PMID: 29224152 DOI: 10.1007/978-1-4939-7481-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many methods exist for examining CpG DNA methylation. However, many of these are qualitative, laborious to apply to a large number of genes simultaneously, or are not easy to target to specific regions of interest. Microdroplet PCR-based bisulfite sequencing allows for quantitative single base resolution analysis of investigator selected regions of interest. Following bisulfite conversion of genomic DNA, targeted microdroplet PCR is conducted with custom primer libraries. Samples are then fragmented, concatenated, and sequenced by high-throughput sequencing. The most recent technology allows for this method to be conducted with as little as 250 ng of bisulfite-converted DNA. The primary advantage of this method is the ability to hand-select the targeted regions covered by up to 10,000 amplicons of 500-600 bp. Moreover, the nature of microdroplet PCR virtually eliminates PCR bias and allows for the amplification of all targets simultaneously in a single tube.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Traver Hart
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada, M5G 1L6
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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60
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Jiang Y, Du L, Li Y, Mu Q, Cui Z, Zhou J, Wu W. A novel mechanism for user-friendly and self-activated microdroplet generation capable of programmable control. Analyst 2018; 143:3798-3807. [DOI: 10.1039/c8an00035b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The real-time continuous-flow PCR inside a 3D spiral microchannel is realized by a novel self-activated microdroplet generation/transport mechanism.
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Affiliation(s)
- Yangyang Jiang
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Lin Du
- State Key Laboratory of ASIC and Systems
- Fudan University
- Shanghai 200433
- China
| | - Yuanming Li
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Quanquan Mu
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Zhongxu Cui
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
| | - Jia Zhou
- State Key Laboratory of ASIC and Systems
- Fudan University
- Shanghai 200433
- China
| | - Wenming Wu
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
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61
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Coarsey CT, Esiobu N, Narayanan R, Pavlovic M, Shafiee H, Asghar W. Strategies in Ebola virus disease (EVD) diagnostics at the point of care. Crit Rev Microbiol 2017; 43:779-798. [PMID: 28440096 PMCID: PMC5653233 DOI: 10.1080/1040841x.2017.1313814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/21/2016] [Accepted: 03/25/2017] [Indexed: 12/13/2022]
Abstract
Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.
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Affiliation(s)
- Chad T. Coarsey
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Nwadiuto Esiobu
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Ramswamy Narayanan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Mirjana Pavlovic
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Waseem Asghar
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
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Nicolini AM, Toth TD, Kim SY, Mandel MA, Galbraith DW, Yoon JY. Mie Scatter and Interfacial Tension Based Real-Time Quantification of Colloidal Emulsion Nucleic Acid Amplification. ADVANCED BIOSYSTEMS 2017; 1:e1700098. [PMID: 32646190 DOI: 10.1002/adbi.201700098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Indexed: 06/11/2023]
Abstract
This work demonstrates for the first time rapid, real-time Mie scatter sensing of colloidal emulsion nucleic acid amplification directly from emulsion droplets. Loop-mediated isothermal amplification is used in this study, and, to our knowledge, has not previously been used in a colloidal emulsion platform. Interfacial tension values (γ) associated with bulk protein adsorption and denaturation at the oil-water interface exhibit characteristic changes in the absence or presence of amplification. In the presence of target and amplicon, emulsions maintain a constant 300-400 nm diameter, whereas emulsions formed with no target control show a rapid decrease in droplet diameter to <100 nm over the first 20 min of incubation. This method is validated using whole bacteria (Staphylococcus aureus MSSA and Escherichia coli O157:H7) and whole virus (Potato virus Y and Zika virus) samples suspended in water, buffer, or serum-like matrices. Short-term formation of colloidal emulsion is quantified via 60° scatter monitoring, where the initial slope of scattering intensity is utilized to confirm target amplification in less than 5 min. The unique benefits of this method render it more cost-effective and field-deployable than existing methods, while being adaptable to a multitude of targets, sample matrices, and nucleic acid amplification tests.
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Affiliation(s)
- Ariana M Nicolini
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Tyler D Toth
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Samuel Y Kim
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - M Alejandra Mandel
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - David W Galbraith
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jeong-Yeol Yoon
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
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63
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Lefever S, Pattyn F, De Wilde B, Coppieters F, De Keulenaer S, Hellemans J, Vandesompele J. High-throughput PCR assay design for targeted resequencing using primerXL. BMC Bioinformatics 2017; 18:400. [PMID: 28877663 PMCID: PMC5588703 DOI: 10.1186/s12859-017-1809-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 08/27/2017] [Indexed: 11/15/2022] Open
Abstract
Background Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only the regions of interest decreases both costs and the complexity of the downstream data-analysis. Various target enrichment strategies are available, but none of them obtain the degree of coverage uniformity, flexibility and specificity of PCR-based enrichment. On the other hand, the biggest limitation of target enrichment by PCR is the need to design large numbers of partially overlapping assays to cover the target. Results To overcome the aforementioned hurdles, we have developed primerXL, a state-of-the-art PCR primer design pipeline for targeted resequencing. It uses an optimized design criteria relaxation cascade and a thorough downstream in silico evaluation process to generate high quality singleplex PCR assays, reducing the need for amplicon normalization, and outperforming other target enrichment strategies and similar primer design tools when considering assay quality, coverage uniformity and target coverage. Results of four different sequencing projects with 2348 amplicons in total covering 470 kb are presented. PrimerXL can be accessed at www.primerxl.org. Conclusion PrimerXL is an state-of-the-art, easy to use primer design webtool capable of generating high-quality targeted resequencing assays. The workflow is fully customizable to suit every researchers’ needs, while an innovative relaxation cascade ensures maximal target coverage. Electronic supplementary material The online version of this article doi:(10.1186/s12859-017-1809-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steve Lefever
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium. .,pxlence, 9200, Dendermonde, Belgium. .,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium. .,Bioinformatics Institute Ghent (BIG), 9000, Ghent, Belgium.
| | - Filip Pattyn
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Present address: Ontoforce, Ottergemsesteenweg-Zuid 808, 9000, Ghent, Belgium
| | - Bram De Wilde
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium.,Bioinformatics Institute Ghent (BIG), 9000, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,pxlence, 9200, Dendermonde, Belgium
| | - Sarah De Keulenaer
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Present address: NXTGNT, UGent, FFW Building 3th floor, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Jan Hellemans
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Present address: Biogazelle, Technologiepark 3, 9052, Zwijnaarde, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,pxlence, 9200, Dendermonde, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium.,Bioinformatics Institute Ghent (BIG), 9000, Ghent, Belgium
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64
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Peikon ID, Kebschull JM, Vagin VV, Ravens DI, Sun YC, Brouzes E, Corrêa IR, Bressan D, Zador AM. Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res 2017; 45:e115. [PMID: 28449067 PMCID: PMC5499584 DOI: 10.1093/nar/gkx292] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/20/2017] [Accepted: 04/13/2017] [Indexed: 01/16/2023] Open
Abstract
The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost.
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Affiliation(s)
- Ian D. Peikon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justus M. Kebschull
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vasily V. Vagin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Diana I. Ravens
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu-Chi Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Dario Bressan
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Anthony M. Zador
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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65
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Emerman AB, Bowman SK, Barry A, Henig N, Patel KM, Gardner AF, Hendrickson CL. NEBNext Direct: A Novel, Rapid, Hybridization-Based Approach for the Capture and Library Conversion of Genomic Regions of Interest. ACTA ACUST UNITED AC 2017; 119:7.30.1-7.30.24. [PMID: 28678441 DOI: 10.1002/cpmb.39] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Next-generation sequencing (NGS) is a powerful tool for genomic studies, translational research, and clinical diagnostics that enables the detection of single nucleotide polymorphisms, insertions and deletions, copy number variations, and other genetic variations. Target enrichment technologies improve the efficiency of NGS by only sequencing regions of interest, which reduces sequencing costs while increasing coverage of the selected targets. Here we present NEBNext Direct® , a hybridization-based, target-enrichment approach that addresses many of the shortcomings of traditional target-enrichment methods. This approach features a simple, 7-hr workflow that uses enzymatic removal of off-target sequences to achieve a high specificity for regions of interest. Additionally, unique molecular identifiers are incorporated for the identification and filtering of PCR duplicates. The same protocol can be used across a wide range of input amounts, input types, and panel sizes, enabling NEBNext Direct to be broadly applicable across a wide variety of research and diagnostic needs. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | | | - Noa Henig
- Directed Genomics, Inc, Ipswich, Massachusetts
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66
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Molecular Techniques for the Detection of Organisms in Aquatic Environments, with Emphasis on Harmful Algal Bloom Species. SENSORS 2017; 17:s17051184. [PMID: 28531156 PMCID: PMC5470929 DOI: 10.3390/s17051184] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 02/08/2023]
Abstract
Molecular techniques to detect organisms in aquatic ecosystems are being gradually considered as an attractive alternative to standard laboratory methods. They offer faster and more accurate means of detecting and monitoring species, with respect to their traditional homologues based on culture and microscopic counting. Molecular techniques are particularly attractive when multiple species need to be detected and/or are in very low abundance. This paper reviews molecular techniques based on whole cells, such as microscope-based enumeration and Fluorescence In-Situ Hybridization (FISH) and molecular cell-free formats, such as sandwich hybridization assay (SHA), biosensors, microarrays, quantitative polymerase chain reaction (qPCR) and real time PCR (RT-PCR). Those that combine one or several laboratory functions into a single integrated system (lab-on-a-chip) and techniques that generate a much higher throughput data, such as next-generation systems (NGS), were also reviewed. We also included some other approaches that enhance the performance of molecular techniques. For instance, nano-bioengineered probes and platforms, pre-concentration and magnetic separation systems, and solid-phase hybridization offer highly pre-concentration capabilities. Isothermal amplification and hybridization chain reaction (HCR) improve hybridization and amplification techniques. Finally, we presented a study case of field remote sensing of harmful algal blooms (HABs), the only example of real time monitoring, and close the discussion with future directions and concluding remarks.
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67
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Zhu Q, Xu Y, Qiu L, Ma C, Yu B, Song Q, Jin W, Jin Q, Liu J, Mu Y. A scalable self-priming fractal branching microchannel net chip for digital PCR. LAB ON A CHIP 2017; 17:1655-1665. [PMID: 28418438 DOI: 10.1039/c7lc00267j] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods. A special 10 nm nano-waterproof layer was created to prevent the solution from evaporating. A vacuum pre-packaging method called self-priming reagent introduction is used to passively drive the reagent flow into the microchannel nets, so that this chip can realize sequential reagent loading and isolation within a couple of minutes, which is very suitable for point-of-care detection. When the number of positive microwells stays in the range of 100 to 4000, the relative uncertainty is below 5%, which means that one panel can detect an average of 101 to 15 374 molecules by the Poisson distribution. This chip is proved to have an excellent ability for single molecule detection and quantification of low expression of hHF-MSC stem cell markers. Due to its potential for high throughput, high density, low cost, lack of sample and reagent loss, self-priming even compartmentalization and simple operation, we envision that this device will significantly expand and extend the application range of digital PCR involving rare samples, liquid biopsy detection and point-of-care detection with higher sensitivity and accuracy.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
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68
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Chen X, Ren CL. Experimental study on droplet generation in flow focusing devices considering a stratified flow with viscosity contrast. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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69
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Abstract
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error. The remainder focuses on digital PCR (dPCR) for quantification of nucleic acids. We discuss five commercial instruments that partition samples into physically isolated chambers (cdPCR) or droplet emulsions (ddPCR). We compare the strengths of dPCR (absolute quantitation, precision, and ability to detect rare or mutant targets) with those of its predecessor, quantitative real-time PCR (dynamic range, larger sample volumes, and throughput). Lastly, we describe several promising applications of dPCR, including copy number variation, quantitation of circulating tumor DNA and viral load, RNA/miRNA quantitation with reverse transcription dPCR, and library preparation for next-generation sequencing. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows. Part II focuses on digital protein and cell assays.
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Affiliation(s)
- Amar S Basu
- 1 Department of Electrical and Computer Engineering, and Department of Biomedical Engineering, Wayne State University, Detroit, MI, USA
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70
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Multiple pathogen biomarker detection using an encoded bead array in droplet PCR. J Microbiol Methods 2017; 139:22-28. [PMID: 28434824 DOI: 10.1016/j.mimet.2017.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/19/2017] [Accepted: 04/19/2017] [Indexed: 11/23/2022]
Abstract
We present a droplet PCR workflow for detection of multiple pathogen DNA biomarkers using fluorescent color-coded Luminex® beads. This strategy enables encoding of multiple singleplex droplet PCRs using a commercially available bead set of several hundred distinguishable fluorescence codes. This workflow provides scalability beyond the limited number offered by fluorescent detection probes such as TaqMan probes, commonly used in current multiplex droplet PCRs. The workflow was validated for three different Luminex bead sets coupled to target specific capture oligos to detect hybridization of three microorganisms infecting poultry: avian influenza, infectious laryngotracheitis virus and Campylobacter jejuni. In this assay, the target DNA was amplified with fluorescently labeled primers by PCR in parallel in monodisperse picoliter droplets, to avoid amplification bias. The color codes of the Luminex detection beads allowed concurrent and accurate classification of the different bead sets used in this assay. The hybridization assay detected target DNA of all three microorganisms with high specificity, from samples with average target concentration of a single DNA template molecule per droplet. This workflow demonstrates the possibility of increasing the droplet PCR assay detection panel to detect large numbers of targets in parallel, utilizing the scalability offered by the color-coded Luminex detection beads.
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71
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Ding Y, Choo J, deMello AJ. From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis. MICROFLUIDICS AND NANOFLUIDICS 2017; 21:58. [PMID: 32214953 PMCID: PMC7087872 DOI: 10.1007/s10404-017-1889-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/22/2017] [Indexed: 05/27/2023]
Abstract
Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter-nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets.
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan, 15588 Republic of Korea
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
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72
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Chandrani P, Prabhash K, Prasad R, Sethunath V, Ranjan M, Iyer P, Aich J, Dhamne H, Iyer DN, Upadhyay P, Mohanty B, Chandna P, Kumar R, Joshi A, Noronha V, Patil V, Ramaswamy A, Karpe A, Thorat R, Chaudhari P, Ingle A, Choughule A, Dutt A. Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Ann Oncol 2017; 28:597-603. [PMID: 27998968 PMCID: PMC5391708 DOI: 10.1093/annonc/mdw636] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths across the world. In this study, we present therapeutically relevant genetic alterations in lung adenocarcinoma of Indian origin. MATERIALS AND METHODS Forty-five primary lung adenocarcinoma tumors were sequenced for 676 amplicons using RainDance cancer panel at an average coverage of 1500 × (reads per million mapped reads). To validate the findings, 49 mutations across 23 genes were genotyped in an additional set of 363 primary lung adenocarcinoma tumors using mass spectrometry. NIH/3T3 cells over expressing mutant and wild-type FGFR3 constructs were characterized for anchorage independent growth, constitutive activation, tumor formation and sensitivity to FGFR inhibitors using in vitro and xenograft mouse models. RESULTS We present the first spectrum of actionable alterations in lung adenocarcinoma tumors of Indian origin, and shows that mutations of FGFR3 are present in 20 of 363 (5.5%) patients. These FGFR3 mutations are constitutively active and oncogenic when ectopically expressed in NIH/3T3 cells and using a xenograft model in NOD/SCID mice. Inhibition of FGFR3 kinase activity inhibits transformation of NIH/3T3 overexpressing FGFR3 constructs and growth of tumors driven by FGFR3 in the xenograft models. The reduction in tumor size in the mouse is paralleled by a reduction in the amounts of phospho-ERK, validating the in vitro findings. Interestingly, the FGFR3 mutations are significantly higher in a proportion of younger patients and show a trend toward better overall survival, compared with patients lacking actionable alterations or those harboring KRAS mutations. CONCLUSION We present the first actionable mutation spectrum in Indian lung cancer genome. These findings implicate FGFR3 as a novel therapeutic in lung adenocarcinoma.
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Affiliation(s)
- P. Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - K. Prabhash
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - V. Sethunath
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - M. Ranjan
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - J. Aich
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - H. Dhamne
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - D. N. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - B. Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Chandna
- AceProbe Technologies Pvt. Ltd, New Delhi, India
| | - R. Kumar
- Department of Pathology, Tata Memorial Hospital
| | - A. Joshi
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Noronha
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Patil
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Ramaswamy
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Karpe
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Thorat
- Department of Pathology, Tata Memorial Hospital
| | - P. Chaudhari
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Ingle
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Choughule
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Correspondence to: Dr Amit Dutt, Wellcome Trust/DBT India Alliance Intermediate Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai 410 210, India. Tel: +91-22-27405056; E-mail:
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73
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Ma S, Murphy TW, Lu C. Microfluidics for genome-wide studies involving next generation sequencing. BIOMICROFLUIDICS 2017; 11:021501. [PMID: 28396707 PMCID: PMC5346105 DOI: 10.1063/1.4978426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/16/2017] [Indexed: 05/11/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.
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Affiliation(s)
- Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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Abe Y, Zhang B, Gordillo L, Karim AM, Francis LF, Cheng X. Dynamic self-assembly of charged colloidal strings and walls in simple fluid flows. SOFT MATTER 2017; 13:1681-1692. [PMID: 28145557 DOI: 10.1039/c6sm02524b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing the general principles of self-assembly under non-equilibrium conditions. Here, we report a simple microfluidic experiment, where charged colloidal particles self-assemble into flow-aligned 1D strings with regular particle spacing near a solid boundary. Using high-speed confocal microscopy, we systematically investigate the influence of flow rates, electrostatics and particle polydispersity on the observed string structures. By studying the detailed dynamics of stable flow-driven particle pairs, we quantitatively characterize interparticle interactions. Based on the results, we construct a simple model that explains the intriguing non-equilibrium self-assembly process. Our study shows that the colloidal strings arise from a delicate balance between attractive hydrodynamic coupling and repulsive electrostatic interaction between particles. Finally, we demonstrate that, with the assistance of transverse electric fields, a similar mechanism also leads to the formation of 2D colloidal walls.
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Affiliation(s)
- Yu Abe
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA. and Films & Film Products Research Laboratories, Toray Industries, Inc, 1-1, Sonoyama 1-chome, Otsu, Shiga 520-8558, Japan
| | - Bo Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Leonardo Gordillo
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alireza Mohammad Karim
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Lorraine F Francis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Xiang Cheng
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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75
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Droplet Microfluidics Approach for Single-DNA Molecule Amplification and Condensation into DNA-Magnesium-Pyrophosphate Particles. MICROMACHINES 2017. [PMCID: PMC6189807 DOI: 10.3390/mi8020062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein expression in vitro has broad applications in directed evolution, synthetic biology, proteomics and drug screening. However, most of the in vitro expression systems rely on relatively high DNA template concentrations to obtain sufficient amounts of proteins, making it harder to perform in vitro screens on gene libraries. Here, we report a technique for the generation of condensed DNA particles that can serve as efficient templates for in vitro gene expression. We apply droplet microfluidics to encapsulate single-DNA molecules in 3-picoliter (pL) volume droplets and convert them into 1 μm-sized DNA particles by the multiple displacement amplification reaction driven by phi29 DNA polymerase. In the presence of magnesium ions and inorganic pyrophosphate, the amplified DNA condensed into the crystalline-like particles, making it possible to purify them from the reaction mix by simple centrifugation. Using purified DNA particles, we performed an in vitro transcription-translation reaction and successfully expressed complex enzyme β-galactosidase in droplets and in the 384-well format. The yield of protein obtained from DNA particles was significantly higher than from the corresponding amount of free DNA templates, thus opening new possibilities for high throughput screening applications.
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76
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Jung JH, Destgeer G, Park J, Ahmed H, Park K, Sung HJ. On-Demand Droplet Capture and Release Using Microwell-Assisted Surface Acoustic Waves. Anal Chem 2017; 89:2211-2215. [DOI: 10.1021/acs.analchem.6b04542] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jin Ho Jung
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
| | - Ghulam Destgeer
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
| | - Jinsoo Park
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
| | - Husnain Ahmed
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
| | - Kwangseok Park
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
| | - Hyung Jin Sung
- Department of Mechanical
Engineering, KAIST, Daejeon 34141, Korea
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77
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Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2. J Hum Genet 2017; 62:561-567. [DOI: 10.1038/jhg.2017.5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/26/2016] [Accepted: 12/05/2016] [Indexed: 12/30/2022]
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78
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Shao N, Chen J, Hu J, Li R, Zhang D, Guo S, Hui J, Liu P, Yang L, Tao SC. Visual detection of multiple genetically modified organisms in a capillary array. LAB ON A CHIP 2017; 17:521-529. [PMID: 28092385 DOI: 10.1039/c6lc01330a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
There is an urgent need for rapid, low-cost multiplex methodologies for the monitoring of genetically modified organisms (GMOs). Here, we report a C[combining low line]apillary A[combining low line]rray-based L[combining low line]oop-mediated isothermal amplification for M[combining low line]ultiplex visual detection of nucleic acids (CALM) platform for the simple and rapid monitoring of GMOs. In CALM, loop-mediated isothermal amplification (LAMP) primer sets are pre-fixed to the inner surface of capillaries. The surface of the capillary array is hydrophobic while the capillaries are hydrophilic, enabling the simultaneous loading and separation of the LAMP reaction mixtures into each capillary by capillary forces. LAMP reactions in the capillaries are then performed in parallel, and the results are visually detected by illumination with a hand-held UV device. Using CALM, we successfully detected seven frequently used transgenic genes/elements and five plant endogenous reference genes with high specificity and sensitivity. Moreover, we found that measurements of real-world blind samples by CALM are consistent with results obtained by independent real-time PCRs. Thus, with an ability to detect multiple nucleic acids in a single easy-to-operate test, we believe that CALM will become a widely applied technology in GMO monitoring.
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Affiliation(s)
- Ning Shao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China. and State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianwei Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China. and State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaying Hu
- Collaborative Innovation center for biosafety of GMOs, National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Rong Li
- Collaborative Innovation center for biosafety of GMOs, National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Collaborative Innovation center for biosafety of GMOs, National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China. and State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junhou Hui
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Liu
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Litao Yang
- Collaborative Innovation center for biosafety of GMOs, National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China. and State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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79
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Song Y, Jeong Y, Kwon T, Lee D, Oh DY, Park TJ, Kim J, Kim J, Kwon S. Liquid-capped encoded microcapsules for multiplex assays. LAB ON A CHIP 2017; 17:429-437. [PMID: 27995235 DOI: 10.1039/c6lc01268j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Although droplet microfludics is a promising technology for handling a number of liquids of a single type of analyte, it has limitations in handling thousands of different types of analytes for multiplex assay. Here, we present a novel "liquid-capped encoded microcapsule", which is applicable to various liquid format assays. Various liquid drops can be graphically encoded and arrayed without repeated dispensing processes, evaporation, and the risk of cross-contamination. Millions of nanoliter-scale liquids are encapsulated within encoded microcapsules and self-assembled in microwells in a single dispensing process. The graphical code on the microcapsule enables identification of randomly assembled microcapsules in each microwell. We conducted various liquid phase assays including enzyme inhibitor screening, virus transduction, and drug-induced apoptosis tests. The results showed that our liquid handling technology can be utilized widely for various solution phase assays.
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Affiliation(s)
- Younghoon Song
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Department of Electrical and Computer Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yunjin Jeong
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Department of Electrical and Computer Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Taehong Kwon
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Department of Electrical and Computer Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Daewon Lee
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Dong Yoon Oh
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Tae-Joon Park
- Nano Systems Institute, Seoul National University, Seoul 151-742, Republic of Korea
| | - Junhoi Kim
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Department of Electrical and Computer Science, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jiyun Kim
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sunghoon Kwon
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 151-742, Republic of Korea. and Department of Electrical and Computer Science, Seoul National University, Seoul 151-742, Republic of Korea and Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea and Nano Systems Institute, Seoul National University, Seoul 151-742, Republic of Korea and Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital, Seoul 151-742, Republic of Korea and Quantamatrix Inc., Seoul 151-742, Republic of Korea
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80
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Feber A, Dhami P, Dong L, de Winter P, Tan WS, Martínez-Fernández M, Paul DS, Hynes-Allen A, Rezaee S, Gurung P, Rodney S, Mehmood A, Villacampa F, de la Rosa F, Jameson C, Cheng KK, Zeegers MP, Bryan RT, James ND, Paramio JM, Freeman A, Beck S, Kelly JD. UroMark-a urinary biomarker assay for the detection of bladder cancer. Clin Epigenetics 2017; 9:8. [PMID: 28163793 PMCID: PMC5282868 DOI: 10.1186/s13148-016-0303-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Bladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, and several studies have shown the potential utility of urinary biomarkers by detecting epigenetic alterations in voided urine. The aim of this study is to develop a targeted bisulfite next-generation sequencing assay to diagnose BC from urine with high sensitivity and specificity. Results We defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The 150 loci UroMark assay was validated in an independent cohort (n = 274, non-cancer (n = 167) and bladder cancer (n = 107)) voided urine samples with an AUC of 97%. The UroMark classifier sensitivity of 98%, specificity of 97% and NPV of 97% for the detection of primary BC was compared to non-BC urine. Conclusions Epigenetic urinary biomarkers for detection of BC have the potential to revolutionise the management of this disease. In this proof of concept study, we show the development and utility of a novel high-throughput, next-generation sequencing-based biomarker for the detection of BC-specific epigenetic alterations in urine. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0303-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Feber
- UCL Cancer Institute, University College London, London, UK
| | - Pawan Dhami
- UCL Cancer Institute, University College London, London, UK
| | - Liqin Dong
- UCL Cancer Institute, University College London, London, UK
| | - Patricia de Winter
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Wei Shen Tan
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Mónica Martínez-Fernández
- Molecular Oncology Unit, CIEMAT (ed70A), Madrid, Spain & Biomedical Research Institute I+12, Universitary Hospistal 12 de Octubre, Av Cordoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Dirk S Paul
- UCL Cancer Institute, University College London, London, UK
| | - Antony Hynes-Allen
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Sheida Rezaee
- UCL Cancer Institute, University College London, London, UK
| | - Pratik Gurung
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK.,School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Simon Rodney
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Ahmed Mehmood
- Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
| | - Felipe Villacampa
- Uro-oncology Section & Biomedical Research Institute I+12, Universitary Hospital 12 de Octubre, Av Córdoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Federico de la Rosa
- Uro-oncology Section & Biomedical Research Institute I+12, Universitary Hospital 12 de Octubre, Av Córdoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Charles Jameson
- Department of Histopathology, University College London Hospital, London, UK
| | - Kar Keung Cheng
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Maurice P Zeegers
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK.,School for Public Health and Primary Care, Maastricht University, Maastricht, Netherlands
| | - Richard T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | | | - Jesus M Paramio
- Molecular Oncology Unit, CIEMAT (ed70A), Madrid, Spain & Biomedical Research Institute I+12, Universitary Hospistal 12 de Octubre, Av Cordoba s/n. 28041, Madrid, Spain.,Centro de Investigación, Biomédica en Red de Cáncer (CIBER ONC), Madrid, Spain
| | - Alex Freeman
- Department of Histopathology, University College London Hospital, London, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK
| | - John D Kelly
- UCL Cancer Institute, University College London, London, UK.,Division of Surgery & Interventional Science, UCL Medical School, University College London, London, UK
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81
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High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time. PLoS One 2017; 12:e0168910. [PMID: 28045987 PMCID: PMC5207663 DOI: 10.1371/journal.pone.0168910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/08/2016] [Indexed: 12/17/2022] Open
Abstract
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials.
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82
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Ding R, Ung WL, Heyman JA, Weitz DA. Sensitive and predictable separation of microfluidic droplets by size using in-line passive filter. BIOMICROFLUIDICS 2017; 11:014114. [PMID: 28344725 PMCID: PMC5336469 DOI: 10.1063/1.4976723] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/04/2017] [Indexed: 05/30/2023]
Abstract
Active manipulation of droplets is crucial in droplet microfluidics. However, droplet polydispersity decreases the accuracy of active manipulation. We develop a microfluidic "droplet filter" that accurately separates droplets by size. The droplet filter has a sharp size cutoff and is capable of distinguishing droplets differing in volume by 20%. A simple model explains the behavior of the droplets as they pass through the filter. We show application of the filter in improving dielectric sorting efficiency.
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Affiliation(s)
- Ruihua Ding
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, USA
| | - W Lloyd Ung
- John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, USA
| | | | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, USA
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83
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Çakir Ö, Meriç S, Meriç S, Ari Ş. GMO Analysis Methods for Food: From Today to Tomorrow. Food Saf (Tokyo) 2016. [DOI: 10.1002/9781119160588.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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84
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Perkins G, Lu H, Garlan F, Taly V. Droplet-Based Digital PCR: Application in Cancer Research. Adv Clin Chem 2016; 79:43-91. [PMID: 28212714 DOI: 10.1016/bs.acc.2016.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient characterization of genetic and epigenetic alterations in oncology, virology, or prenatal diagnostics requires highly sensitive and specific high-throughput approaches. Nevertheless, with the use of conventional methods, sensitivity and specificity were largely limited. By partitioning individual target molecules within distinct compartments, digital PCR (dPCR) could overcome these limitations and detect very rare sequences with unprecedented precision and sensitivity. In dPCR, the sample is diluted such that each individual partition will contain no more than one target sequence. Following the assay reaction, the dPCR process provides an absolute value and analyzable quantitative data. The recent coupling of dPCR with microfluidic systems in commercial platforms should lead to an essential tool for the management of patients with cancer, especially adapted to the analysis of precious samples. Applications in cancer research range from the analysis of tumor heterogeneity to that of a range of body fluids. Droplet-based dPCR is indeed particularly appropriate for the emerging field of liquid biopsy analysis. In this review, following an overview of the development in dPCR technology and different strategies based on the use of microcompartments, we will focus particularly on the applications and latest development of microfluidic droplet-based dPCR in oncology.
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Affiliation(s)
- G Perkins
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France; European Georges Pompidou Hospital, AP-HP - Paris Descartes University, Paris, France
| | - H Lu
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - F Garlan
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - V Taly
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France.
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85
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High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 2016; 12:e1006321. [PMID: 27898685 PMCID: PMC5127505 DOI: 10.1371/journal.pgen.1006321] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/24/2016] [Indexed: 11/30/2022] Open
Abstract
The active sites of multisubunit RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins. Proper regulation of Pol II transcription, the first step of gene expression, is essential for life. Extensive evidence has revealed a widely conserved and dynamic polymerase active site component, termed the Trigger Loop (TL), in balancing transcription rate and fidelity while possibly allowing control of transcription elongation. Coupling high-throughput sequencing with our previously established genetic system, we are able to assess the in vivo phenotypes for almost all possible single substitution Pol II TL mutants in the budding yeast Saccharomyces cerevisiae. We show that mutants in the TL nucleotide interacting and linker regions widely confer dominant and severe growth defects. Clustering of TL mutants’ transcription-related and general stress phenotypes reveals three main classes of TL mutants, including previously identified fast and slow elongating mutants. Comprehensive analyses of the distribution of fast and slow elongation mutants in light of existing Pol II crystal structures reveal critical regions contributing to proper TL dynamics and function. Evidence is presented linking a previously observed hydrophobic pocket to NTP substrate-induced TL closing, the mechanism critical for correct substrates selection and transcription fidelity. Finally, we assess the functional interplay between TL and its proximal domains, and their presumptive roles in the function and evolution of the TL. Utilizing the Pol II TL as a case study, we present a structural genetics approach that reveals insights into a complex, multi-functional, and essential domain in yeast.
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86
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Carapito R, Radosavljevic M, Bahram S. Next-Generation Sequencing of the HLA locus: Methods and impacts on HLA typing, population genetics and disease association studies. Hum Immunol 2016; 77:1016-1023. [DOI: 10.1016/j.humimm.2016.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/15/2016] [Accepted: 04/04/2016] [Indexed: 12/30/2022]
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87
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Borsu L, Intrieri J, Thampi L, Yu H, Riely G, Nafa K, Chandramohan R, Ladanyi M, Arcila ME. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples. J Mol Diagn 2016; 18:903-911. [PMID: 27631691 PMCID: PMC5807920 DOI: 10.1016/j.jmoldx.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/08/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA.
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Affiliation(s)
- Laetitia Borsu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Julie Intrieri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Linta Thampi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Helena Yu
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Gregory Riely
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
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88
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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89
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Dapprich J, Ferriola D, Mackiewicz K, Clark PM, Rappaport E, D’Arcy M, Sasson A, Gai X, Schug J, Kaestner KH, Monos D. The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity. BMC Genomics 2016; 17:486. [PMID: 27393338 PMCID: PMC4938946 DOI: 10.1186/s12864-016-2836-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 06/15/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The ability to capture and sequence large contiguous DNA fragments represents a significant advancement towards the comprehensive characterization of complex genomic regions. While emerging sequencing platforms are capable of producing several kilobases-long reads, the fragment sizes generated by current DNA target enrichment technologies remain a limiting factor, producing DNA fragments generally shorter than 1 kbp. The DNA enrichment methodology described herein, Region-Specific Extraction (RSE), produces DNA segments in excess of 20 kbp in length. Coupling this enrichment method to appropriate sequencing platforms will significantly enhance the ability to generate complete and accurate sequence characterization of any genomic region without the need for reference-based assembly. RESULTS RSE is a long-range DNA target capture methodology that relies on the specific hybridization of short (20-25 base) oligonucleotide primers to selected sequence motifs within the DNA target region. These capture primers are then enzymatically extended on the 3'-end, incorporating biotinylated nucleotides into the DNA. Streptavidin-coated beads are subsequently used to pull-down the original, long DNA template molecules via the newly synthesized, biotinylated DNA that is bound to them. We demonstrate the accuracy, simplicity and utility of the RSE method by capturing and sequencing a 4 Mbp stretch of the major histocompatibility complex (MHC). Our results show an average depth of coverage of 164X for the entire MHC. This depth of coverage contributes significantly to a 99.94 % total coverage of the targeted region and to an accuracy that is over 99.99 %. CONCLUSIONS RSE represents a cost-effective target enrichment method capable of producing sequencing templates in excess of 20 kbp in length. The utility of our method has been proven to generate superior coverage across the MHC as compared to other commercially available methodologies, with the added advantage of producing longer sequencing templates amenable to DNA sequencing on recently developed platforms. Although our demonstration of the method does not utilize these DNA sequencing platforms directly, our results indicate that the capture of long DNA fragments produce superior coverage of the targeted region.
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Affiliation(s)
| | - Deborah Ferriola
- />Generation Biotech, Lawrenceville, NJ 08648 USA
- />Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kate Mackiewicz
- />Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Peter M. Clark
- />Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Eric Rappaport
- />Nucleic Acids & Protein Core Facility, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Monica D’Arcy
- />The Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Ariella Sasson
- />The Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Xiaowu Gai
- />The Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Jonathan Schug
- />Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Klaus H. Kaestner
- />Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Dimitri Monos
- />Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- />The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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90
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Tay A, Pavesi A, Yazdi SR, Lim CT, Warkiani ME. Advances in microfluidics in combating infectious diseases. Biotechnol Adv 2016; 34:404-421. [PMID: 26854743 PMCID: PMC7125941 DOI: 10.1016/j.biotechadv.2016.02.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/11/2022]
Abstract
One of the important pursuits in science and engineering research today is to develop low-cost and user-friendly technologies to improve the health of people. Over the past decade, research efforts in microfluidics have been made to develop methods that can facilitate low-cost diagnosis of infectious diseases, especially in resource-poor settings. Here, we provide an overview of the recent advances in microfluidic devices for point-of-care (POC) diagnostics for infectious diseases and emphasis is placed on malaria, sepsis and AIDS/HIV. Other infectious diseases such as SARS, tuberculosis, and dengue are also briefly discussed. These infectious diseases are chosen as they contribute the most to disability-adjusted life-years (DALYs) lost according to the World Health Organization (WHO). The current state of research in this area is evaluated and projection toward future applications and accompanying challenges are also discussed.
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Affiliation(s)
- Andy Tay
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore 117575, Singapore; Department of Bioengineering, University of California Los Angeles, CA 90025, United States
| | - Andrea Pavesi
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602, Singapore
| | - Saeed Rismani Yazdi
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602, Singapore; Polytechnic University of Milan, Milan 20133, Italy
| | - Chwee Teck Lim
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602, Singapore; Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore 117575, Singapore
| | - Majid Ebrahimi Warkiani
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602, Singapore; School of Mechanical and Manufacturing Engineering, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia.
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91
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Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis. Mar Genomics 2016; 30:15-26. [PMID: 27346185 DOI: 10.1016/j.margen.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/11/2016] [Accepted: 06/11/2016] [Indexed: 12/25/2022]
Abstract
High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest. Specifically, we exploited sequence capture and Illumina sequencing to characterize the evolution of key components from the insulin-like growth (IGF) signalling axis of salmonid fish at unprecedented phylogenetic resolution. The IGF axis represents a central governor of vertebrate growth and its core components were expanded by whole genome duplication in the salmonid ancestor ~95Ma. Using RNA baits synthesised to genes encoding the complete family of IGF binding proteins (IGFBP) and an IGF hormone (IGF2), we captured, sequenced and assembled orthologous and paralogous exons from species representing all ten salmonid genera. This approach generated 299 novel sequences, most as complete or near-complete protein-coding sequences. Phylogenetic analyses confirmed congruent evolutionary histories for all nineteen recognized salmonid IGFBP family members and identified novel salmonid-specific IGF2 paralogues. Moreover, we reconstructed the evolution of duplicated IGF axis paralogues across a replete salmonid phylogeny, revealing complex historic selection regimes - both ancestral to salmonids and lineage-restricted - that frequently involved asymmetric paralogue divergence under positive and/or relaxed purifying selection. Our findings add to an emerging literature highlighting diverse applications for targeted sequencing in comparative-evolutionary genomics. We also set out a viable approach to obtain large sets of nuclear genes for any member of the salmonid family, which should enable insights into the evolutionary role of whole genome duplication before additional nuclear genome sequences become available.
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92
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Abstract
Digital PCR (dPCR) is an emerging technology for genetic analysis and clinical diagnostics. To facilitate the widespread application of dPCR, here we developed a new micropatterned superporous absorbent array chip (μSAAC) which consists of an array of microwells packed with highly porous agarose microbeads. The packed beads construct a hierarchically porous microgel which confers superior water adsorption capacity to enable spontaneous filling of PDMS microwells for fluid compartmentalization without the need of sophisticated microfluidic equipment and operation expertise. Using large λ-DNA as the model template, we validated the μSAAC for stochastic partitioning and quantitative digital detection of DNA molecules. Furthermore, as a proof-of-concept, we conducted dPCR detection and single-molecule sequencing of a mutation prevalent in blood cancer, the chromosomal translocation t(14;18), demonstrating the feasibility of the μSAAC for analysis of disease-associated mutations. These experiments were carried out using the standard molecular biology techniques and instruments. Because of its low cost, ease of fabrication, and equipment-free liquid partitioning, the μSAAC is readily adaptable to general lab settings, which could significantly facilitate the widespread application of dPCR technology in basic research and clinical practice.
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Affiliation(s)
- Yazhen Wang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
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93
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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94
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Bernasconi-Elias P, Hu T, Jenkins D, Firestone B, Gans S, Kurth E, Capodieci P, Deplazes-Lauber J, Petropoulos K, Thiel P, Ponsel D, Hee Choi S, LeMotte P, London A, Goetcshkes M, Nolin E, Jones MD, Slocum K, Kluk MJ, Weinstock DM, Christodoulou A, Weinberg O, Jaehrling J, Ettenberg SA, Buckler A, Blacklow SC, Aster JC, Fryer CJ. Characterization of activating mutations of NOTCH3 in T-cell acute lymphoblastic leukemia and anti-leukemic activity of NOTCH3 inhibitory antibodies. Oncogene 2016; 35:6077-6086. [PMID: 27157619 PMCID: PMC5102827 DOI: 10.1038/onc.2016.133] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/07/2016] [Indexed: 01/07/2023]
Abstract
Notch receptors have been implicated as oncogenic drivers in several cancers, the most notable example being NOTCH1 in T-cell acute lymphoblastic leukemia (T-ALL). To characterize the role of activated NOTCH3 in cancer, we generated an antibody that detects the neo-epitope created upon gamma-secretase cleavage of NOTCH3 to release its intracellular domain (ICD3), and sequenced the negative regulatory region (NRR) and PEST domain coding regions of NOTCH3 in a panel of cell lines. We also characterize NOTCH3 tumor-associated mutations that result in activation of signaling and report new inhibitory antibodies. We determined the structural basis for receptor inhibition by obtaining the first co-crystal structure of a NOTCH3 antibody with the NRR protein and defined two distinct epitopes for NRR antibodies. The antibodies exhibit potent anti-leukemic activity in cell lines and tumor xenografts harboring NOTCH3 activating mutations. Screening of primary T-ALL samples reveals that two of 40 tumors examined show active NOTCH3 signaling. We also identified evidence of NOTCH3 activation in 12 of 24 patient-derived orthotopic xenograft models, two of which exhibit activation of NOTCH3 without activation of NOTCH1. Our studies provide additional insights into NOTCH3 activation and offer a path forward for identification of cancers that are likely to respond to therapy with NOTCH3 selective inhibitory antibodies.
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Affiliation(s)
- P Bernasconi-Elias
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - T Hu
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - D Jenkins
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - B Firestone
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - S Gans
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - E Kurth
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - P Capodieci
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - J Deplazes-Lauber
- Discovery Alliances and Technologies, MorphoSys AG, Martinsried, Germany
| | - K Petropoulos
- Discovery Alliances and Technologies, MorphoSys AG, Martinsried, Germany
| | - P Thiel
- Discovery Alliances and Technologies, MorphoSys AG, Martinsried, Germany
| | - D Ponsel
- Discovery Alliances and Technologies, MorphoSys AG, Martinsried, Germany
| | - S Hee Choi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - P LeMotte
- Department of Biologics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - A London
- Department of Biologics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - M Goetcshkes
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - E Nolin
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - M D Jones
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - K Slocum
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - M J Kluk
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - D M Weinstock
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - A Christodoulou
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - O Weinberg
- Pathology Children Hospital Boston, Boston, MA, USA
| | - J Jaehrling
- Discovery Alliances and Technologies, MorphoSys AG, Martinsried, Germany
| | - S A Ettenberg
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - A Buckler
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - S C Blacklow
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - J C Aster
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - C J Fryer
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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95
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Chen K, Zhou YX, Li K, Qi LX, Zhang QF, Wang MC, Xiao JH. A novel three-round multiplex PCR for SNP genotyping with next generation sequencing. Anal Bioanal Chem 2016; 408:4371-7. [PMID: 27113460 DOI: 10.1007/s00216-016-9536-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/27/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
Owing to the high throughput and low cost, next generation sequencing has attracted much attention for SNP genotyping application for researchers. Here, we introduce a new method based on three-round multiplex PCR to precisely genotype SNPs with next generation sequencing. This method can as much as possible consume the equivalent amount of each pair of specific primers to largely eliminate the amplification discrepancy between different loci. After the PCR amplification, the products can be directly subjected to next generation sequencing platform. We simultaneously amplified 37 SNP loci of 757 samples and sequenced all amplicons on ion torrent PGM platform; 90.5 % of the target SNP loci were accurately genotyped (at least 15×) and 90.4 % amplicons had uniform coverage with a variation less than 50-fold. Ligase detection reaction (LDR) was performed to genotype the 19 SNP loci (as part of the 37 SNP loci) with 91 samples randomly selected from the 757 samples, and 99.5 % genotyping data were consistent with the next generation sequencing results. Our results demonstrate that three-round PCR coupled with next generation sequencing is an efficient and economical genotyping approach. Graphical Abstract The schematic diagram of three-round PCR.
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Affiliation(s)
- Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 05003365, China
| | - Yu-Xun Zhou
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Li-Xin Qi
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Qi-Fei Zhang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Mao-Chun Wang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Jun-Hua Xiao
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China.
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96
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Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine. Pharmaceutics 2016; 8:E15. [PMID: 27110816 PMCID: PMC4932478 DOI: 10.3390/pharmaceutics8020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.
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Affiliation(s)
- Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Leihong Wu
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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97
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Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids. PLoS One 2016; 11:e0153359. [PMID: 27074005 PMCID: PMC4830604 DOI: 10.1371/journal.pone.0153359] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/29/2016] [Indexed: 11/28/2022] Open
Abstract
Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm2 area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10-1 to 4 × 10-3 copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings.
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98
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Mashaghi S, van Oijen AM. Droplet microfluidics for kinetic studies of viral fusion. BIOMICROFLUIDICS 2016; 10:024102. [PMID: 27014395 PMCID: PMC4788598 DOI: 10.1063/1.4943126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Viral infections remain a major threat to public health. The speed with which viruses are evolving drug-resistant mutations necessitates the further development of antiviral therapies with a large emphasis on drug discovery. To facilitate these efforts, there is a need for robust, high-throughput assays that allow the screening of large libraries of compounds, while enabling access to detailed kinetic data on their antiviral activity. We report here the development of a droplet-based microfluidic platform to probe viral fusion, an early critical step in infection by membrane-enveloped viruses such as HIV, Hepatitis C, and influenza. Using influenza A, we demonstrate the measurement of the kinetics of fusion of virions with target liposomes with sub-second temporal resolution. In analogy with acidification of the endosome that triggers fusion in a cellular context, we acidify the content of aqueous droplets containing virions and liposomes in situ by introducing acid from the dispersed phase and visualize the kinetics of fusion by using fluorescent probes.
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99
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Abstract
The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.
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Affiliation(s)
- Songzi Kou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Danhui Cheng
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fei Sun
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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100
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A three-dimensional electrode for highly efficient electrocoalescence-based droplet merging. Biomed Microdevices 2016; 17:35. [PMID: 25681970 DOI: 10.1007/s10544-014-9921-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Droplet merging is one of the key functions in the ever-widening applications of droplet microfluidics. Enhancing the efficiency of electric field-based droplet merging, namely electrocoalescence, can lead to an increase in platform stability and overcome one of the major bottlenecks in further improving throughputs of droplet microfluidic systems. In this work, a paired three-dimensional (3D) electrode design that can provide a uniform electric field within a droplet merging region, which is also properly aligned with the droplet dipole moments for highly efficient electrocoalescence is presented. A systematic study was conducted to compare the droplet merging performance of the presented 3D electrode design to other commonly used planar electrode, coplanar electrode, dual-coplanar electrode, and liquid metal 3D electrode designs. The presented 3D electrode design reduced the threshold input voltage required to obtain droplet fusion by up to 75%. In addition, a droplet merging efficiency of higher than 95% was consistently observed, compared to less than 85% merging efficiency for the conventionally used electrode designs. We expect that this droplet electrocoalescence design will improve the overall throughput and merging success rate in droplet microfluidic based high-throughput assays.
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