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Wang Z, He S, Zhang C, Xu D. A label-free aptasensing method for detecting SARS-CoV-2 virus antigen by using dumbbell probe-mediated circle-to-circle amplification. Anal Bioanal Chem 2024; 416:1961-1970. [PMID: 38349532 DOI: 10.1007/s00216-024-05195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
Controlling the spread of pathogen requires an efficient and accurate diagnosis. Compared with nucleic acid and antibody detection, antigen assays are more convenient to meet clinical diagnostic needs. However, antigen detection is often difficult to achieve high sensitivity in a limited time. In this work, a novel aptasensing method was designed for the purpose of SARS-CoV-2 antigen detection, using a dumbbell padlock probe-mediated circle-to-circle amplification (C2CA) approach. A sandwich complex of antibody-antigen-aptamer is first formed on the magnetic beads. Afterwards, the signal is amplified by a C2CA reaction involving two tandem rolling circle amplifications. Without special instruments or nanomaterials, a detection limit of 575 fg/mL for S1 protein can be achieved in less than 2 h. In the case of the spike pseudovirus SARS-CoV-2 in artificial saliva, the detection limit is 272 TU/μL, which is much lower than average viral load in patients. Therefore, our method provides a timely, efficient and accurate approach for the clinical diagnosis of SARS-CoV-2. It also opens up the application of C2CA in aptamer sensing and antigen detection.
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Affiliation(s)
- Zecheng Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, People's Republic of China
| | - Si He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, People's Republic of China
| | - Chenchen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, People's Republic of China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, People's Republic of China.
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2
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Ordóñez CD, Mayoral-Campos C, Egas C, Redrejo-Rodríguez M. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences. NAR Genom Bioinform 2023; 5:lqad073. [PMID: 37608803 PMCID: PMC10440786 DOI: 10.1093/nargab/lqad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023] Open
Abstract
Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.
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Affiliation(s)
- Carlos D Ordóñez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Carmen Mayoral-Campos
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Biocant, Transfer Technology Association, Cantanhede, Portugal
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
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3
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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Czado N, LaRue B, Wheeler A, Houston R, Holmes A, Grisedale K, Hughes S. The effectiveness of various strategies to improve DNA analysis of formaldehyde-damaged tissues from embalmed cadavers for human identification purposes. J Forensic Sci 2023; 68:596-607. [PMID: 36725687 DOI: 10.1111/1556-4029.15200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023]
Abstract
Formalin-fixed tissues provide the medical and forensic communities with alternative and often last resort sources of DNA for identification or diagnostic purposes. The DNA in these samples can be highly degraded and chemically damaged, making downstream genotyping using short tandem repeats (STRs) challenging. Therefore, the use of alternative genetic markers, methods that pre-amplify the low amount of good quality DNA present, or methods that repair the damaged DNA template may provide more probative genetic information. This study investigated whether whole genome amplification (WGA) and DNA repair could improve STR typing of formaldehyde-damaged (FD) tissues from embalmed cadavers. Additionally, comparative genotyping success using bi-allelic markers, including INDELs and SNPs, was explored. Calculated random match probabilities (RMPs) using traditional STRs, INDEL markers, and two next generation sequencing (NGS) panels were compared across all samples. Overall, results showed that neither WGA nor DNA repair substantially improved STR success rates from formalin-fixed tissue samples. However, when DNA from FD samples was genotyped using INDEL and SNP-based panels, the RMP of each sample was markedly lower than the RMPs calculated from partial STR profiles. Therefore, the results of this study suggest that rather than attempting to improve the quantity and quality of severely damaged and degraded DNA prior to STR typing, a more productive approach may be to target smaller amplicons to provide more discriminatory DNA identifications. Furthermore, an NGS panel with less loci may yield better results when examining FD samples, due to more optimized chemistries that result in greater allelic balance and amplicon coverage.
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Affiliation(s)
- Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Bobby LaRue
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA.,Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Amanda Wheeler
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Amy Holmes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Kelly Grisedale
- Chemistry and Physics Department, Western Carolina University,1 University Drive, Cullowhee, North Carolina, USA
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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Circular Whole-Transcriptome Amplification (cWTA) and mNGS Screening Enhanced by a Group Testing Algorithm (mEGA) Enable High-Throughput and Comprehensive Virus Identification. mSphere 2022; 7:e0033222. [PMID: 36005385 PMCID: PMC9599668 DOI: 10.1128/msphere.00332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance.
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Wang K, Jiang Y, Guo Y, Geng M, Wu W. An Optimized Thermal Feedback Methodology for Accurate Temperature Control and High Amplification Efficiency during Fluorescent qPCR. Bioengineering (Basel) 2022; 9:bioengineering9060237. [PMID: 35735480 PMCID: PMC9220086 DOI: 10.3390/bioengineering9060237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
Traditional qPCR instrument is combined with CMOS and a personal computer, and a photoelectric feedback automatic fluorescence detection system is designed to realize quantitative real-time PCR. The key to reaction efficiency lies in how to ensure that the temperature of the detection reagent completely matches the set temperature. However, for most traditional real-time fluorescent PCR systems, the temperature cycling is controlled by detecting the temperature of the heating well plate. It cannot directly measure the temperature in the reaction reagent PCR tube, which will cause the deviation in the actual temperature of the reagent to be as expected. Therefore, in this paper, we raise a method of directly detecting the temperature in the reaction tube of the reagent during the temperature cycling is adopted. According to the deviation from the expected value, the set temperature of the PCR instrument is adjusted to make the actual temperature of the reagent closer to the expected value. Through this method, we also realized the temperature calibration and optimization of the TEC circulation system we built. Experiments show that this low-cost, portable real-time quantitative PCR system can detect and analyze pathogens in situ.
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Affiliation(s)
- Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yangyang Jiang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou 510006, China;
| | - Mingkun Geng
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China;
- Graduate School, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
- Correspondence:
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Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing. Microorganisms 2021; 9:microorganisms9091979. [PMID: 34576874 PMCID: PMC8467633 DOI: 10.3390/microorganisms9091979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis.
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9
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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10
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Cheng YH, Liu SJ, Jiang JH. Enzyme-free electrochemical biosensor based on amplification of proximity-dependent surface hybridization chain reaction for ultrasensitive mRNA detection. Talanta 2020; 222:121536. [PMID: 33167244 DOI: 10.1016/j.talanta.2020.121536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
Abstract
The ability to recognize mRNA with high efficiency in cells would greatly facilitate the elucidation of mRNA-mediated cellular cascades and their disease associations. However, most traditional electrochemical strategies targeting nucleotides are always confronted with cumbersome interface operation and washing procedures, as well as the high cost of labeling and the strict reaction conditions of tool enzymes, limiting their potential applications. To address these issues, herein we reported, for the first time, a simple label-free, isothermal, non-enzymatic, and ultrasensitive homogeneous electrochemical biosensor based on autonomous proximity-dependent surface hybridization chain reaction (HCR), for sensitive signal amplification and highly specific detection of target survivin mRNA with a detection limit of 3 fM. The target triggers hybridization chain reaction and mRNA-fueled surface hybridization of ferrocene-tagged metastable DNA hairpin probes on proximity-dependent surface hybridization, resulting in the formation of multiple long-range duplex DNA chains which are immobilized onto the gold electrodes with a substantially stable ferrocene-mediated redox current. Thus, a significant electrochemical signal increase is observed dependent on the concentration of the target RNA, with a very low detection limit. Mo-reover, this molecular biosensor also exhibits excellent specificity to distinguish even single base mismatched, with strong reliability. The developed biosensor provides a novel promising tool for ultra-sensitive and selective detection, and it has great potential to be applied in mRNA-related biochemical research and clinical cancer diagnostics in more detail.
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Affiliation(s)
- Yu-Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Si-Jia Liu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Key Laboratory of Regenerative Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, School of Basic Medical Sciences, Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. PLoS Negl Trop Dis 2019; 13:e0007480. [PMID: 31158221 PMCID: PMC6564047 DOI: 10.1371/journal.pntd.0007480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/13/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reaction tube. Using this system, the CHIKV genome was effectively amplified under isothermal conditions, and used as a template for MinION sequencing with a laptop computer. Our in-house RT-LAMP method and MinION sequencing system were also validated with RNAs and serum samples from recent outbreaks of CHIKV patients in Brazil. The obtained sequence data confirmed the CHIKV outbreaks and identified the genotype. In summary, our established inexpensive on-site genome detection and sequencing system is applicable for both diagnosis of CHIKV infected patients and genotyping of the CHIKV virus in future outbreak in remote areas. Chikungunya virus has re-emerged as an important pathogen causing several outbreaks in the world. As the clinical symptoms of chikungunya is similar to other mosquito-borne febrile diseases, the definitive diagnosis of the disease is based on the detection of viral genome from the patient blood. Loop-mediated isothermal amplification (LAMP) is a method that rapidly amplify nucleic acids under isothermal condition. In the present work, a simple dried format LAMP test for chikungunya diagnosis was developed which can be directly amplified from human blood. Combining with the portable sequencer MinION sequencing system, a method to identify the viral genotype was also established. The developed on-site diagnosis and genotyping system is easy to perform, sensitive, and rapid. Therefore, it offers great promise as a routine simple tool for diagnosis and disease management of chikungunya.
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12
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Höpke J, Brewer G, Dodsworth S, Ortiz E, Albach D. DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae). UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj75.06.564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Fan Y, Dong D, Li Q, Si H, Pei H, Li L, Tang B. Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips. LAB ON A CHIP 2018; 18:1151-1173. [PMID: 29541737 DOI: 10.1039/c7lc01333g] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.
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Affiliation(s)
- Yuanyuan Fan
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
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Özay B, Robertus CM, Negri JL, McCalla SE. First characterization of a biphasic, switch-like DNA amplification. Analyst 2018; 143:1820-1828. [PMID: 29577124 PMCID: PMC5969907 DOI: 10.1039/c8an00130h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.
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Affiliation(s)
- Burcu Özay
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717, USA.
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15
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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16
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Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping. J Hum Genet 2018; 63:407-416. [PMID: 29440707 DOI: 10.1038/s10038-018-0411-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 11/08/2022]
Abstract
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.
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Al-Hashimi F, J. Diaz-Cano S. Multi-target analysis of neoplasms for the evaluation of tumor progression: stochastic approach of biologic processes. AIMS MOLECULAR SCIENCE 2018. [DOI: 10.3934/molsci.2018.1.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Qu X, Wang S, Ge Z, Wang J, Yao G, Li J, Zuo X, Shi J, Song S, Wang L, Li L, Pei H, Fan C. Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions. J Am Chem Soc 2017; 139:10176-10179. [DOI: 10.1021/jacs.7b04040] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiangmeng Qu
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Shaopeng Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jianbang Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Guangbao Yao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Jiye Shi
- Kellogg
College, University of Oxford, Oxford, OX2 6PN, U.K
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Li Li
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Hao Pei
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
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Nie X, Zhang C, Wang Y, Guo C, Zhou J, Chen G. Application of hyper-branched rolling circle amplification (HRCA) and HRCA-based strip test for the detection of Chattonella marina. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:15678-15688. [PMID: 28527138 DOI: 10.1007/s11356-017-9152-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Harmful algal blooms (HABs) are global threats to marine ecosystems, fisheries, and human health. Therefore, developing effective and accurate methods for identifying causative algae and monitoring seawater quality is urgent. However, traditional, microscopy-based methods are complex, inaccurate, and time-consuming. Here, we present a novel method for effective and sensitive detection of Chattonella marina using hyper-branched rolling circle amplification (HRCA) and HRCA-based strip test (HBST). The large subunit (LSU) ribosomal DNA (rDNA) D1-D2 region of C. marina was firstly sequenced to design a species-specific padlock probe (PLP). The HRCA reaction with two amplification primers and further HBST for C. marina was established. The optimized reaction conditions for HRCA were PLP concentration, 20 pM; ligation temperature, 65 °C; ligation time, 60 min; amplification temperature, 61 °C; and amplification time, 60 min. The developed HBST detection procedure involved HRCA reaction, test strip preparation, hybridization, coloration, and judgment of hybridization by the naked eye. Specificity and sensitivity of the established methods were validated. Moreover, the results showed that the established detection methods were specific and sensitive to C. marina. The detection limits of HRCA and HBST assays were 10 copies and 1 copy μL-1 of plasmid with LSU rDNA of C. marina, which are of two and three respective magnitude orders higher than conventional PCR. Finally, the protocols were applied to the simulated field samples and the results showed that the developed HBST assay had higher detection sensitivity than HRCA and PCR. In conclusion, the methods presented in this study are promising for sensitive, intuitive, and specific detection of C. marina in field monitoring natural samples and may provide a good detection model for other harmful algae in the future.
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Affiliation(s)
- Xiaoli Nie
- College of Oceanology, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Chunyun Zhang
- College of Oceanology, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
| | - Yuanyuan Wang
- College of Oceanology, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Changlu Guo
- College of Oceanology, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Jin Zhou
- Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Xili Town, Shenzhen City, 518055, Guangdong Province, People's Republic of China
| | - Guofu Chen
- College of Oceanology, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
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Mikulasova A, Wardell CP, Murison A, Boyle EM, Jackson GH, Smetana J, Kufova Z, Pour L, Sandecka V, Almasi M, Vsianska P, Gregora E, Kuglik P, Hajek R, Davies FE, Morgan GJ, Walker BA. The spectrum of somatic mutations in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape than that in multiple myeloma. Haematologica 2017; 102:1617-1625. [PMID: 28550183 PMCID: PMC5685224 DOI: 10.3324/haematol.2017.163766] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/16/2017] [Indexed: 01/10/2023] Open
Abstract
Monoclonal gammopathy of undetermined significance is a pre-malignant precursor of multiple myeloma with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS gene mutations, little is known about the molecular mechanism of malignant transformation. We performed whole exome sequencing together with comparative genomic hybridization plus single nucleotide polymorphism array analysis in 33 flow-cytometry-separated abnormal plasma cell samples from patients with monoclonal gammopathy of undetermined significance to describe somatic gene mutations and chromosome changes at the genome-wide level. Non-synonymous mutations and copy-number alterations were present in 97.0% and in 60.6% of cases, respectively. Importantly, the number of somatic mutations was significantly lower in monoclonal gammopathy of undetermined significance than in myeloma (P<10-4) and we identified six genes that were significantly mutated in myeloma (KRAS, NRAS, DIS3, HIST1H1E, EGR1 and LTB) within the monoclonal gammopathy of undetermined significance dataset. We also found a positive correlation with increasing chromosome changes and somatic gene mutations. IGH translocations, comprising t(4;14), t(11;14), t(14;16) and t(14;20), were present in 27.3% of cases and in a similar frequency to myeloma, consistent with the primary lesion hypothesis. MYC translocations and TP53 deletions or mutations were not detected in samples from patients with monoclonal gammopathy of undetermined significance, indicating that they may be drivers of progression to myeloma. Data from this study show that monoclonal gammopathy of undetermined significance is genetically similar to myeloma, however overall genetic abnormalities are present at significantly lower levels in monoclonal gammopathy of undetermined significant than in myeloma.
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Affiliation(s)
- Aneta Mikulasova
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Czech Republic.,Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christopher P Wardell
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alexander Murison
- Center for Myeloma Research, Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Eileen M Boyle
- Center for Myeloma Research, Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Graham H Jackson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Czech Republic
| | - Zuzana Kufova
- Faculty of Medicine, University of Ostrava, Czech Republic.,Department of Hematooncology, University Hospital Ostrava, Czech Republic
| | - Ludek Pour
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Viera Sandecka
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Martina Almasi
- Department of Clinical Hematology, University Hospital Brno, Czech Republic
| | - Pavla Vsianska
- Department of Clinical Hematology, University Hospital Brno, Czech Republic
| | - Evzen Gregora
- Department of Internal Medicine and Hematology, University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Czech Republic
| | - Roman Hajek
- Faculty of Medicine, University of Ostrava, Czech Republic.,Department of Hematooncology, University Hospital Ostrava, Czech Republic
| | - Faith E Davies
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Comparison of whole genome amplification techniques for human single cell exome sequencing. PLoS One 2017; 12:e0171566. [PMID: 28207771 PMCID: PMC5313163 DOI: 10.1371/journal.pone.0171566] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/21/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. DISCUSSION In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.
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22
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Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells. Oncotarget 2016; 8:56066-56080. [PMID: 28915574 PMCID: PMC5593545 DOI: 10.18632/oncotarget.10701] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/09/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation. Although MDA-based WGA yielded the highest DNA amount, DNA quality was not adequate for downstream analysis. PCR-based WGA demonstrates superiority over MDA-PCR combining technique for SNP and indel analysis in single cells. However, SNP calling performance of MDA-PCR WGA improves with increasing amount of input DNA, whereas CNA analysis does not. The performance of PCR-based WGA did not significantly improve with increase of input material. CNA profiles of single cells, amplified with MDA-PCR technique and sequenced on both HiSeq2000 and IonProton platforms, resembled unamplified DNA the most. MATERIALS AND METHODS We analyzed the performance of PCR-based, multiple-displacement amplification (MDA)-based, and MDA-PCR combining WGA techniques (WGA kits Ampli1, REPLI-g, and PicoPlex, respectively) on single and pooled tumor cells obtained from EDTA- and CellSave-preserved blood and archival material. Amplified DNA underwent exome-Seq with the Illumina HiSeq2000 and ThermoFisher IonProton platforms. CONCLUSION We demonstrate the feasibility of single cell genotyping of differently preserved material, nevertheless, WGA and NGS approaches have to be chosen carefully depending on the study aims.
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Development of a bench-top extra-cleanroom for DNA amplification. Biotechniques 2016; 61:42-6. [DOI: 10.2144/000114433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 03/21/2016] [Indexed: 11/23/2022] Open
Abstract
Prevention of airborne contamination has become an important factor in biotechnology; however, conventional laminar-airflow cabinets (LAF-cabinets) are no longer sufficient as a countermeasure against nano-sized airborne contaminants in the laboratory. Here we present a bench-top extra-cleanroom classified as ISO-1 that can prevent contamination from airborne nanoparticles. This bench-top extra-cleanroom consists of a novel clean-zone-creating system that is equipped with nanofibrous, nonwoven filters. In addition, the cleanroom is also equipped with an ionizer to prevent plasticware from collecting dust by electrostatic charge attraction. This combination of features allows the cleanroom to prevent DNA contamination derived from airborne nanoparticles. Our extra-cleanroom with ionizer could be useful in various areas of biotechnology that are easily affected by airborne contaminants.
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24
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Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. PLoS One 2016; 11:e0153699. [PMID: 27144304 PMCID: PMC4856258 DOI: 10.1371/journal.pone.0153699] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/03/2016] [Indexed: 12/17/2022] Open
Abstract
Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.
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25
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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26
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Morinishi LS, Blainey P. Simple Bulk Readout of Digital Nucleic Acid Quantification Assays. J Vis Exp 2015. [PMID: 26436576 DOI: 10.3791/52925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays. We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout. Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology.
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Affiliation(s)
| | - Paul Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology;
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27
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Zhang CZ, Spektor A, Cornils H, Francis JM, Jackson EK, Liu S, Meyerson M, Pellman D. Chromothripsis from DNA damage in micronuclei. Nature 2015; 522:179-84. [PMID: 26017310 PMCID: PMC4742237 DOI: 10.1038/nature14493] [Citation(s) in RCA: 768] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 04/20/2015] [Indexed: 01/01/2023]
Abstract
Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis. Chromothripsis is characterized by extensive genomic rearrangements and an oscillating pattern of DNA copy number levels, all curiously restricted to one or a few chromosomes. The mechanism for chromothripsis is unknown, but we previously proposed that it could occur through the physical isolation of chromosomes in aberrant nuclear structures called micronuclei. Here, using a combination of live cell imaging and single-cell genome sequencing, we demonstrate that micronucleus formation can indeed generate a spectrum of genomic rearrangements, some of which recapitulate all known features of chromothripsis. These events are restricted to the mis-segregated chromosome and occur within one cell division. We demonstrate that the mechanism for chromothripsis can involve the fragmentation and subsequent reassembly of a single chromatid from a micronucleus. Collectively, these experiments establish a new mutational process of which chromothripsis is one extreme outcome.
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Affiliation(s)
- Cheng-Zhong Zhang
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [4] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexander Spektor
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hauke Cornils
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joshua M Francis
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Emily K Jackson
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Shiwei Liu
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew Meyerson
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA [4] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David Pellman
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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Calibrating genomic and allelic coverage bias in single-cell sequencing. Nat Commun 2015; 6:6822. [PMID: 25879913 DOI: 10.1038/ncomms7822] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/03/2015] [Indexed: 02/07/2023] Open
Abstract
Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.
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29
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Sørensen KM. Whole Genome Amplification from Blood Spot Samples. Methods Mol Biol 2015; 1347:163-178. [PMID: 26374317 DOI: 10.1007/978-1-4939-2990-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole genome amplification is an invaluable technique when working with DNA extracted from blood spots, as the DNA obtained from this source often is too limited for extensive genetic analysis. Two techniques that amplify the entire genome are common. Here, both are described with focus on the benefits and drawbacks of each system. However, in order to obtain the best possible WGA result the quality of input DNA extracted from the blood spot is essential, but also time consumption, flexibility in format and elution volume and price of the technology are factors influencing system choice. Here, three DNA extraction techniques are described and the above aspects are compared between the systems.
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Affiliation(s)
- Karina Meden Sørensen
- The Danish National Biobank, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Danmark.
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30
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Abstract
The increasing interest towards cellular heterogeneity within cell populations has pushed the development of new protocols to isolate and analyze single cells. PCR-based amplification techniques are widely used in this field. However, setting up an experiment and analyzing the results can sometimes be challenging. The aim of this chapter is to provide a general overview on single-cell PCR analysis focusing on the potential pitfalls and on the possible solutions to successfully perform the analysis.
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31
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Abstract
Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.
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Affiliation(s)
| | - John H Leamon
- CyVek Inc., 2 Barnes Industrial Road South, Wallingford, CT, 06492, USA.
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32
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Kroneis T, El-Heliebi A. Whole Genome Amplification by Isothermal Multiple Strand Displacement Using Phi29 DNA Polymerase. Methods Mol Biol 2015; 1347:111-117. [PMID: 26374313 DOI: 10.1007/978-1-4939-2990-0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The here described method of isothermal whole genome amplification (iWGA) uses a Phi29 DNA polymerase-based kit (Illustra GenomiPhi V2 DNA Amplification Kit) that amplifies minute quantities of DNA by multiple strand displacement upon random hexamer primer binding. Starting from genomic DNA or single cells this amplification yields up to 5 μg of iWGA product with fragment lengths of 10 kb and longer. As this amplification lacks the need of fragmenting DNA, its products are well suited for many downstream applications (e.g. sequencing and DNA profiling). On the contrary, degraded DNA samples are not supported by the nature of the amplification and are not well suited.
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Affiliation(s)
- Thomas Kroneis
- Research Unit for Single Cell Analysis, Institute of Cell Biology, Histology & Embryology, Medical University of Graz, Harrachgasse 21, Graz, 8010, Austria.
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden.
| | - Amin El-Heliebi
- Research Unit for Single Cell Analysis, Institute of Cell Biology, Histology & Embryology, Medical University of Graz, Harrachgasse 21, Graz, 8010, Austria
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Abstract
Modern molecular biology relies on large amounts of high-quality genomic DNA. However, in a number of clinical or biological applications this requirement cannot be met, as starting material is either limited (e.g., preimplantation genetic diagnosis (PGD) or analysis of minimal residual cancer) or of insufficient quality (e.g., formalin-fixed paraffin-embedded tissue samples or forensics). As a consequence, in order to obtain sufficient amounts of material to analyze these demanding samples by state-of-the-art modern molecular assays, genomic DNA has to be amplified. This chapter summarizes available technologies for whole-genome amplification (WGA), bridging the last 25 years from the first developments to currently applied methods. We will especially elaborate on research application, as well as inherent advantages and limitations of various WGA technologies.
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Affiliation(s)
- Zbigniew Tadeusz Czyz
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany
| | - Stefan Kirsch
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany
| | - Bernhard Polzer
- Project Group, Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Josef-Engert-Straße 9, 93053, Regensburg, Germany.
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Walter MC, Öhrman C, Myrtennäs K, Sjödin A, Byström M, Larsson P, Macellaro A, Forsman M, Frangoulidis D. Genome sequence of Coxiella burnetii strain Namibia. Stand Genomic Sci 2014; 9:22. [PMID: 25593636 PMCID: PMC4286197 DOI: 10.1186/1944-3277-9-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022] Open
Abstract
We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438 bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics.
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Affiliation(s)
- Mathias C Walter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Genome-Oriented Bioinformatics, Center of Life and Food Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mona Byström
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Pär Larsson
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Anna Macellaro
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
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Furtak VA, Dabrazhynetskaya A, Volokhov DV, Chizhikov V. Use of tangential flow filtration for improving detection of viral adventitious agents in cell substrates. Biologicals 2014; 43:23-30. [PMID: 25432087 DOI: 10.1016/j.biologicals.2014.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/03/2014] [Accepted: 10/27/2014] [Indexed: 11/28/2022] Open
Abstract
In this study, we assessed the feasibility of tangential flow filtration (TFF) for primary concentration of viral adventitious agents (AAs) from large volumes of cell substrate-derived samples, such as cell-free Chinese hamster ovary (CHO) culture supernatants (500 mL) and CHO cell lysates (50 mL), prior to virus detection in them by nucleic acid-based methods (i.e., qPCR and massively parallel sequencing (MPS). The study was conducted using the samples spiked with four model DNA viruses (bovine herpesvirus type 4, human adenovirus type 5, simian polyomavirus SV-40, and bovine parvovirus). The results showed that the combined TFF/MPS approach enables reliable detection of as low as 1000 genome equivalents (GE) of each of the four viruses spiked into the cell substrate samples. The final achieved sensitivities of 2 GE/mL for cell culture supernatant and 20 GE/mL for cell lysate make this approach more sensitive than virus-specific PCR and qPCR assays. The study results allowed us to propose that TFF might be useful and valuable method for simple and rapid concentration of potential AAs in cell substrate samples prior to AAs detection by conventional in vivo, in vitro, or molecular methods.
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Affiliation(s)
- Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Alena Dabrazhynetskaya
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Vladimir Chizhikov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA.
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A de novo genome assembly algorithm for repeats and nonrepeats. BIOMED RESEARCH INTERNATIONAL 2014; 2014:736473. [PMID: 24967398 PMCID: PMC4055594 DOI: 10.1155/2014/736473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/01/2014] [Accepted: 04/08/2014] [Indexed: 11/18/2022]
Abstract
Background. Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses. Up to now, the performances of assembling repeats of these current assemblers are very poor. Results. To improve this problem, we proposed a new genome assembly algorithm, named SWA, which has four properties: (1) assembling repeats and nonrepeats; (2) adopting a new overlapping extension strategy to extend each seed; (3) adopting sliding window to filter out the sequencing bias; and (4) proposing a compensational mechanism for low coverage datasets. SWA was evaluated and validated in both simulations and real sequencing datasets. The accuracy of assembling repeats and estimating the copy numbers is up to 99% and 100%, respectively. Finally, the extensive comparisons with other eight leading assemblers show that SWA outperformed others in terms of completeness and correctness of assembling repeats and nonrepeats. Conclusions. This paper proposed a new de novo genome assembly method for resolving complex repeats. SWA not only can detect where repeats or nonrepeats are but also can assemble them completely from NGS data, especially for assembling repeats. This is the advantage over other assemblers.
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Takahashi H, Yamazaki H, Akanuma S, Kanahara H, Saito T, Chimuro T, Kobayashi T, Ohtani T, Yamamoto K, Sugiyama S, Kobori T. Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose. PLoS One 2014; 9:e82624. [PMID: 24505243 PMCID: PMC3915000 DOI: 10.1371/journal.pone.0082624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/25/2013] [Indexed: 11/25/2022] Open
Abstract
We previously reported that multiply-primed rolling circle amplification (MRPCA) using modified random RNA primers can amplify tiny amounts of circular DNA without producing any byproducts. However, contaminating DNA in recombinant Phi29 DNA polymerase adversely affects the outcome of MPRCA, especially for negative controls such as non-template controls. The amplified DNA in negative control casts doubt on the result of DNA amplification. Since Phi29 DNA polymerase has high affinity for both single-strand and double-stranded DNA, some amount of host DNA will always remain in the recombinant polymerase. Here we describe a procedure for preparing Phi29 DNA polymerase which is essentially free of amplifiable DNA. This procedure is realized by a combination of host DNA removal using appropriate salt concentrations, inactivation of amplifiable DNA using ethidium monoazide, and irradiation with visible light from a light-emitting diode lamp. Any remaining DNA, which likely exists as oligonucleotides captured by the Phi29 DNA polymerase, is degraded by the 3'-5' exonuclease activity of the polymerase itself in the presence of trehalose, used as an anti-aggregation reagent. Phi29 DNA polymerase purified by this procedure has little amplifiable DNA, resulting in reproducible amplification of at least ten copies of plasmid DNA without any byproducts and reducing reaction volume. This procedure could aid the amplification of tiny amounts DNA, thereby providing clear evidence of contamination from laboratory environments, tools and reagents.
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Affiliation(s)
- Hirokazu Takahashi
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Yamazaki
- Isehara Research Laboratory, Technology & Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa, Japan
| | - Satoshi Akanuma
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroko Kanahara
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Toshiyuki Saito
- Transcriptome Profiling Group, National Institute of Radiological Sciences, Chiba, Chiba, Japan
| | - Tomoyuki Chimuro
- Isehara Research Laboratory, Technology & Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa, Japan
| | - Takayoshi Kobayashi
- Bio-Chemical Department, Reagent Division, Kanto Chemical Co., Inc. Tokyo, Japan
| | - Toshio Ohtani
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kimiko Yamamoto
- Insect Genome Laboratory, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Shigeru Sugiyama
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Toshiro Kobori
- Nanobiotechnology Laboratory, Food Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, Wommack KE. Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. MICROBIOME 2014; 2:3. [PMID: 24475755 PMCID: PMC3937105 DOI: 10.1186/2049-2618-2-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/17/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. RESULTS Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. CONCLUSIONS MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.
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Affiliation(s)
- Rachel Marine
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19716, USA
| | - Coleen McCarren
- Washington College, 300 Washington Avenue, Chestertown, MD 21620, USA
| | - Vansay Vorrasane
- Delaware Technical Community College, 400 Stanton-Christiana Road, Newark, DE 19713, USA
| | - Dan Nasko
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19716, USA
| | - Erin Crowgey
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19716, USA
| | - Shawn W Polson
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19716, USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19716, USA
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Direito SOL, Zaura E, Little M, Ehrenfreund P, Röling WFM. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification. Environ Microbiol 2014; 16:643-57. [PMID: 24372985 DOI: 10.1111/1462-2920.12365] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 11/28/2022]
Abstract
Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement amplification (MDA)] and one new primer-free method [primase-based whole genome amplification (pWGA)] were compared using a polymerase chain reaction (PCR)-based method as control. Pyrosequencing of an environmental sample and principal component analysis revealed that MDA impacted community profiles more strongly than pWGA and indicated that this related to species GC content, although an influence of DNA integrity could not be excluded. Subsequently, biases by species GC content, DNA integrity and fragment size were separately analysed using defined mixtures of DNA from various species. We found significantly less amplification of species with the highest GC content for MDA-based templates and, to a lesser extent, for pWGA. DNA fragmentation also interfered severely: species with more fragmented DNA were less amplified with MDA and pWGA. pWGA was unable to amplify low molecular weight DNA (< 1.5 kb), whereas MDA was inefficient. We conclude that pWGA is the most promising method for characterization of microbial communities in low-biomass environments and for currently planned astrobiological missions to Mars.
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Affiliation(s)
- Susana O L Direito
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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40
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Reliable single cell array CGH for clinical samples. PLoS One 2014; 9:e85907. [PMID: 24465780 PMCID: PMC3897541 DOI: 10.1371/journal.pone.0085907] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/07/2013] [Indexed: 12/19/2022] Open
Abstract
Background Disseminated cancer cells (DCCs) and circulating tumor cells (CTCs) are extremely rare, but comprise the precursors cells of distant metastases or therapy resistant cells. The detailed molecular analysis of these cells may help to identify key events of cancer cell dissemination, metastatic colony formation and systemic therapy escape. Methodology/Principal Findings Using the Ampli1™ whole genome amplification (WGA) technology and high-resolution oligonucleotide aCGH microarrays we optimized conditions for the analysis of structural copy number changes. The protocol presented here enables reliable detection of numerical genomic alterations as small as 0.1 Mb in a single cell. Analysis of single cells from well-characterized cell lines and single normal cells confirmed the stringent quantitative nature of the amplification and hybridization protocol. Importantly, fixation and staining procedures used to detect DCCs showed no significant impact on the outcome of the analysis, proving the clinical usability of our method. In a proof-of-principle study we tracked the chromosomal changes of single DCCs over a full course of high-dose chemotherapy treatment by isolating and analyzing DCCs of an individual breast cancer patient at four different time points. Conclusions/Significance The protocol enables detailed genome analysis of DCCs and thereby assessment of the clonal evolution during the natural course of the disease and under selection pressures. The results from an exemplary patient provide evidence that DCCs surviving selective therapeutic conditions may be recruited from a pool of genomically less advanced cells, which display a stable subset of specific genomic alterations.
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41
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McCaughan F. Molecular copy-number counting: potential of single-molecule diagnostics. Expert Rev Mol Diagn 2014; 9:309-12. [DOI: 10.1586/erm.09.14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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42
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Džunková M, Garcia-Garcerà M, Martínez-Priego L, D’Auria G, Calafell F, Moya A. Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate. PLoS One 2014; 9:e97379. [PMID: 24887077 PMCID: PMC4041646 DOI: 10.1371/journal.pone.0097379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/17/2014] [Indexed: 02/07/2023] Open
Abstract
The large amount of DNA needed to prepare a library in next generation sequencing protocols hinders direct sequencing of small DNA samples. This limitation is usually overcome by the enrichment of such samples with whole genome amplification (WGA), mostly by multiple displacement amplification (MDA) based on φ29 polymerase. However, this technique can be biased by the GC content of the sample and is prone to the development of chimeras as well as contamination during enrichment, which contributes to undesired noise during sequence data analysis, and also hampers the proper functional and/or taxonomic assignments. An alternative to MDA is direct DNA sequencing (DS), which represents the theoretical gold standard in genome sequencing. In this work, we explore the possibility of sequencing the genome of Escherichia coli fs 24 from the minimum number of DNA molecules required for pyrosequencing, according to the notion of one-bead-one-molecule. Using an optimized protocol for DS, we constructed a shotgun library containing the minimum number of DNA molecules needed to fill a selected region of a picotiterplate. We gathered most of the reference genome extension with uniform coverage. We compared the DS method with MDA applied to the same amount of starting DNA. As expected, MDA yielded a sparse and biased read distribution, with a very high amount of unassigned and unspecific DNA amplifications. The optimized DS protocol allows unbiased sequencing to be performed from samples with a very small amount of DNA.
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Affiliation(s)
- Mária Džunková
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Marc Garcia-Garcerà
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Llúcia Martínez-Priego
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Giussepe D’Auria
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- * E-mail:
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Gadkar VJ, Filion M. A linear concatenation strategy to construct 5'-enriched amplified cDNA libraries using multiple displacement amplification. Mol Biotechnol 2013; 54:541-50. [PMID: 22941734 DOI: 10.1007/s12033-012-9594-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In various experimental systems, limiting available amounts of RNA may prevent a researcher from performing large-scale analyses of gene transcripts. One way to circumvent this is to 'pre-amplify' the starting RNA/cDNA, so that sufficient amounts are available for any downstream analysis. In the present study, we report the development of a novel protocol for constructing amplified cDNA libraries using the Phi29 DNA polymerase based multiple displacement amplification (MDA) system. Using as little as 200 ng of total RNA, we developed a linear concatenation strategy to make the single-stranded cDNA template amenable for MDA. The concatenation, made possible by the template switching property of the reverse transcriptase enzyme, resulted in the amplified cDNA library with intact 5' ends. MDA generated micrograms of template, allowing large-scale polymerase chain reaction analyses or other large-scale downstream applications. As the amplified cDNA library contains intact 5' ends, it is also compatible with 5' RACE analyses of specific gene transcripts. Empirical validation of this protocol is demonstrated on a highly characterized (tomato) and an uncharacterized (corn gromwell) experimental system.
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Affiliation(s)
- Vijay J Gadkar
- Department of Biology, Université de Moncton, Moncton, Canada
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Gadkar VJ, Arseneault T, Filion M. Fidelity and representativeness of two isothermal multiple displacement amplification systems to preamplify limiting amounts of total RNA. Mol Biotechnol 2013; 56:377-85. [PMID: 24198216 DOI: 10.1007/s12033-013-9718-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this study we investigated the fidelity and representativeness of two novel multiple displacement amplification (MDA) protocols leading to whole transcriptome amplification (WTA). WTA is used to amplify a limiting amount of experimental RNA, allowing its use in downstream applications. Using Phi29 and Bst DNA polymerase-based MDA, henceforth referred to as WTA-Phi and WTA-Bst, respectively, we successfully amplified very low amounts of linearly concatenated cDNA originating from 10 to 100 ng of starting RNA. The average yield obtained from 10 ng was 3.5 and 4.7 μg for WTA-Phi and WTA-Bst, respectively, while 100 ng of starting RNA yielded 7.0 and 12.4 μg for WTA-Phi and WTA-Bst, respectively. Representational distortion of the templates, analyzed via conventional PCR, showed robust amplification of 11 different transcripts when either WTA-Phi or WTA-Bst synthesized templates were used, while some transcripts were not detected from unamplified templates. Loci representation, a measure of amplification consistency, was evaluated using TaqMan RT-qPCR amplification of five different transcripts, yielding values ranging from 96.4 to 189.3 %, comparable to those obtained using genomic target-based MDA systems. The two MDA protocols described in this study efficiently lead to representative WTA, using as little as 10 ng of starting RNA.
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Affiliation(s)
- Vijay J Gadkar
- Department of Biology, Université de Moncton, 18 Antonine-Maillet Ave, Moncton, NB, E1A 3E9, Canada
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Sujayanont P, Chininmanu K, Tassaneetrithep B, Tangthawornchaikul N, Malasit P, Suriyaphol P. Comparison of phi29-based whole genome amplification and whole transcriptome amplification in dengue virus. J Virol Methods 2013; 195:141-7. [PMID: 24129073 DOI: 10.1016/j.jviromet.2013.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 12/11/2022]
Abstract
Dengue virus is responsible for 50-100 million new infections annually worldwide. The virus uses error-prone RNA polymerase during genome replication in a host, resulting in the formation of closely related viruses known as quasispecies. The availability of next-generation sequencing technology provides opportunities to analyze viral quasispecies. Before analysis, it is crucial to increase the amount of DNA because of the limited amounts of viral genomic material that can be isolated from a patient. However, using specific primers may overlook the occurrence of possible variations at primer binding sites. To address this problem, the performance of two sequence-independent amplification methods was compared for whole genome amplification (WGA): phi29 DNA polymerase-based WGA and whole transcriptome amplification (WTA). Both methods have the ability to provide complete coverage of the dengue genome from template amounts as low as 1 ng. However, WTA showed greater efficiency in terms of yield (WTA: ~10 μg; phi29-based WGA: ~500 ng) and lower amplification bias. In conclusion, the WTA amplification kit was shown to perform substantially better than phi29 DNA polymerase-based WGA in terms of both final concentration and amplification bias in amplifying small genomes, such as that of the dengue virus.
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Affiliation(s)
- Patcharawan Sujayanont
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand; Division of Bioinformatics and Data Management for Research, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand; Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand.
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A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH. PLoS One 2013; 8:e67031. [PMID: 23825608 PMCID: PMC3692546 DOI: 10.1371/journal.pone.0067031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/14/2013] [Indexed: 12/31/2022] Open
Abstract
Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH) of single cells. The protocol is based on an established adapter-linker PCR (WGAM) and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS) could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost-) effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.
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Kaewmanee M, Phoksawat W, Romphruk A, Romphruk AV, Jumnainsong A, Leelayuwat C. Development of a multiplex polymerase chain reaction-sequence-specific primer method for NKG2D and NKG2F single-nucleotide polymorphism typing using isothermal multiple displacement amplification products. ACTA ACUST UNITED AC 2013; 81:419-27. [PMID: 23530727 DOI: 10.1111/tan.12105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
Abstract
Natural killer group 2 member D (NKG2D) on immune effector cells recognizes multiple stress-inducible ligands. NKG2D single-nucleotide polymorphism (SNP) haplotypes were related to the levels of cytotoxic activity of peripheral blood mononuclear cells. Indeed, these polymorphisms were also located in NKG2F. Isothermal multiple displacement amplification (IMDA) is used for whole genome amplification (WGA) that can amplify very small genomic DNA templates into microgram with whole genome coverage. This is particularly useful in the cases of limited amount of valuable DNA samples requiring multi-locus genotyping. In this study, we evaluated the quality and applicability of IMDA to genetic studies in terms of sensitivity, efficiency of IMDA re-amplification and stability of IMDA products. The smallest amount of DNA to be effectively amplified by IMDA was 200 pg yielding final DNA of approximately 16 µg within 1.5 h. IMDA could be re-amplified only once (second round of amplification), and could be kept for 5 months at 4°C and more than a year at -20°C without loosing genome coverage. The amplified products were used successfully to setup a multiplex polymerase chain reaction-sequence-specific primer for SNP typing of the NKG2D/F genes. The NKG2D/F multiplex polymerase chain reaction (PCR) contained six PCR mixtures for detecting 10 selected SNPs, including 8 NKG2D/F SNP haplotypes and 2 additional NKG2D coding SNPs. This typing procedure will be applicable in both clinical and research laboratories. Thus, our data provide useful information and limitations for utilization of genome-wide amplification using IMDA and its application for multiplex NKG2D/F typing.
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Affiliation(s)
- M Kaewmanee
- Biomedical Sciences Program, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
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A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing. PLoS One 2013; 8:e54236. [PMID: 23372689 PMCID: PMC3553135 DOI: 10.1371/journal.pone.0054236] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/10/2012] [Indexed: 02/02/2023] Open
Abstract
Copy number variations (CNVs), a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA) and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%). Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb) at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.
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Rosenquist R, Ehrencrona H, Hasle H, Palle J, Kanduri M. Whole-genome-amplified DNA as a source for mutational analysis underestimates the frequency of mutations in pediatric acute myeloid leukemia. Leukemia 2012; 27:510-2. [PMID: 22996295 DOI: 10.1038/leu.2012.250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Whole genome amplification of degraded and nondegraded DNA for forensic purposes. Int J Legal Med 2012; 127:309-19. [PMID: 22940764 PMCID: PMC3578730 DOI: 10.1007/s00414-012-0764-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/14/2012] [Indexed: 11/06/2022]
Abstract
Degraded DNA is often analyzed in forensic genetics laboratories. Reliable analysis of degraded DNA is of great importance, since its results impact the quality and reliability of expert testimonies. Recently, a number of whole genome amplification (WGA) methods have been proposed as preamplification tools. They work on the premise of being able to generate microgram quantities of DNA from as little as the quantity of DNA from a single cell. We chose, investigated, and compared seven WGA methods to evaluate their ability to “recover” degraded and nondegraded DNA: degenerate oligonucleotide-primed PCR, primer extension preamplification PCR, GenomePlex™ WGA commercial kit (Sigma), multiple displacement amplification, GenomiPhi™ Amplification kit (Amersham Biosciences), restriction and circularization-aided rolling circle amplification, and blunt-end ligation-mediated WGA. The efficiency and reliability of those methods were analyzed and compared using SGMPlus, YFiler, mtDNA, and Y-chromosome SNP typing. The best results for nondegraded DNA were obtained with GenomiPhi and PEP methods. In the case of degraded DNA (200 bp), the best results were obtained with GenomePlex which successfully amplified also severely degraded DNA (100 bp), thus enabling correct typing of mtDNA and Y-SNP loci. WGA may be very useful in analysis of low copy number DNA or degraded DNA in forensic genetics, especially after introduction of some improvements (sample pooling and replicate DNA typing).
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