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Sharaf SA, Kantoush NA, Ayoub DF, Ibrahim AA, Abdelaal AA, Aziz RA, ElHefnawi MM, Ahmed AN. Altered expression of WFS1 and NOTCH2 genes associated with diabetic nephropathy in T2DM patients. Diabetes Res Clin Pract 2018; 140:304-313. [PMID: 29626590 DOI: 10.1016/j.diabres.2018.03.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/18/2018] [Accepted: 03/29/2018] [Indexed: 12/13/2022]
Abstract
AIM The increased incidence of type 2 diabetes mellitus (T2DM) and the importance of early identification and management of its complications, especially diabetic nephropathy (DN), have spotted the light on genetic factors that increase risk of T2DM and its related nephropathy. The present study aimed at investigating expression of (KCNJ11, ABCC8, JAZF1, WFS1, PPARG, NOTCH2 and EXOSC4) genes in peripheral blood of T2DM patients. METHOD The study included 30 non-complicated T2DM patients, 30 patients with DN and 40 healthy controls. Quantitative Real Time PCR Array was used to study gene expression. RESULTS NOTCH2 showed higher expression while KCNJ11, JAZF1, WFS1 and PPARG genes showed lower expression in DN patients compared to non-complicated patients. KCNJ11, JAZF1, WFS1, PPARG, and EXOSC4 expression showed significant negative correlation with microalbumin, while NOTCH2 expression was significantly positively correlated with microalbumin. AS regard HbA1c and studied genes expression, there was significant negative correlation between WFS1 expression and HbA1c, while NOTCH2, KCNJ11, JAZF1, PPARG, EXOSC4 expression didn't show significant correlation with HbA1c. Risk ratio of studied genes expression showed that WFS1 and NOTCH2 had highest risk ratio (30) and highest sensitivity and specificity, in relation to DN and they were the best predictors in the group of studied genes at cut off value of ≤0.861 for WFS1 and ≥0.678 for NOTCH2. CONCLUSION Altered expression of WFS1 and NOTCH2 genes may play a role in pathogenesis and development of DN in patients with T2DM. These results may contribute in early identification and management of DN.
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Affiliation(s)
- Sahar A Sharaf
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nagwa A Kantoush
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
| | - Dina F Ayoub
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
| | - Alshaymaa A Ibrahim
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt.
| | - Amaal A Abdelaal
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rokaya Abdel Aziz
- Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mahmoud M ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, Division of Engineering Research, National Research Centre, Cairo, Egypt
| | - Amira N Ahmed
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
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102
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Bahder BW, Helmick EE, Mou DF, Harrison NA, Davis R. Digital PCR Technology for Detection of Palm-Infecting Phytoplasmas Belonging to Group 16SrIV that Occur in Florida. PLANT DISEASE 2018; 102:1008-1014. [PMID: 30673395 DOI: 10.1094/pdis-06-17-0787-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytoplasmas are an economically important group of plant pathogens that negatively impact a wide variety of plants in agricultural and natural ecosystems. In Florida, palm trees are essential elements in the nursery and landscaping industries that suffer from diseases caused by phytoplasmas that are related to each other but are classified in two different subgroups, 16SrIV-A and 16SrIV-D. In this study, a TaqMan assay was developed for digital polymerase chain reaction (dPCR) to detect both palm-infecting phytoplasmas found in Florida. When compared with real-time PCR assays and nested PCR assays, dPCR was capable of detecting the phytoplasmas at much lower concentrations than was possible by using real-time PCR and nested PCR. Additionally, the assay was capable of detecting 16SrIV-B phytoplasma as well as isolates representing the 16SrI and 16SrIII phytoplasma groups. Due to sequence identity of primer annealing regions across diverse phytoplasmas, the assay is likely to be successful for detection of a wide variety of phytoplasmas. The increased sensitivity of this dPCR assay over real-time PCR will allow for earlier detection of phytoplasma infection in palm trees, as well as for screening of salivary glands of candidate insect vector species. These advantages should aid timely management decisions to reduce disease spread and rapid determination of phytoplasma transmission by vectors.
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Affiliation(s)
- Brian W Bahder
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | - Ericka E Helmick
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | - De-Fen Mou
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | | | - Robert Davis
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
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103
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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104
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Monico J, Miller B, Rezeanu L, May W, Sullivan DC. Fibroblast growth factor receptor 1 amplification in laryngeal squamous cell carcinoma. PLoS One 2018; 13:e0186185. [PMID: 29351293 PMCID: PMC5774678 DOI: 10.1371/journal.pone.0186185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) has been noted to be amplified in a variety of squamous cell carcinomas (SCCa) of the head, neck, and lung and increased copy number (CN) is a predictor of poor outcomes. FGFR1 is a therapeutic target for lung SCCa and inhibition therapy is currently in clinical trials. Absolute quantification of FGFR1 from formalin fixed paraffin embedded (FFPE) tissue of laryngeal SCCa was examined in this retrospective study. A droplet digital polymerase chain reaction (ddPCR) was used for absolute quantitation of the FGFR1 gene CN. Of the 74 samples analyzed, FGFR1 CN analysis revealed 54% of samples had CN greater than 2 copies/cell (1.8-2.2 copies/cell), and 38% had CN values greater than 3. The mean and standard deviation FGFR1 CN was 4.17 ± 1.46 CN for African American patients (n = 41) and 3.78 ±1.85 CN for Caucasian patients (n = 31). Further, 60.9% of specimens from African Americans demonstrated increased FGFR1 CN compared to 48.4% of Caucasians. Two SCCA samples from Native American demonstrated increased FGFR1 CN (4.19 and 3.01 CN). The level of FGFR1 amplification did not correlate with tumor stage, lymph node staging, or metastasis. In this population, the proportion of patient samples with an FGFR1 amplification was three times higher than in reported for SCCA of the head and neck. Further, increased FGFR1 CN was observed in two racial groups not previously reported: African Americans and Native Americans. However, FGFR1 amplification is not prognostic in laryngeal squamous cell carcinomas.
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Affiliation(s)
- Jesus Monico
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Brandon Miller
- Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Luminita Rezeanu
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Warren May
- Department of Biostatistics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Donna C. Sullivan
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
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105
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Abstract
Recent advances in miRNA detection methods and new applications.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Lijuan Dong
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Jiangyan Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yaqing Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
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106
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Zhou B, Haney MS, Zhu X, Pattni R, Abyzov A, Urban AE. Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. Methods Mol Biol 2018; 1768:173-190. [PMID: 29717444 DOI: 10.1007/978-1-4939-7778-9_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here, we describe approaches using droplet digital polymerase chain reaction (ddPCR) to validate and quantify somatic mosaic events contributed by transposable-element insertions, copy-number variants, and single-nucleotide variants. In the ddPCR assay, sample or template DNA is partitioned into tens of thousands of individual droplets such that when DNA input is low, the vast majority of droplets contains no more than one copy of template DNA. PCR takes place in each individual droplet and produces a fluorescent readout to indicate the presence or absence of the target of interest allowing for the accurate "counting" of the number of copies present in the sample. The number of partitions is large enough to assay somatic mosaic events with frequencies down to less than 1%.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Michael S Haney
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA. .,Program on Genetics of Brain Function, Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Palo Alto, CA, USA.
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107
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Lau HY, Botella JR. Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection. FRONTIERS IN PLANT SCIENCE 2017; 8:2016. [PMID: 29375588 PMCID: PMC5770625 DOI: 10.3389/fpls.2017.02016] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/13/2017] [Indexed: 05/07/2023]
Abstract
Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.
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Affiliation(s)
- Han Yih Lau
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute, Serdang, Malaysia
| | - Jose R. Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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108
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Lau BT, Wood-Bouwens C, Ji HP. Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding. Anal Chem 2017; 89:11913-11917. [PMID: 29083143 DOI: 10.1021/acs.analchem.7b02688] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Digital PCR (dPCR) relies on the analysis of individual partitions to accurately quantify nucleic acid species. The most widely used analysis method requires manual clustering through individual visual inspection. Some automated analysis methods have emerged but do not robustly account for multiplexed targets, low target concentration, and assay noise. In this study, we describe an open source analysis software called Calico that uses "data gridding" to increase the sensitivity of clustering toward small clusters. Our workflow also generates quality score metrics in order to gauge and filter individual assay partitions by how well they were classified. We applied our analysis algorithm to multiplexed droplet-based digital PCR data sets in both EvaGreen and probes-based schemes, and targeted the oncogenic BRAF V600E and KRAS G12D mutations. We demonstrate an automated clustering sensitivity of down to 0.1% mutant fraction and filtering of artifactual assay partitions from low quality DNA samples. Overall, we demonstrate a vastly improved approach to analyzing ddPCR data that can be applied to clinical use, where automation and reproducibility are critical.
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Affiliation(s)
- Billy T Lau
- Stanford Genome Technology Center, Stanford University , Palo Alto, California 94304, United States
| | - Christina Wood-Bouwens
- Division of Oncology, Stanford School of Medicine , Stanford, California 94305, United States
| | - Hanlee P Ji
- Division of Oncology, Stanford School of Medicine , Stanford, California 94305, United States
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109
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Wu H, Sugata K, Hirai M, Yoshiura Y, Hibi K, Endo H. Ultra highly sensitive method for detecting Edwardsiella ictaluri using high-gradient immunomagnetic separation with polymerase chain reaction. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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110
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Yang Q, Xi J, Chen X, Hu S, Chen N, Qiao S, Wan S, Bao D. The development of a sensitive droplet digital PCR for quantitative detection of porcine reproductive and respiratory syndrome virus. Int J Biol Macromol 2017; 104:1223-1228. [DOI: 10.1016/j.ijbiomac.2017.06.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 11/29/2022]
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111
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Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence. Nat Med 2017; 23:1319-1330. [PMID: 28967919 DOI: 10.1038/nm.4405] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022]
Abstract
Tumor recurrence remains the main reason for breast cancer-associated mortality, and there are unmet clinical demands for the discovery of new biomarkers and development of treatment solutions to benefit patients with breast cancer at high risk of recurrence. Here we report the identification of chromosomal copy-number amplification at 1q21.3 that is enriched in subpopulations of breast cancer cells bearing characteristics of tumor-initiating cells (TICs) and that strongly associates with breast cancer recurrence. Amplification is present in ∼10-30% of primary tumors but in more than 70% of recurrent tumors, regardless of breast cancer subtype. Detection of amplification in cell-free DNA (cfDNA) from blood is strongly associated with early relapse in patients with breast cancer and could also be used to track the emergence of tumor resistance to chemotherapy. We further show that 1q21.3-encoded S100 calcium-binding protein (S100A) family members, mainly S100A7, S100A8, and S100A9 (S100A7/8/9), and IL-1 receptor-associated kinase 1 (IRAK1) establish a reciprocal feedback loop driving tumorsphere growth. Notably, this functional circuitry can be disrupted by the small-molecule kinase inhibitor pacritinib, leading to preferential impairment of the growth of 1q21.3-amplified breast tumors. Our study uncovers the 1q21.3-directed S100A7/8/9-IRAK1 feedback loop as a crucial component of breast cancer recurrence, serving as both a trackable biomarker and an actionable therapeutic target for breast cancer.
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112
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Liu Q, Liu G, Wang T, Fu J, Li R, Song L, Wang ZG, Ding B, Chen F. Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs. Chemphyschem 2017; 18:2977-2980. [DOI: 10.1002/cphc.201700809] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/25/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Qing Liu
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Guocheng Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
| | - Ting Wang
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
| | - Jing Fu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Rujiao Li
- Big Data Center, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
| | - Linlin Song
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Zhen-Gang Wang
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
| | - Baoquan Ding
- CAS Center for Excellence in Nanoscience; National Center for Nanoscience and Technology; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
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113
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Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li X, Altmüller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol 2017; 26:4712-4724. [PMID: 28390096 PMCID: PMC5638112 DOI: 10.1111/mec.14134] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022]
Abstract
Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy-number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents. This coincided with increased expression for three genes related to vision, detoxification and muscle development, suggesting possible gene dosage effects. Copy number increases of putative transposons were assessed by comparative mapping of genomic DNA reads against a de novo assembly of 1,005 repetitive elements. In contrast to exons, copy number increases of repetitive elements were common (20.7%) in invasive Cottus, whereas decrease was very rare (0.01%). Among the increased repetitive elements, 53.8% occurred at higher numbers in C. perifretum compared to C. rhenanus, while only 1.4% were more abundant in C. rhenanus. This implies a biased mutational process that amplifies genetic material from one ancestor. To assess the frequency of de novo mutations through hybridization, we screened 64 laboratory-bred F2 offspring between the parental species for copy-number changes at five candidate loci. We found no evidence for new structural variants, indicating that they are too rare to be detected given our sampling scheme. Instead, they must have accumulated over more generations than we observed in a controlled cross.
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Affiliation(s)
- Stefan Dennenmoser
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Institute for BiologyCarl von Ossietzky University OldenburgOldenburgGermany
| | | | - Elzbieta Iwaszkiewicz
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Xiang‐Yi Li
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human GeneticsUniversity of CologneCologneGermany
| | - Arne W. Nolte
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Institute for BiologyCarl von Ossietzky University OldenburgOldenburgGermany
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114
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Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA. J Mol Diagn 2017; 19:697-710. [PMID: 28818432 PMCID: PMC6593258 DOI: 10.1016/j.jmoldx.2017.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023] Open
Abstract
We describe a single-color digital PCR assay that detects and quantifies cancer mutations directly from circulating DNA collected from the plasma of cancer patients. This approach relies on a double-stranded DNA intercalator dye and paired allele-specific DNA primer sets to determine an absolute count of both the mutation and wild-type–bearing DNA molecules present in the sample. The cell-free DNA assay uses an input of 1 ng of nonamplified DNA, approximately 300 genome equivalents, and has a molecular limit of detection of three mutation DNA genome-equivalent molecules per assay reaction. When using more genome equivalents as input, we demonstrated a sensitivity of 0.10% for detecting the BRAF V600E and KRAS G12D mutations. We developed several mutation assays specific to the cancer driver mutations of patients' tumors and detected these same mutations directly from the nonamplified, circulating cell-free DNA. This rapid and high-performance digital PCR assay can be configured to detect specific cancer mutations unique to an individual cancer, making it a potentially valuable method for patient-specific longitudinal monitoring.
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115
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116
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DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS One 2017; 12:e0180467. [PMID: 28683077 PMCID: PMC5500342 DOI: 10.1371/journal.pone.0180467] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
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117
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Wong YK, Tsang HF, Xue VW, Chan CM, Au TC, Cho WC, Chan LW, Wong SC. Applications of digital PCR in precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2017.1347482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Y. K. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - H. F. Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - V. W. Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - C. M. Chan
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - T. C. Au
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - W. C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China
| | - L. W. Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - S. C. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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Seo JW, Moon H, Kim SY, Moon JY, Jeong KH, Lee YH, Kim YG, Lee TW, Ihm CG, Kim CD, Chung BH, Kim YH, Lee SH. Both absolute and relative quantification of urinary mRNA are useful for non-invasive diagnosis of acute kidney allograft rejection. PLoS One 2017; 12:e0180045. [PMID: 28654700 PMCID: PMC5487057 DOI: 10.1371/journal.pone.0180045] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 06/08/2017] [Indexed: 12/02/2022] Open
Abstract
Urinary mRNA analysis with three-gene set (18S rRNA, CD3ε, and IP-10) has been suggested as a non-invasive biomarker of acute rejection (AR) in kidney transplant recipients using quantitative real-time PCR (qPCR). Application of droplet digital PCR (ddPCR), which has been suggested to provide higher sensitivity, accuracy, and absolute quantification without standard curves, could be a useful method for the quantifying low concentration of urinary mRNA. We investigated the urinary expression of these three genes in Korean patients with kidney transplantation and also evaluated the usefulness of ddPCR. 90 urine samples were collected at time of allograft biopsy in kidney recipients (n = 67) and from patients with stable renal function more than 10 years (n = 23). Absolute quantification with both PCR system showed significant higher mRNA levels of CD3ε and IP-10 in AR patients compared with stable transplants (STA), but there was no difference in 18S rRNA expression across the patient groups. To evaluate discrimination between AR and STA, ROC curve analyses of CTOT-4 formula yielded area under the curve values of 0.72 (95% CI 0.60–0.83) and 0.77 (95% CI 0.66–0.88) for qPCR and ddPCR, respectively. However, 18S normalization of absolute quantification and relative quantification with 18S showed better discrimination of AR from STA than those of the absolute method. Our data indicate that ddPCR system without standard curve would be useful to determine the absolute quantification of urinary mRNA from kidney transplant recipients. However, comparative method also could be useful and convenient in both qPCR and ddPCR analysis.
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Affiliation(s)
- Jung-Woo Seo
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Haena Moon
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, South Korea
| | - Se-Yun Kim
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Ju-Young Moon
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Kyung Hwan Jeong
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Yu-Ho Lee
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Yang-Gyun Kim
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Tae-Won Lee
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Chun-Gyoo Ihm
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Chan-Duck Kim
- Department of Internal Medicine, Division of Nephrology, Kyung-pook National University School of Medicine, Daegu, South Korea
| | - Byung Ha Chung
- Department of Internal Medicine, Division of Nephrology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yeong Hoon Kim
- Department of Internal Medicine, Division of Nephrology, Busan Paik Hospital, College of Medicine, Inje University, Busan, South Korea
| | - Sang Ho Lee
- Department of Internal Medicine, Division of Nephrology, College of Medicine, Kyung Hee University, Seoul, South Korea
- * E-mail:
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119
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Li X, Zhao J, Yuan Q, Xia N. Detection of HBV Covalently Closed Circular DNA. Viruses 2017; 9:E139. [PMID: 28587292 PMCID: PMC5490816 DOI: 10.3390/v9060139] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/19/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection affects approximately 240 million people worldwide and remains a serious public health concern because its complete cure is impossible with current treatments. Covalently closed circular DNA (cccDNA) in the nucleus of infected cells cannot be eliminated by present therapeutics and may result in persistence and relapse. Drug development targeting cccDNA formation and maintenance is hindered by the lack of efficient cccDNA models and reliable cccDNA detection methods. Southern blotting is regarded as the gold standard for quantitative cccDNA detection, but it is complicated and not suitable for high-throughput drug screening, so more sensitive and simple methods, including polymerase chain reaction (PCR)-based methods, Invader assays, in situ hybridization and surrogates, have been developed for cccDNA detection. However, most methods are not reliable enough, and there are no unified standards for these approaches. This review will summarize available methods for cccDNA detection. It is hoped that more robust methods for cccDNA monitoring will be developed and that standard operation procedures for routine cccDNA detection in scientific research and clinical monitoring will be established.
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Affiliation(s)
- Xiaoling Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jinghua Zhao
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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Abstract
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error. The remainder focuses on digital PCR (dPCR) for quantification of nucleic acids. We discuss five commercial instruments that partition samples into physically isolated chambers (cdPCR) or droplet emulsions (ddPCR). We compare the strengths of dPCR (absolute quantitation, precision, and ability to detect rare or mutant targets) with those of its predecessor, quantitative real-time PCR (dynamic range, larger sample volumes, and throughput). Lastly, we describe several promising applications of dPCR, including copy number variation, quantitation of circulating tumor DNA and viral load, RNA/miRNA quantitation with reverse transcription dPCR, and library preparation for next-generation sequencing. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows. Part II focuses on digital protein and cell assays.
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Affiliation(s)
- Amar S Basu
- 1 Department of Electrical and Computer Engineering, and Department of Biomedical Engineering, Wayne State University, Detroit, MI, USA
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121
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Ding Y, Choo J, deMello AJ. From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis. MICROFLUIDICS AND NANOFLUIDICS 2017; 21:58. [PMID: 32214953 PMCID: PMC7087872 DOI: 10.1007/s10404-017-1889-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/22/2017] [Indexed: 05/27/2023]
Abstract
Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter-nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets.
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan, 15588 Republic of Korea
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
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A novel duplex ddPCR assay for the diagnosis of schistosomiasis japonica: proof of concept in an experimental mouse model. Parasitology 2017; 144:1005-1015. [DOI: 10.1017/s003118201700021x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SUMMARYThe current World Health Organization strategic plan targets the elimination of schistosomiasis as a public health problem by 2025 and accurate diagnostics will play a pivotal role in achieving this goal. DNA-based detection methods provide a viable alternative to some of the commonly used tests, notably microscopy and serology, for the diagnosis of schistosomiasis. The detection of parasite cell-free DNA in different clinical samples is a recent valuable advance, which provides significant benefits for accurate disease diagnosis. Here we validated a novel duplex droplet digital PCR assay for the diagnosis of Chinese (SjC) and Philippine (SjP) strains of Schistosoma japonicum infection in a mouse model. The assay proved applicable for both SjC and SjP infections and capable of detecting infection at a very early intra-mammalian stage in conveniently obtainable samples (urine and saliva) as well as in serum and feces. The target DNA copy numbers obtained in the assay showed a positive correlation with the infection burden assessed by direct traditional parasitology. The potential to detect parasite DNA in urine and saliva has important practical implications for large-scale epidemiological screening programmes in the future, particularly in terms of logistical convenience, and the assay has the potential to be a valuable additional tool for the diagnosis of schistosomiasis japonica.
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123
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Fu W, Wei S, Wang C, Du Z, Zhu P, Wu X, Wu G, Zhu S. A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis. Food Chem 2017; 229:396-402. [PMID: 28372191 DOI: 10.1016/j.foodchem.2017.02.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/17/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023]
Abstract
High throughput screening systems are the preferred solution to meet the urgent requirement of increasing number of genetically modified organisms (GMOs). In this study, we have successfully developed a multiplex GMO element screening system with dual priming oligonucleotide (DPO) primers. This system can detect the cauliflower mosaic virus 35S (CaMV 35S), terminator of nopaline synthase gene (NOS), figwort mosaic virus 35S (FMV 35S) promoter, neomycin phosphotransferaseII (NPTII), Bt Cry 1Ab, phosphinothricin acetyltransferase genes (bar) and Streptomyces viridochromogenes (pat) simultaneously, which covers more than 90% of all authorized GMO species worldwide. This system exhibits a high tolerance to annealing temperatures, high specificity and a limit of detection equal to conventional PCR. A total of 214 samples from markets, national entry-exit agencies, the Institute for Reference Materials and Measurement (IRMM) and the American Oil Chemists' Society (AOCS) were also tested for applicability. This screening system is therefore suitable for GMO screening.
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Affiliation(s)
- Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuang Wei
- Shantou Entry-exit Inspection and Quarantine Bureau, Shantou 515041, China
| | - Chenguang Wang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhixin Du
- Guangxi Entry-exit Inspection and Quarantine Bureau, Nanning 530028, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xiyang Wu
- Department of Food Science and Engineering, College of Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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124
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Droplet Microfluidics Approach for Single-DNA Molecule Amplification and Condensation into DNA-Magnesium-Pyrophosphate Particles. MICROMACHINES 2017. [PMCID: PMC6189807 DOI: 10.3390/mi8020062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein expression in vitro has broad applications in directed evolution, synthetic biology, proteomics and drug screening. However, most of the in vitro expression systems rely on relatively high DNA template concentrations to obtain sufficient amounts of proteins, making it harder to perform in vitro screens on gene libraries. Here, we report a technique for the generation of condensed DNA particles that can serve as efficient templates for in vitro gene expression. We apply droplet microfluidics to encapsulate single-DNA molecules in 3-picoliter (pL) volume droplets and convert them into 1 μm-sized DNA particles by the multiple displacement amplification reaction driven by phi29 DNA polymerase. In the presence of magnesium ions and inorganic pyrophosphate, the amplified DNA condensed into the crystalline-like particles, making it possible to purify them from the reaction mix by simple centrifugation. Using purified DNA particles, we performed an in vitro transcription-translation reaction and successfully expressed complex enzyme β-galactosidase in droplets and in the 384-well format. The yield of protein obtained from DNA particles was significantly higher than from the corresponding amount of free DNA templates, thus opening new possibilities for high throughput screening applications.
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125
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Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR. PLoS One 2017; 12:e0169846. [PMID: 28085908 PMCID: PMC5234771 DOI: 10.1371/journal.pone.0169846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Bacteria can be considered as biological nanofactories that manufacture a cornucopia of bioproducts most notably recombinant proteins. As such, they must perfectly match with appropriate plasmid vectors to ensure successful overexpression of target genes. Among many parameters that correlate positively with protein productivity plasmid copy number plays pivotal role. Therefore, development of new and more accurate methods to assess this critical parameter will result in optimization of expression of plasmid-encoded genes. In this study, we present a simple and highly accurate method for quantifying plasmid copy number utilizing an EvaGreen single colour, droplet digital PCR. We demonstrate the effectiveness of this method by examining the copy number of the pBR322 vector within Escherichia coli DH5α cells. The obtained results were successfully validated by real-time PCR. However, we observed a strong dependency of the plasmid copy number on the method chosen for isolation of the total DNA. We found that application of silica-membrane-based columns for DNA purification or DNA isolation with use of bead-beating, a mechanical cell disruption lead to determination of an average of 20.5 or 7.3 plasmid copies per chromosome, respectively. We found that recovery of the chromosomal DNA from purification columns was less efficient than plasmid DNA (46.5 ± 1.9% and 87.4 ± 5.5%, respectively) which may lead to observed differences in plasmid copy number. Besides, the plasmid copy number variations dependent on DNA template isolation method, we found that droplet digital PCR is a very convenient method for measuring bacterial plasmid content. Careful determination of plasmid copy number is essential for better understanding and optimization of recombinant proteins production process. Droplet digital PCR is a very precise method that allows performing thousands of individual PCR reactions in a single tube. The ddPCR does not depend on running standard curves and is a straightforward and reliable method to quantify the plasmid copy number. Therefore we believe that the ddPCR designed in this study will be widely used for any plasmid copy number calculation in the future.
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126
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Abstract
Droplet digital PCR (ddPCR) is based on the isolated amplification of thousands of individual DNA molecules simultaneously, with each molecule compartmentalized in a droplet. The presence of amplified product in each droplet is indicated by a fluorescent signal, and the proportion of positive droplets allows the precise quantification of a given sequence. In this chapter we briefly outline the basis of ddPCR, and describe two different applications using the Bio-Rad QX200 system: genotyping copy number variation and quantification of Illumina sequencing libraries.
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Affiliation(s)
- Rolf H A M Vossen
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Stefan J White
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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127
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Perkins G, Lu H, Garlan F, Taly V. Droplet-Based Digital PCR: Application in Cancer Research. Adv Clin Chem 2016; 79:43-91. [PMID: 28212714 DOI: 10.1016/bs.acc.2016.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient characterization of genetic and epigenetic alterations in oncology, virology, or prenatal diagnostics requires highly sensitive and specific high-throughput approaches. Nevertheless, with the use of conventional methods, sensitivity and specificity were largely limited. By partitioning individual target molecules within distinct compartments, digital PCR (dPCR) could overcome these limitations and detect very rare sequences with unprecedented precision and sensitivity. In dPCR, the sample is diluted such that each individual partition will contain no more than one target sequence. Following the assay reaction, the dPCR process provides an absolute value and analyzable quantitative data. The recent coupling of dPCR with microfluidic systems in commercial platforms should lead to an essential tool for the management of patients with cancer, especially adapted to the analysis of precious samples. Applications in cancer research range from the analysis of tumor heterogeneity to that of a range of body fluids. Droplet-based dPCR is indeed particularly appropriate for the emerging field of liquid biopsy analysis. In this review, following an overview of the development in dPCR technology and different strategies based on the use of microcompartments, we will focus particularly on the applications and latest development of microfluidic droplet-based dPCR in oncology.
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Affiliation(s)
- G Perkins
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France; European Georges Pompidou Hospital, AP-HP - Paris Descartes University, Paris, France
| | - H Lu
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - F Garlan
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France
| | - V Taly
- Université Sorbonne Paris Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, Equipe labélisée LIGUE Contre le Cancer, Paris, France.
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128
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Köppel R, Peterseil V, Dagand E, Schütz E, Kolberg N, Milavec M, Moor D. Collaborative trial to assess the performance of digital PCR in the field of GMO analysis using an artificial sample material. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2824-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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129
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Tian H, Sun Y, Liu C, Duan X, Tang W, Li Z. Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction. Anal Chem 2016; 88:11384-11389. [DOI: 10.1021/acs.analchem.6b01225] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hui Tian
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Yuanyuan Sun
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Chenghui Liu
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Xinrui Duan
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Wei Tang
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Zhengping Li
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
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130
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Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 2016; 17:893. [PMID: 27825302 PMCID: PMC5101643 DOI: 10.1186/s12864-016-3221-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022] Open
Abstract
Background Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted. Results We analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2–14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV. Conclusions We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of AT3G18530-AT3G18535 duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Maja Szymanska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
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131
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Tang H, Cai Q, Li H, Hu P. Comparison of droplet digital PCR to real-time PCR for quantification of hepatitis B virus DNA. Biosci Biotechnol Biochem 2016; 80:2159-2164. [DOI: 10.1080/09168451.2016.1196576] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Abstract
Quantitative real-time PCR (qPCR) has been widely implemented for clinical hepatitis B viral load testing, but a lack of standardization and relatively poor precision hinder its usefulness. Droplet digital PCR (ddPCR) is a promising tool that offers high precision and direct quantification. In this study, we compared the ddPCR QX100 platform by Bio-Rad with the CFX384 Touch Real-Time PCR Detection System (Bio-Rad, USA) to detect serial plasmid DNA dilutions of known concentrations as well as HBV DNA extracted from patient serum samples. Both methods showed a high degree of linearity and quantitative correlation. However, ddPCR assays generated more reproducible results and detected lower copy numbers than qPCR assays. Patient sample quantifications by ddPCR and qPCR were highly agreeable based on the Bland–Altman analysis. Collectively, our findings demonstrate that ddPCR offers improved analytical sensitivity and specificity for HBV measurements and is suitable for clinical HBV detection.
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Affiliation(s)
- Hui Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Qingchun Cai
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Hu Li
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Peng Hu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
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132
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Dobnik D, Štebih D, Blejec A, Morisset D, Žel J. Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection. Sci Rep 2016; 6:35451. [PMID: 27739510 PMCID: PMC5064307 DOI: 10.1038/srep35451] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/30/2016] [Indexed: 11/25/2022] Open
Abstract
The advantages of the digital PCR technology are already well documented until now. One way to achieve better cost efficiency of the technique is to use it in a multiplexing strategy. Droplet digital PCR platforms, which include two fluorescence filters, support at least duplex reactions and with some developments and optimization higher multiplexing is possible. The present study not only shows a development of multiplex assays in droplet digital PCR, but also presents a first thorough evaluation of several parameters in such multiplex digital PCR. Two 4-plex assays were developed for quantification of 8 different DNA targets (7 genetically modified maize events and maize endogene). Per assay, two of the targets were labelled with one fluorophore and two with another. As current analysis software does not support analysis of more than duplex, a new R- and Shiny-based web application analysis tool (http://bit.ly/ddPCRmulti) was developed that automates the analysis of 4-plex results. In conclusion, the two developed multiplex assays are suitable for quantification of GMO maize events and the same approach can be used in any other field with a need for accurate and reliable quantification of multiple DNA targets.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dejan Štebih
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Andrej Blejec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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133
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Cheng N, Zhu P, Xu Y, Huang K, Luo Y, Yang Z, Xu W. High-sensitivity assay for Hg (II) and Ag (I) ion detection: A new class of droplet digital PCR logic gates for an intelligent DNA calculator. Biosens Bioelectron 2016; 84:1-6. [DOI: 10.1016/j.bios.2016.04.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 12/21/2022]
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134
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Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biol 2016; 17:180. [PMID: 27566673 PMCID: PMC5000403 DOI: 10.1186/s13059-016-1039-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 08/05/2016] [Indexed: 11/16/2022] Open
Abstract
Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necessary tools as stand-alone components as well as integrate them into the Galaxy platform. All analyses performed in this manuscript can be repeated exactly as described at http://usegalaxy.org/duplex .
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Affiliation(s)
- Nicholas Stoler
- Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA
| | | | - Wilfried Guiblet
- Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, 310 Wartik Lab, University Park, PA, 16802, USA.
| | - Anton Nekrutenko
- Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA.
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.
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135
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Poh CF, Haynes C. A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens. PLoS One 2016; 11:e0161274. [PMID: 27537682 PMCID: PMC4990255 DOI: 10.1371/journal.pone.0161274] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.
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Affiliation(s)
- Curtis B. Hughesman
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - X. J. David Lu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kelly Y. P. Liu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Yuqi Zhu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Catherine F. Poh
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
- * E-mail: (CH); (CP)
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- RES’EAU NSERC Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- * E-mail: (CH); (CP)
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136
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Lau HY, Wang Y, Wee EJH, Botella JR, Trau M. Field Demonstration of a Multiplexed Point-of-Care Diagnostic Platform for Plant Pathogens. Anal Chem 2016; 88:8074-81. [PMID: 27403651 DOI: 10.1021/acs.analchem.6b01551] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Effective disease management strategies to prevent catastrophic crop losses require rapid, sensitive, and multiplexed detection methods for timely decision making. To address this need, a rapid, highly specific and sensitive point-of-care method for multiplex detection of plant pathogens was developed by taking advantage of surface-enhanced Raman scattering (SERS) labeled nanotags and recombinase polymerase amplification (RPA), which is a rapid isothermal amplification method with high specificity. In this study, three agriculturally important plant pathogens (Botrytis cinerea, Pseudomonas syringae, and Fusarium oxysporum) were used to demonstrate potential translation into the field. The RPA-SERS method was faster, more sensitive than polymerase chain reaction, and could detect as little as 2 copies of B. cinerea DNA. Furthermore, multiplex detection of the three pathogens was demonstrated for complex systems such as the Arabidopsis thaliana plant and commercial tomato crops. To demonstrate the potential for on-site field applications, a rapid single-tube RPA/SERS assay was further developed and successfully performed for a specific target outside of a laboratory setting.
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Affiliation(s)
- Han Yih Lau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Eugene J H Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane QLD 4072, Australia
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137
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Zhao Y, Xia Q, Yin Y, Wang Z. Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri. PLoS One 2016; 11:e0159004. [PMID: 27427975 PMCID: PMC4948846 DOI: 10.1371/journal.pone.0159004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/24/2016] [Indexed: 11/19/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a novel molecular biology technique providing absolute quantification of target nucleic acids without the need for an external calibrator. Despite its emerging applications in medical diagnosis, there are few reports of its use for the detection of plant pathogens. This work was designed to assess the diagnosis potential of the ddPCR for absolute quantitative detection of Xanthomonas citri subsp. citri, a quarantine plant pathogenic bacterium that causes citrus bacterial canker in susceptible Citrus species. We transferred an established quantitative PCR (qPCR) assay for citrus bacterial canker diagnosis directly to the ddPCR format and compared the performance of the two methods. The qPCR assay has a broader dynamic range compared to the ddPCR assay and the ddPCR assay has a significantly higher degree of sensitivity compared to the qPCR assay. The influence of PCR inhibitors can be reduced considerably in the ddPCR assay because the collection of end-point fluorescent signals and the counting of binomial events (positive or negative droplets) are associated with a Poisson algorithm. The ddPCR assay also shows lower coefficient of variation compared to the qPCR assay especially in low target concentration. The linear association of the measurements by ddPCR and qPCR assays is strong (Pearson correlation = 0.8633; P<0.001). Receiver operating characteristic analysis indicates the ddPCR methodology is a more robust approach for diagnosis of citrus bacterial canker. In summary, the results demonstrated that the ddPCR assay has the potential for the quantitative detection of X. citri subsp. citri with high precision and accuracy as compared with the results from qPCR assay. Further studies are required to evaluate and validate the value of ddPCR technology in the diagnosis of plant disease and quarantine applications.
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Affiliation(s)
- Yun Zhao
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Qingyan Xia
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Youping Yin
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Zhongkang Wang
- School of Life Science, Chongqing University, Chongqing, 400030, China
- * E-mail:
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138
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Goh SK, Musafer A, Witkowski T, Muralidharan V, Christophi C, Do H, Dobrovic A. Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms. Clin Chem 2016; 62:1012-9. [DOI: 10.1373/clinchem.2016.256388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/16/2022]
Abstract
Abstract
BACKGROUND
The quantification of genomic chimerism is increasingly recognized for its clinical significance after transplantation. Before the measurement of chimerism, accurate genotyping of genetic polymorphisms for informative alleles that can distinguish donor DNA from recipient DNA is essential. The ease of allelic discrimination of small deletion and insertion polymorphisms (DIPs) makes DIPs attractive markers to track chimerism. Current methodologies for the genotyping of DIPs are largely based on “open-tube” approaches. “Closed-tube” approaches involving no or minimal post-PCR handling are preferred. We compared 3 distinct methodologies to determine an optimal platform for DIP genotyping.
METHODS
Genomic DNA from 19 normal individuals was genotyped for 6 small biallelic DIPs using high-resolution melting analysis (HRMA), probe-free droplet digital PCR (ddPCR), and microfluidic electrophoresis of PCR products. For HRMA, 3 different platforms were compared.
RESULTS
Our newly developed probe-free ddPCR approach allowed the genotype of each DIP to be determined by fluorescence intensity based on amplicon size. Microfluidic electrophoresis also allowed genotypes to be determined by amplicon size. HRMA assays allowed the genotype of each DIP to be determined by melting profile. Genotyping results were concordant between the 3 methodologies. HRMA was the most readily performed methodology and was robust across 3 separate HRMA-capable platforms.
CONCLUSIONS
We demonstrated the effectiveness of probe-free ddPCR to accurately genotype small biallelic DIPs. Nevertheless, HRMA proved to be the optimal approach for genotyping small DIPs because closed-tube approaches are preferred owing to rapid and less laborious workflows and least risk of PCR contamination.
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Affiliation(s)
- Su Kah Goh
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Ashan Musafer
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Tom Witkowski
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | | | - Christopher Christophi
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
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139
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Fundamentals of multiplexing with digital PCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:15-23. [PMID: 27990345 PMCID: PMC5154634 DOI: 10.1016/j.bdq.2016.05.002] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
Abstract
Over the past decade numerous publications have demonstrated how digital PCR (dPCR) enables precise and sensitive quantification of nucleic acids in a wide range of applications in both healthcare and environmental analysis. This has occurred in parallel with the advances in partitioning fluidics that enable a reaction to be subdivided into an increasing number of partitions. As the majority of dPCR systems are based on detection in two discrete optical channels, most research to date has focused on quantification of one or two targets within a single reaction. Here we describe ‘higher order multiplexing’ that is the unique ability of dPCR to precisely measure more than two targets in the same reaction. Using examples, we describe the different types of duplex and multiplex reactions that can be achieved. We also describe essential experimental considerations to ensure accurate quantification of multiple targets.
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140
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Detection and quantification of Wuchereria bancrofti and Brugia malayi DNA in blood samples and mosquitoes using duplex droplet digital polymerase chain reaction. Parasitol Res 2016; 115:2967-72. [PMID: 27085707 DOI: 10.1007/s00436-016-5051-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/07/2016] [Indexed: 01/29/2023]
Abstract
Lymphatic filariasis, a mosquito-borne disease, is still a major public health problem in tropical and sub-tropical countries. Effective diagnostic tools are required for identification of infected individuals, for epidemiological assessment, and for monitoring of control programs. A duplex droplet digital polymerase chain reaction (ddPCR) was conducted to differentiate and quantify Wuchereria bancrofti DNA by targeting the long DNA repeat (LDR) element and Brugia malayi DNA by targeting the HhaI element in blood samples and mosquito vectors. The analytical sensitivity and specificity were evaluated. Our results indicated that the duplex ddPCR assay could differentiate and quantify W. bancrofti and B. malayi DNA from blood samples and mosquitoes. DNA from a single larva in 50 μl of a blood sample, or in one mosquito vector, could be detected. The analytical sensitivity and specificity for W. bancrofti are both 100 %. Corresponding values for B. malayi are 100 and 98.3 %, respectively. Therefore, duplex ddPCR is a potential tool for simultaneous diagnosis and monitoring of bancroftian and brugian filariasis in endemic areas.
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141
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Weerakoon KG, Gordon CA, Gobert GN, Cai P, McManus DP. Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: A duplex approach with DNA binding dye chemistry. J Microbiol Methods 2016; 125:19-27. [PMID: 27021661 DOI: 10.1016/j.mimet.2016.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/03/2016] [Accepted: 03/21/2016] [Indexed: 11/19/2022]
Abstract
Schistosomiasis is a chronically debilitating helminth infection with a significant socio-economic and public health impact. Accurate diagnostics play a pivotal role in achieving current schistosomiasis control and elimination goals. However, many of the current diagnostic procedures, which rely on detection of schistosome eggs, have major limitations including lack of accuracy and the inability to detect pre-patent infections. DNA-based detection methods provide a viable alternative to the current tests commonly used for schistosomiasis diagnosis. Here we describe the optimisation of a novel droplet digital PCR (ddPCR) duplex assay for the diagnosis of Schistosoma japonicum infection which provides improved detection sensitivity and specificity. The assay involves the amplification of two specific and abundant target gene sequences in S. japonicum; a retrotransposon (SjR2) and a portion of a mitochondrial gene (nad1). The assay detected target sequences in different sources of schistosome DNA isolated from adult worms, schistosomules and eggs, and exhibits a high level of specificity, thereby representing an ideal tool for the detection of low levels of parasite DNA in different clinical samples including parasite cell free DNA in the host circulation and other bodily fluids. Moreover, being quantitative, the assay can be used to determine parasite infection intensity and, could provide an important tool for the detection of low intensity infections in low prevalence schistosomiasis-endemic areas.
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Affiliation(s)
- Kosala G Weerakoon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Public Health, University of Queensland, Brisbane, Australia; Department of Parasitology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka.
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Geoffrey N Gobert
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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142
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Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PCM, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Res 2016; 26:530-40. [PMID: 26934921 PMCID: PMC4817776 DOI: 10.1101/gr.199448.115] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 01/25/2023]
Abstract
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
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Affiliation(s)
- Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Samarth Rangavittal
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Monika Cechova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rebeca Campos Sanchez
- Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard W Fescemyer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Danling Ye
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Rayan Chikhi
- University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France; Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | | | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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143
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Schuler F, Trotter M, Zengerle R, von Stetten F. Monochrome Multiplexing in Polymerase Chain Reaction by Photobleaching of Fluorogenic Hydrolysis Probes. Anal Chem 2016; 88:2590-5. [DOI: 10.1021/acs.analchem.5b02960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Friedrich Schuler
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Martin Trotter
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS-Centre
for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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144
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The Rise of CRISPR/Cas for Genome Editing in Stem Cells. Stem Cells Int 2016; 2016:8140168. [PMID: 26880991 PMCID: PMC4736575 DOI: 10.1155/2016/8140168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 12/26/2022] Open
Abstract
Genetic manipulation is a powerful tool to establish the causal relationship between a genetic lesion and a particular pathological phenotype. The rise of CRISPR/Cas9 genome-engineering tools overcame the traditional technical bottleneck for routine site-specific genetic manipulation in cells. To create the perfect in vitro cell model, there is significant interest from the stem cell research community to adopt this fast evolving technology. This review addresses this need directly by providing both the up-to-date biochemical rationale of CRISPR-mediated genome engineering and detailed practical guidelines for the design and execution of CRISPR experiments in cell models. Ultimately, this review will serve as a timely and comprehensive guide for this fast developing technology.
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145
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Cao Y, Griffith JF, Weisberg SB. The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR. Methods Mol Biol 2016; 1452:113-30. [PMID: 27460373 DOI: 10.1007/978-1-4939-3774-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - John F Griffith
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA.
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Djogbénou LS, Assogba B, Essandoh J, Constant EAV, Makoutodé M, Akogbéto M, Donnelly MJ, Weetman D. Estimation of allele-specific Ace-1 duplication in insecticide-resistant Anopheles mosquitoes from West Africa. Malar J 2015; 14:507. [PMID: 26682913 PMCID: PMC4683970 DOI: 10.1186/s12936-015-1026-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/02/2015] [Indexed: 11/25/2022] Open
Abstract
Background
Identification of variation in Ace-1 copy number and G119S mutation genotype from samples of Anopheles gambiae and Anopheles coluzzii across West Africa are important diagnostics of carbamate and organophosphate resistance at population and individual levels. The most widespread and economical method, PCR–RFLP, suffers from an inability to discriminate true heterozygotes from heterozygotes with duplication.
Methods In addition to PCR–RFLP, in this study three different molecular techniques were applied on the same mosquito specimens: TaqMan qPCR, qRTPCR and ddPCR. To group heterozygous individuals recorded from the PCR–RFLP analysis into different assumptive genotypes K-means clustering was applied on the Z-scores of data obtained from both the TaqMan and ddPCR methods. The qRTPCR analysis was used for absolute quantification of copy number variation. Results The results indicate that most heterozygotes are duplicated and that G119S mutation must now be regarded as a complex genotype ranging from primarily single-copy susceptible Glycine homozygotes to balanced and imbalanced heterozygotes, and multiply-amplified resistant Serine allele homozygotes. Whilst qRTPCR-based gene copy analysis suffers from some imprecision, it clearly illustrates differences in copy number among genotype groups identified by TaqMan or ddPCR. Based on TaqMan method properties, and by coupling TaqMan and ddPCR methods simultaneously on the same type of mosquito specimens, it demonstrated that the TaqMan genotype assays associated with the K-means clustering algorithm could provide a useful semi-quantitative estimate method to investigate the level of allele-specific duplication in mosquito populations. Conclusions Ace-1 gene duplication is evidently far more complex in An. gambiae and An. coluzzii than the better-studied mosquito Culex quinquefasciatus, which consequently can no longer be considered an appropriate model for prediction of phenotypic consequences. These require urgent further evaluation in Anopheles. To maintain the sustained effectiveness carbamates and organophosphates as alternative products to pyrethroids for malaria vector control, monitoring of duplicated resistant alleles in natural populations is essential to guide the rational use of these insecticides. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-1026-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luc S Djogbénou
- Institut Regional de Santé Publique de Ouidah/Université d'Abomey-Calavi, Cotonou, Benin. .,Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
| | - Benoît Assogba
- Institut Regional de Santé Publique de Ouidah/Université d'Abomey-Calavi, Cotonou, Benin.
| | - John Essandoh
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
| | - Edi A V Constant
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
| | - Michel Makoutodé
- Institut Regional de Santé Publique de Ouidah/Université d'Abomey-Calavi, Cotonou, Benin.
| | - Martin Akogbéto
- Centre de Recherche Entomologique de Cotonou, Cotonou, Benin.
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
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147
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Duplex digital droplet PCR for the determination of non-Basmati rice in Basmati rice (Oryza sativa) on the base of a deletion in the fragrant gene. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2599-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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148
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Minimal Residual Disease Detection by Droplet Digital PCR in Multiple Myeloma, Mantle Cell Lymphoma, and Follicular Lymphoma. J Mol Diagn 2015; 17:652-60. [DOI: 10.1016/j.jmoldx.2015.05.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/26/2015] [Accepted: 05/22/2015] [Indexed: 01/27/2023] Open
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149
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Rajasekaran N, Oh MR, Kim SS, Kim SE, Kim YD, Choi HJ, Byun B, Shin YK. Employing Digital Droplet PCR to Detect BRAF V600E Mutations in Formalin-fixed Paraffin-embedded Reference Standard Cell Lines. J Vis Exp 2015. [PMID: 26484710 DOI: 10.3791/53190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
ddPCR is a highly sensitive PCR method that utilizes a water-oil emulsion system. Using a droplet generator, an extracted nucleic acid sample is partitioned into ~20,000 nano-sized, water-in-oil droplets, and PCR amplification occurs in individual droplets. The ddPCR approach is in identifying sequence mutations, copy number alterations, and select structural rearrangements involving targeted genes. Here, we demonstrate the use of ddPCR as a powerful technique for precisely quantitating rare BRAF V600E mutations in FFPE reference standard cell lines, which is helpful in identifying individuals with cancer. In conclusion, ddPCR technique offers the potential to precisely profile the specific rare mutations in different genes in various types of FFPE samples.
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Affiliation(s)
- Nirmal Rajasekaran
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University
| | | | - Sung-Su Kim
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University
| | | | | | - Hyun-Jeung Choi
- The Center for Anti-Cancer CDx, N-Bio, Seoul National University
| | - Bohyun Byun
- The Center for Anti-Cancer CDx, N-Bio, Seoul National University
| | - Young Kee Shin
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University; The Center for Anti-Cancer CDx, N-Bio, Seoul National University;
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150
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Zhao S, Lin H, Chen S, Yang M, Yan Q, Wen C, Hao Z, Yan Y, Sun Y, Hu J, Chen Z, Xi L. Sensitive detection of Porcine circovirus-2 by droplet digital polymerase chain reaction. J Vet Diagn Invest 2015; 27:784-8. [PMID: 26391713 DOI: 10.1177/1040638715608358] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sensitive detection of Porcine circovirus-2 (PCV-2) is very important for surveillance of postweaning multisystemic wasting syndrome. Droplet digital polymerase chain reaction (ddPCR) is novel PCR method that can achieve high precision. Our study aimed to develop a sensitive assay utilizing ddPCR to detect PCV-2. Specificity of the assay was confirmed by the failure of amplification of DNA of other relevant viruses. The detection limit for ddPCR was 25 copies/μL, a 4-fold greater sensitivity than TaqMan real-time PCR. Both methods showed a high degree of linearity (R(2) = ~1), although TaqMan real-time PCR showed less sensitivity than ddPCR for clinical detection. Our findings indicate that ddPCR might represent a promising platform for detecting PCV-2 viral loads.
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Affiliation(s)
- Shan Zhao
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Hua Lin
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Shijie Chen
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Miao Yang
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Qigui Yan
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Caifang Wen
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Zhongxiang Hao
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Yubao Yan
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Yingjie Sun
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Juan Hu
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Zhenrong Chen
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
| | - Lixin Xi
- College of Veterinary Medicine (Zhao, Q Yan, Wen, Hao, Z Chen, Xi) and Key Laboratory of Animal Disease and Human Health of Sichuan Province (Q Yan), Sichuan Agricultural University, Chengdu, ChinaSichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, S Chen, Yang, Y Yan, Sun, Hu)
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