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Huang K, Zhang J, Li J, Qiu H, Wei L, Yang Y, Wang C. Exploring the Impact of Primer-Template Mismatches on PCR Performance of DNA Polymerases Varying in Proofreading Activity. Genes (Basel) 2024; 15:215. [PMID: 38397205 PMCID: PMC10888005 DOI: 10.3390/genes15020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Polymerase chain reaction (PCR) is a widely used technique in gene expression analysis, diagnostics, and various molecular biology applications. However, the accuracy and sensitivity of PCR can be compromised by primer-template mismatches, potentially leading to erroneous results. In this study, we strategically designed 111 primer-template combinations with varying numbers, types, and locations of mismatches to meticulously assess their impact on qPCR performance while two distinctly different types of DNA polymerases were used. Notably, when a single-nucleotide mismatch occurred at the 3' end of the primer, we observed significant decreases in the analytical sensitivity (0-4%) with Invitrogen™ Platinum™ Taq DNA Polymerase High Fidelity, while the analytical sensitivity remained unchanged with Takara Ex Taq Hot Start Version DNA Polymerase. Leveraging these findings, we designed a highly specific PCR to amplify Babesia while effectively avoiding the genetically close Theileria. Through elucidating the critical interplay between types of DNA polymerases and primer-template mismatches, this research provides valuable insights for improving PCR accuracy and performance. These findings have important implications for researchers aiming to achieve robust qPCR results in various molecular biology applications.
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Affiliation(s)
- Ke Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
- Center of Animal Disease Control and Prevention, Songjiang District, Shanghai 201600, China
| | - Jilei Zhang
- College of Medicine, University of Illinois Chicago, Chicago, IL 60607, USA;
| | - Jing Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Haixiang Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Lanjing Wei
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA;
| | - Yi Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225012, China; (K.H.); (J.L.); (H.Q.)
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
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2
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Zanatta CB, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. Specificity Testing for NGT PCR-Based Detection Methods in the Context of the EU GMO Regulations. Foods 2023; 12:4298. [PMID: 38231759 DOI: 10.3390/foods12234298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems' specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations.
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Affiliation(s)
- Caroline Bedin Zanatta
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
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3
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Xu EY, Schneper LM, Notterman DA. A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions. PLoS One 2023; 18:e0292559. [PMID: 37812635 PMCID: PMC10561853 DOI: 10.1371/journal.pone.0292559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
In quantitative polymerase chain reaction (qPCR) experiments, primers containing mismatches with respect to the template are widely used in measuring repetitive DNA elements. Primer-template mismatches may lead to underestimation of the input sample quantity due to inefficient annealing and amplification. But how primer-template mismatches affect quantification accuracy has not been rigorously investigated. In this study, we performed a series of qPCR experiments in which we tested three pairs of mismatched telomere primers (tel1/tel2, tel1b/tel2b and telg/telc) and two pairs of perfect-match reference gene primers (36B4-F/-R and IFNB1-F/-R) at three different primer concentrations under four cycling conditions. Templates used were genomic DNA from two human cell lines and oligo duplexes which contained telomere sequences, reference gene sequences, or both. We demonstrated that the underestimation of input sample quantity from reactions containing mismatched primers was not due to lower amplification efficiency (E), but due to ineffective usage of the input sample. We defined a novel concept of amplification efficacy (f) which quantifies the effectiveness of input sample amplification by primers. We have modified the conventional qPCR kinetic formula to include f, which corrects the effects of primer mismatches. We demonstrated that reactions containing mismatched telomere primer pairs had similar efficiency (E), but varying degrees of reduced efficacy (f) in comparison to those with the perfect-match gene primer pairs. Using the quantitative parameter f, underestimation of initial target by telomere primers can be adjusted to provide a more accurate measurement. Additionally, we found that the tel1b/tel2b primer set at concentration of 500 nM and 900 nM exhibited the best amplification efficacy f. This study provides a novel way to incorporate an evaluation of amplification efficacy into qPCR analysis. In turn, it improves mismatched primer selection and quantification accuracy in amplifying DNA repeats using qPCR methods.
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Affiliation(s)
- Eugenia Y. Xu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Lisa M. Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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4
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Latham S, Hughes E, Budgen B, Morley A. Inhibition of the PCR by genomic DNA. PLoS One 2023; 18:e0284538. [PMID: 37083935 PMCID: PMC10120932 DOI: 10.1371/journal.pone.0284538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
AIMS qPCR, is widely used for quantifying minimal residual disease (MRD) and is conventionally performed according to guidelines proposed by the EuroMRD consortium. However it often fails when quantifying MRD levels below 10-4. By contrast, HAT-PCR, a recent modification designed to minimise false-positive results, can quantify MRD down to 10-6. METHODS The factors leading to failure of conventional qPCR to quantify low levels of MRD were studied by analysing PCR reagents, protocol and primers and by testing for inhibition by adding primers to a plasmid amplification system. Complementary primers, ending in either G/C or A/T, were used to determine the effect of the 3' end of a primer. RESULTS Inhibition of conventional PCR resulted from interaction of primers with genomic DNA leading to exponential amplification of nonspecific amplicons. It was observed with approximately half of the EuroMRD J primers tested. Inhibition by a primer was significantly related to primer Tm and G/C content and was absent when extension at the 3' end was blocked. Nonspecificity and inhibition were decreased or abolished by increasing the annealing temperature and inhibition was decreased by increasing the concentration of polymerase. Primers terminating with G/C produced significantly more nonspecificity and inhibition than primers terminating with A/T. HAT-PCR produced minimal nonspecificity and no inhibition. CONCLUSIONS Inhibition of the PCR may result from the presence of genomic DNA and resultant exponential amplification of nonspecific amplicons. Factors contributing to the phenomenon include suboptimal annealing temperature, suboptimal primer design, and suboptimal polymerase concentration. Optimisation of these factors, as in HAT-PCR, enables sensitive quantification of MRD. PCR assays are increasingly used for sensitive detection of other rare targets against a background of genomic DNA and such assays may benefit from similar improvement in PCR design.
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Affiliation(s)
- Sue Latham
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Elizabeth Hughes
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Bradley Budgen
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Alexander Morley
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
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5
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. Microbiol Spectr 2022; 10:e0158321. [PMID: 35708340 PMCID: PMC9430505 DOI: 10.1128/spectrum.01583-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/06/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high-throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false-negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multitarget redundancy and an internal amplification control. A convenient and cost-effective target-specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-CoV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high-frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multitarget redundancy. When challenged with extracted human samples the multiplex assay showed 87% or better sensitivity (of 30 positive samples), with 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction (of 21 positive samples), and 100% specificity (of 60 negative samples). These results are further evidence that conventional laboratory methodologies can be leveraged at the point of care for robust performance and diagnostic stability over time. IMPORTANCE The COVID-19 pandemic has had tremendous impact, and the ability to perform molecular diagnostics in resource limited settings has emerged as a key resource for mitigating spread of the disease. One challenge in COVID-19 diagnosis, as well as other viruses, is ongoing mutation that can allow viruses to evade detection by diagnostic tests. We developed a test that detects multiple parts of the virus genome in a single test to reduce the chance of missing a virus due to mutation, and it is designed to be simpler and faster than typical laboratory tests while maintaining high sensitivity. This capability is enabled by a novel fluorescent probe technology that works with a simple constant temperature reaction condition.
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Affiliation(s)
- Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health for Women Adolescents and Children, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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6
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In Silico Evaluation of CRISPR-Based Assays for Effective Detection of SARS-CoV-2. Pathogens 2022; 11:pathogens11090968. [PMID: 36145402 PMCID: PMC9506389 DOI: 10.3390/pathogens11090968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease (COVID-19) caused by the SARS-CoV-2 has been an outbreak since late 2019 up to now. This pandemic causes rapid development in molecular detection technologies to diagnose viral infection for epidemic prevention. In addition to antigen test kit (ATK) and polymerase chain reaction (PCR), CRISPR-based assays for detection of SARS-CoV-2 have gained attention because it has a simple setup but still maintain high specificity and sensitivity. However, the SARS-CoV-2 has been continuing mutating over the past few years. Thus, molecular tools that rely on matching at the nucleotide level need to be reevaluated to preserve their specificity and sensitivity. Here, we analyzed how mutations in different variants of concern (VOC), including Alpha, Beta, Gamma, Delta, and Omicron strains, could introduce mismatches to the previously reported primers and crRNAs used in the CRISPR-Cas system. Over 40% of the primer sets and 15% of the crRNAs contain mismatches. Hence, primers and crRNAs in nucleic acid-based assays must be chosen carefully to pair up with SARS-CoV-2 variants. In conclusion, the data obtained from this study could be useful in selecting the conserved primers and crRNAs for effective detections against the VOC of SARS-CoV-2.
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7
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Abstract
A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and emerging COVID-19 diagnosis tools, such as biosensing platforms, will also be introduced. Considering the extreme relevance that all these technologies assume in pandemic control, it is of the utmost relevance to have an intrinsic knowledge of the parameters that need to be taken into consideration before choosing the most adequate test for a particular situation. Moreover, the new variants of the virus and their potential impact on the detection method’s effectiveness will be discussed. In order to better manage the pandemic, it is essential to maintain continuous research into the SARS-CoV-2 genome and updated genomic surveillance at the global level. This will allow for timely detection of new mutations and viral variants, which may affect the performance of COVID-19 detection tests.
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8
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Ezpeleta J, Garcia Labari I, Villanova GV, Bulacio P, Lavista-Llanos S, Posner V, Krsticevic F, Arranz S, Tapia E. Robust and scalable barcoding for massively parallel long-read sequencing. Sci Rep 2022; 12:7619. [PMID: 35538127 PMCID: PMC9090787 DOI: 10.1038/s41598-022-11656-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
Nucleic-acid barcoding is an enabling technique for many applications, but its use remains limited in emerging long-read sequencing technologies with intrinsically low raw accuracy. Here, we apply so-called NS-watermark barcodes, whose error correction capability was previously validated in silico, in a proof of concept where we synthesize 3840 NS-watermark barcodes and use them to asymmetrically tag and simultaneously sequence amplicons from two evolutionarily distant species (namely Bordetella pertussis and Drosophila mojavensis) on the ONT MinION platform. To our knowledge, this is the largest number of distinct, non-random tags ever sequenced in parallel and the first report of microarray-based synthesis as a source for large oligonucleotide pools for barcoding. We recovered the identity of more than 86% of the barcodes, with a crosstalk rate of 0.17% (i.e., one misassignment every 584 reads). This falls in the range of the index hopping rate of established, high-accuracy Illumina sequencing, despite the increased number of tags and the relatively low accuracy of both microarray-based synthesis and long-read sequencing. The robustness of NS-watermark barcodes, together with their scalable design and compatibility with low-cost massive synthesis, makes them promising for present and future sequencing applications requiring massive labeling, such as long-read single-cell RNA-Seq.
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Affiliation(s)
- Joaquín Ezpeleta
- Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina. .,Facultad de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Ignacio Garcia Labari
- Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Gabriela Vanina Villanova
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina.,Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario - Centro Científico Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
| | - Pilar Bulacio
- Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina.,Facultad de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sofía Lavista-Llanos
- Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
| | - Victoria Posner
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario - Centro Científico Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
| | - Flavia Krsticevic
- Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Silvia Arranz
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario - Centro Científico Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
| | - Elizabeth Tapia
- Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina.,Facultad de Ciencias Exactas, Ingeniería y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina
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9
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Haemogregarines of the genera Haemogregarina, Hemolivia, and Hepatozoon Infecting Vietnamese Freshwater Turtles, with Additional Notes on Primer Specificity and Primer-template Mismatches Affecting Diagnostic Success. Protist 2022; 173:125884. [DOI: 10.1016/j.protis.2022.125884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022]
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10
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Kolter A, Gemeinholzer B. Internal transcribed spacer primer evaluation for vascular plant metabarcoding. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
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11
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34462755 DOI: 10.1101/2021.08.13.21261995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multi-target redundancy and an internal amplification control. A convenient and cost-effective target specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-COV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multi-target redundancy. When challenged with extracted human samples the multiplexed assay showed 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction, and 100% specificity. These results are further evidence that conventional laboratory methodologies can be leveraged at the point-of-care for robust performance and diagnostic stability over time.
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12
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Hu B, Wang Y, Sun S, Luo G, Zhang S, Zhang J, Chen L, Huang Z. Specificity Enhancement of Deoxyribonucleic Acid Polymerization for Sensitive Nucleic Acid Detection. Anal Chem 2020; 92:15872-15879. [PMID: 33236629 DOI: 10.1021/acs.analchem.0c03223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.
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Affiliation(s)
- Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Yitao Wang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shichao Sun
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Lu Chen
- Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China.,Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
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13
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Tan Y, Zhong W, Tang W, Fan J, Zhang X, Guo D, Wu X, Liu Y. Improvement of Molecular Diagnosis Using Domain-Level Single-Nucleotide Variants by Eliminating Unexpected Secondary Structures. Chemistry 2020; 26:16256-16260. [PMID: 32964533 DOI: 10.1002/chem.202003592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Indexed: 01/06/2023]
Abstract
Identification of single-nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain-level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double-stranded structure, specially designed probes are used to detect double-stranded properties and report abundant domain-level oligonucleotide information to improve the effective information in the detection results and complete domain-level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof-of-concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.
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Affiliation(s)
- Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaohui Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Donghua Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaolong Wu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
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14
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Coulton A, Edwards KJ. AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids. BMC Bioinformatics 2020; 21:311. [PMID: 32677889 PMCID: PMC7364506 DOI: 10.1186/s12859-020-03601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/11/2020] [Indexed: 12/02/2022] Open
Abstract
Background Polyploid organisms such as wheat complicate even the simplest of procedures in molecular biology. Whilst knowledge of genomic sequences in crops is increasing rapidly, the scientific community is still a long way from producing a full pan-genome for every species. Polymerase chain reaction and Sanger sequencing therefore remain widely used as methods for characterizing gene sequences in many varieties of crops. High sequence similarity between genomes in polyploids means that if primers are not homeologue-specific via the incorporation of a SNP at the 3’ tail, sequences other than the target sequence will also be amplified. Current consensus for gene cloning in wheat is to manually perform many steps in a long bioinformatics pipeline. Results Here we present AutoCloner (www.autocloner.com), a fully automated pipeline for crop gene cloning that includes a free-to-use web interface for users. AutoCloner takes a sequence of interest from the user and performs a basic local alignment search tool (BLAST) search against the genome assembly for their particular polyploid crop. Homologous sequences are then compiled with the input sequence into a multiple sequence alignment which is mined for single-nucleotide polymorphisms (SNPs). Various combinations of potential primers that cover the entire gene of interest are then created and evaluated by Primer3; the set of primers with the highest score, as well as all possible primers at every SNP location, are then returned to the user for polymerase chain reaction (PCR). We have successfully used AutoCloner to clone various genes of interest in the Apogee wheat variety, which has no current genome sequence. In addition, we have successfully run the pipeline on ~ 80,000 high-confidence gene models from a wheat genome assembly. Conclusion AutoCloner is the first tool to fully-automate primer design for gene cloning in polyploids, where previously the consensus within the wheat community was to perform this process manually. The web interface for AutoCloner provides a simple and effective polyploid primer-design method for gene cloning, with no need for researchers to download software or input any other details other than their sequence of interest.
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Affiliation(s)
- Alexander Coulton
- Biological Sciences Department, The University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Keith J Edwards
- Biological Sciences Department, The University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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15
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Rana DR, Pokhrel N. Sequence mismatch in PCR probes may mask the COVID-19 detection in Nepal. Mol Cell Probes 2020; 53:101599. [PMID: 32425334 PMCID: PMC7233248 DOI: 10.1016/j.mcp.2020.101599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 11/18/2022]
Abstract
Most of the COVID-19 cases in Nepal are in the Southern districts of Nepal bordering India with travel histories to India. Very few positive cases of COVID-19 are detected in Nepal which could either be due to early national lockdown. Low PCR positivity rates could also be due to inefficiency of the PCR methods. Whole genomes of 93 clinical samples from COVID-19 patients were analyzed to find the primer and probe binding sites. Mutations in probe binding sites were found which could impact PCR efficiency resulting in false negative results
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Affiliation(s)
- Divya Rsjb Rana
- Hari Khetan Multiple Campus, Birgunj, Nepal (affiliated to Tribhuvan University, Kirtipur, Nepal).
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16
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Khazan S, Minz-Dub A, Sela H, Manisterski J, Ben-Yehuda P, Sharon A, Millet E. Reducing the size of an alien segment carrying leaf rust and stripe rust resistance in wheat. BMC PLANT BIOLOGY 2020; 20:153. [PMID: 32272895 PMCID: PMC7147030 DOI: 10.1186/s12870-020-2306-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Leaf and stripe rusts are two major wheat diseases, causing significant yield losses. The preferred way for protecting wheat from rust pathogens is by introgression of rust resistance traits from wheat-related wild species. To avoid genetic drag due to replacement of large wheat chromosomal segments by the alien chromatin, it is necessary to shorten the alien chromosome segment in primary recombinants. RESULTS Here we report on shortening of an alien chromosome segment in wheat that carries leaf and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis). Rust resistant wheat introgression lines were selected and the alien region was mapped using genotyping by sequencing. Single polymorphic nucleotides (SNP) were identified and used to generate diagnostic PCR markers. Shortening of the alien fragment was achieved by induced homoeologous pairing and lines with shortened alien chromosome were identified using the PCR markers. Further reduction of the segment was achieved in tertiary recombinants without losing the rust resistance. CONCLUSIONS Alien chromatin in wheat with novel rust resistance genes was characterized by SNP markers and shortened by homoeologous recombination to avoid deleterious traits. The resulting wheat lines are resistant to highly virulent races of leaf and stripe rust pathogens and can be used as both resistant wheat in the field and source for gene transfer to other wheat lines/species.
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Affiliation(s)
- Sofia Khazan
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Anna Minz-Dub
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Hanan Sela
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Jacob Manisterski
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Pnina Ben-Yehuda
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Eitan Millet
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
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17
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Kim KT, Winssinger N. Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS). Chem Sci 2020; 11:4150-4157. [PMID: 34122878 PMCID: PMC8152519 DOI: 10.1039/d0sc00741b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity but compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.
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Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
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18
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Kaundun SS, Hutchings SJ, Marchegiani E, Rauser R, Jackson LV. A derived Polymorphic Amplified Cleaved Sequence assay for detecting the Δ210 PPX2L codon deletion conferring target-site resistance to protoporphyrinogen oxidase-inhibiting herbicides. PEST MANAGEMENT SCIENCE 2020; 76:789-796. [PMID: 31400066 DOI: 10.1002/ps.5581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Resistance to protoporphyrinogen oxidase (PPO)-inhibiting herbicides in Amaranthus rudis from corn/soybean production systems in the USA appears to be mainly due to a codon deletion at position 210 of the target PPX2L gene. In this study, we have developed a simple and cost-effective derived Polymorphic Amplified Cleaved Sequenced (dPACS) marker for detecting this resistance-causing deletion in A. rudis and other relevant weed species. RESULTS Ninety-six plants from 16 diverse fomesafen-sensitive and resistant A. rudis populations from Illinois and Iowa were used to establish the dPACS procedure. The assay requires forced mismatches in both the forward and reverse PCR primers and uses the restriction enzyme XcmI for the positive identification of wild type glycine residue at PPX2L codon position 210. The data from the dPACS method, using either leaf tissues or seeds as starting material, were completely correlated with direct Sanger sequencing results for samples that gave readable nucleotide peaks around codon 210 of PPX2L. Furthermore, the assay was directly transferable to all four other Amaranthus species tested, and to Ambrosia artemisiifolia using species-specific primers. CONCLUSION The proposed assay will allow the rapid detection of the Δ210 codon deletion in the PPX2L gene and the timely development of management strategies for tackling growing resistance to PPO-inhibiting herbicides in A. rudis and other broadleaf weed species. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Shiv S Kaundun
- Herbicide Bioscience, Syngenta, Jealott's Hill International Research Centre, Berkshire, UK
| | - Sarah-Jane Hutchings
- Herbicide Bioscience, Syngenta, Jealott's Hill International Research Centre, Berkshire, UK
| | - Elisabetta Marchegiani
- Herbicide Bioscience, Syngenta, Jealott's Hill International Research Centre, Berkshire, UK
| | - Ruben Rauser
- Herbicide Bioscience, Syngenta, Jealott's Hill International Research Centre, Berkshire, UK
| | - Lucy V Jackson
- Herbicide Bioscience, Syngenta, Jealott's Hill International Research Centre, Berkshire, UK
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19
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Ngatia JN, Lan TM, Ma Y, Dinh TD, Wang Z, Dahmer TD, Chun Xu Y. Distinguishing extant elephants ivory from mammoth ivory using a short sequence of cytochrome b gene. Sci Rep 2019; 9:18863. [PMID: 31827140 PMCID: PMC6906310 DOI: 10.1038/s41598-019-55094-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
Trade in ivory from extant elephant species namely Asian elephant (Elephas maximus), African savanna elephant (Loxodonta africana) and African forest elephant (Loxodonta cyclotis) is regulated internationally, while the trade in ivory from extinct species of Elephantidae, including woolly mammoth, is unregulated. This distinction creates opportunity for laundering and trading elephant ivory as mammoth ivory. The existing morphological and molecular genetics methods do not reliably distinguish the source of ivory items that lack clear identification characteristics or for which the quality of extracted DNA cannot support amplification of large gene fragments. We present a PCR-sequencing method based on 116 bp target sequence of the cytochrome b gene to specifically amplify elephantid DNA while simultaneously excluding non-elephantid species and ivory substitutes, and while avoiding contamination by human DNA. The partial Cytochrome b gene sequence enabled accurate association of ivory samples with their species of origin for all three extant elephants and from mammoth. The detection limit of the PCR system was as low as 10 copy numbers of target DNA. The amplification and sequencing success reached 96.7% for woolly mammoth ivory and 100% for African savanna elephant and African forest elephant ivory. This is the first validated method for distinguishing elephant from mammoth ivory and it provides forensic support for investigation of ivory laundering cases.
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Affiliation(s)
- Jacob Njaramba Ngatia
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Tian Ming Lan
- BGI - Shenzhen, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- China National GeneBank, BGI - Shenzhen, Shenzhen, 518083, China
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thi Dao Dinh
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Wang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thomas D Dahmer
- Ecosystems Ltd, No. 40 Shek Pai Wan Road, Aberdeen, Hong Kong, China
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China.
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China.
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, Harbin, 150040, China.
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20
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Döring M, Kreer C, Lehnen N, Klein F, Pfeifer N. Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features. Sci Rep 2019; 9:10748. [PMID: 31341211 PMCID: PMC6656877 DOI: 10.1038/s41598-019-47173-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/10/2019] [Indexed: 11/09/2022] Open
Abstract
Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efficiently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplification status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifies a template given their nucleotide sequences. The model suggests that the free energy of annealing, ΔG, is the key driver of amplification (p = 7.35e-12) and that 3' mismatches should be considered in dependence on ΔG and the mismatch closest to the 3' terminus (p = 1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR ( http://openPrimeR.mpi-inf.mpg.de ).
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Affiliation(s)
- Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Christoph Kreer
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
| | - Nathalie Lehnen
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
- German Center for Infection Research, Cologne-Bonn Partner Site, Cologne, Germany
| | - Florian Klein
- Institute of Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Robert-Koch-Straße 21, 50931, Cologne, Germany
- German Center for Infection Research, Cologne-Bonn Partner Site, Cologne, Germany
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany.
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
- Medical Faculty, Geissweg 5, University of Tübingen, 72076, Tübingen, Germany.
- German Center for Infection Research, Tübingen Partner Site, Tübingen, Germany.
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21
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Kaundun SS, Marchegiani E, Hutchings SJ, Baker K. Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion-Insertion Polymorphisms. Int J Mol Sci 2019; 20:E3193. [PMID: 31261867 PMCID: PMC6651057 DOI: 10.3390/ijms20133193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion-insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised 'derived Polymorphic Amplified Cleaved Sequence' (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35-55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.
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Affiliation(s)
- Shiv Shankhar Kaundun
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK.
| | - Elisabetta Marchegiani
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
| | - Sarah-Jane Hutchings
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
| | - Ken Baker
- General Bioinformatics, Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
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22
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Zhang L, Dong R, Wei S, Zhou HC, Zhang MX, Alagarsamy K. A novel data processing method CyC* for quantitative real time polymerase chain reaction minimizes cumulative error. PLoS One 2019; 14:e0218159. [PMID: 31185064 PMCID: PMC6559663 DOI: 10.1371/journal.pone.0218159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 05/28/2019] [Indexed: 11/18/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is routinely conducted for DNA quantitative analysis using the cycle-threshold (Ct) method, which assumes uniform/optimum template amplification. In practice, amplification efficiencies vary from cycle to cycle in a PCR reaction, and often decline as the amplification proceeds, which results in substantial errors in measurement. This study reveals the cumulative error for quantification of initial template amounts, due to the difference between the assumed perfect amplification efficiency and actual one in each amplification cycle. The novel CyC* method involves determination of both the earliest amplification cycle detectable above background (“outlier” C*) and the amplification efficiency over the cycle range from C* to the next two amplification cycles; subsequent analysis allows the calculation of initial template amount with minimal cumulative error. Simulation tests indicated that the CyC* method resulted in significantly less variation in the predicted initial DNA level represented as fluorescence intensity F0 when the outlier cycle C* was advanced to an earlier cycle. Performance comparison revealed that CyC* was better than the majority of 13 established qPCR data analysis methods in terms of bias, linearity, reproducibility, and resolution. Actual PCR test also suggested that relative expression levels of nine genes in tea leaves obtained using CyC* were much closer to the real value than those obtained with the conventional 2-ΔΔCt method. Our data indicated that increasing the input of initial template was effective in advancing emergence of the earliest amplification cycle among the tested variants. A computer program (CyC* method) was compiled to perform the data processing. This novel method can minimize cumulative error over the amplification process, and thus, can improve qPCR analysis.
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Affiliation(s)
- Linzhong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- School of Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Rui Dong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- * E-mail:
| | - Han-Chen Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- Tea Research Institution, Anhui Academy of Agricultural Sciences, Huangshan, Anhui, China
| | - Meng-Xian Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Karthikeyan Alagarsamy
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
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23
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Mohsen MG, Ji D, Kool ET. Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA. Chem Sci 2019; 10:3264-3270. [PMID: 30996911 PMCID: PMC6429602 DOI: 10.1039/c8sc03901a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/30/2019] [Indexed: 01/13/2023] Open
Abstract
The identification of single nucleotide polymorphisms (SNP) is increasingly important for diagnosis and treatment of disease. Here we studied the potential use of ATP-releasing nucleotides (ARNs) for identifying SNPs in DNA and RNA targets. Synthesized as derivatives of the four canonical deoxynucleotides, ARNs can be used in the place of deoxynucleoside triphosphates to elongate a primer hybridized to a nucleic acid template, with the leaving group being ATP rather than pyrophosphate. The released ATP is then harnessed in conjunction with luciferase to generate chemiluminescence. Extension on a long target DNA or RNA generates many equivalents of ATP per target strand, providing isothermal amplification of signal. In principle, allele-specific primers could be used in conjunction with ARNs to generate differential luminescence signals with respect to distinct genetic polymorphisms. To test this, varied primer designs, modifications, enzymes and conditions were tested, resulting in an optimized strategy that discriminates between differing nucleic acid templates with single nucleotide resolution. This strategy was then applied to diagnostically relevant alleles resulting in discrimination between known polymorphisms. SNP detection was successfully performed on transcribed mRNA fragments from four different alleles derived from JAK2, BCR-ABL1, BRAF, and HBB. To investigate background interference, wild-type and mutant transcripts of these four alleles were tested and found to be easily distinguishable amid total cellular RNA isolated from human blood. Thus, ARNs have been employed with specialized allele-specific primers to detect diagnostically important SNPs in a novel method that is sensitive, rapid, and isothermal.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Debin Ji
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
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24
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Bai M, Sen B, Wang Q, Xie Y, He Y, Wang G. Molecular Detection and Spatiotemporal Characterization of Labyrinthulomycete Protist Diversity in the Coastal Waters Along the Pearl River Delta. MICROBIAL ECOLOGY 2019; 77:394-405. [PMID: 30083828 DOI: 10.1007/s00248-018-1235-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
The heterotrophic labyrinthulomycete protists have long been known to play an important role in the nutrient cycling of coastal seawater. Yet, their spatiotemporal abundance and diversity in polluted coastal waters remain poorly discussed, due in part to the paucity of a rapid detection method. To this end, we developed a qPCR detection method based on a newly designed primer pair targeting their 18S rRNA gene. Using this method, we studied the population dynamics of labyrinthulomycete protists in nutrient-rich (Shenzhen Bay) and low-nutrient (Daya) coastal habitats along the Pearl River Delta. We found a significantly (P < 0.05) higher abundance of Labyrinthulomycetes in the Shenzhen bay (average 3455 gene copies mL-1) than that in Daya Bay (average 378 gene copies mL-1). Their abundance gradient positively correlated (P < 0.05) with the levels of inorganic nitrogen and phosphates. Further characterization of the molecular diversity of these protists in Shenzhen Bay using different primer sets revealed the presence of several genera besides a large number of unclassified OTUs. Regardless of the primer biases, our results show significant (P < 0.05) spatiotemporal changes in the molecular abundance and diversity of these heterotrophic protists. Overall, this study provides a rapid molecular detection tool for Labyrinthulomycetes and expands our current understanding of their dynamics controlled by physicochemical gradients in coastal waters.
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Affiliation(s)
- Mohan Bai
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Qiuzhen Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yunxuan Xie
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yaodong He
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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25
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Malpartida-Cardenas K, Rodriguez-Manzano J, Yu LS, Delves MJ, Nguon C, Chotivanich K, Baum J, Georgiou P. Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers. Anal Chem 2018; 90:11972-11980. [PMID: 30226760 PMCID: PMC6195307 DOI: 10.1021/acs.analchem.8b02416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022]
Abstract
Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 101 copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Ling-Shan Yu
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Michael J. Delves
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Chea Nguon
- National
Centre for Parasitology, Entomology and
Malaria Control, Phnom Penh 12302, Cambodia
| | - Kesinee Chotivanich
- Department
of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Jake Baum
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Pantelis Georgiou
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
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26
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Ikenaga M, Katsuragi S, Handa Y, Katsumata H, Chishaki N, Kawauchi T, Sakai M. Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique. Microbes Environ 2018; 33:340-344. [PMID: 30146542 PMCID: PMC6167120 DOI: 10.1264/jsme2.me18071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PCR clamping by locked nucleic acid (LNA) oligonucleotides is an effective technique for selectively amplifying the community SSU rRNA genes of plant–associated bacteria. However, the original primer set often shows low amplification efficiency. In order to improve this efficiency, new primers were designed at positions to compete with LNA oligonucleotides. Three new sets displayed higher amplification efficiencies than the original; however, efficiency varied among the primer sets. Two new sets appeared to be available in consideration of bacterial profiles by next-generation sequencing. One new set, KU63f and KU1494r, may be applicable to the selective gene amplification of plant-associated bacteria.
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Affiliation(s)
- Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University
| | | | | | | | - Naoya Chishaki
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University
| | - Tomohiro Kawauchi
- The United Graduate School of Agricultural Sciences, Kagoshima University
| | - Masao Sakai
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University
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27
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Rasmussen HB, Madsen MB. Carboxylesterase 1 genes: systematic review and evaluation of existing genotyping procedures. Drug Metab Pers Ther 2018; 33:3-14. [PMID: 29427553 DOI: 10.1515/dmpt-2017-0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/06/2017] [Indexed: 12/12/2022]
Abstract
The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2). Hence, the CES1 region is complex. Using in silico PCR and alignment, we assessed the specificity of PCR-assisted procedures for genotyping CES1, CES1A2 and CES1P1 in studies identified in PubMed. We identified 33 such studies and excluded those that were not the first to use a procedure or lacked sequence information. After this 17 studies remained. Ten of these used haplotype-specific amplification, restriction enzyme treatment or amplicon sequencing, and included five that were predicted to lack specificity. All procedures for genotyping of single nucleotide polymorphisms in eight studies lacked specificity. One of these studies also used amplicon sequencing, thus being present in the group above. Some primers and their intended targets were mismatched. We provide experimental evidence that one of the procedures lacked specificity. Additionally, a complex pattern of segmental duplications in the CES1 region was revealed. In conclusion, many procedures for CES1, CES1A2 and CES1P1 genotyping appear to lack specificity. Knowledge about the segmental duplications may improve the typing of these genes.
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Affiliation(s)
- Henrik Berg Rasmussen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, Boserupvej 2, 4000 Roskilde, Denmark, Phone: + 45 3864 2284, Fax: +45 3864 2300
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Majbritt Busk Madsen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, Roskilde, Denmark
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28
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Rejali NA, Moric E, Wittwer CT. The Effect of Single Mismatches on Primer Extension. Clin Chem 2018; 64:801-809. [PMID: 29444902 DOI: 10.1373/clinchem.2017.282285] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/26/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Allele-specific PCR is an important diagnostic tool that identifies single-nucleotide variants by preferential amplification of a particular allele, using primers that are mismatched to all but one allele variant. METHODS We applied a fluorescent stopped-flow polymerase assay to measure extension rates from oligonucleotide hairpins to simulate primer-template pairs. Under PCR-applicable conditions, reaction rates were recorded in nucleotides per second per polymerase (nt/s/poly). The effects of temperature, potassium chloride, mismatch type, and position were studied with primarily a deletion mutant of Thermus aquaticus (Taq) DNA polymerase and 135 oligonucleotide sequences. RESULTS Rates at 65 °C were between 205 ± 11 and 177 ± 8 nt/s/poly for matched templates and between 4.55 ± 0.21 and 0.008 ± 0.005 nt/s/poly for 3'-mismatched templates. Although extension rates progressively increased with mismatches further away from the 3' end, rates were still reduced by as much as 84% with a C · C mismatch 6 bases from the 3' end. The optimal extension temperature for matched sequences was 70 °C, shifting to 55-60 °C for 3' mismatches. KCl inhibited mismatch extension. The Michaelis constant (Km) was increased and the apparent unimolecular rate constant (kcat) decreased for 3' mismatches relative to matched templates. CONCLUSIONS Although primer extension of mismatches depends on mismatch type and position, variation also depends on local sequence, KCl concentration, and the type of polymerase. Introduction of 3' mismatches reduces the optimal temperature for extension, suggesting higher annealing temperatures for better allele discrimination. Quantitative descriptions of expected specificity in allele-specific PCR provide additional design direction and suggest when other methods (e.g., high-resolution melting analysis) may be a better choice.
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Affiliation(s)
- Nick A Rejali
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Endi Moric
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT.
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29
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Abstract
Genome editing to introduce specific mutations or to knock out genes in model cell systems has become an efficient platform for research in the fields of molecular biology, genetics, and cell biology. With recent rapid improvements in genome editing techniques, bench-top manipulation of the genome in cell culture has become progressively easier. The application of this knowledge to erythroid cell culture systems now allows the rapid analysis of the downstream effects of virtually any engineered gene disruption or modification in cell systems. Here, we describe a CRISPR/Cas9-based approach to making genomic modifications in erythroid lineage cells which we have successfully used in both murine (MEL) and human (K562) erythroleukaemia immortalized cell lines.
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Affiliation(s)
- Jinfen J Yik
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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30
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Liu Y, Erséus C. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). Ecol Evol 2017; 7:10421-10439. [PMID: 29238565 PMCID: PMC5723599 DOI: 10.1002/ece3.3212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022] Open
Abstract
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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Affiliation(s)
- Yingkui Liu
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
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31
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Dunaeva M, Derksen M, Pruijn GJM. LINE-1 Hypermethylation in Serum Cell-Free DNA of Relapsing Remitting Multiple Sclerosis Patients. Mol Neurobiol 2017; 55:4681-4688. [PMID: 28707075 PMCID: PMC5948235 DOI: 10.1007/s12035-017-0679-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/29/2017] [Indexed: 10/31/2022]
Abstract
Concentrations of cell-free DNA (cfDNA) circulating in blood and its epigenetic variation, such as DNA methylation, may provide useful diagnostic or prognostic information. Long interspersed nuclear element-1 (LINE-1) constitutes approximately 20% of the human genome and its 5'UTR region is CpG rich. Due to its wide distribution, the methylation level of the 5'UTR of LINE-1 can serve as a surrogate marker of global genomic DNA methylation. The aim of the current study was to investigate whether the methylation status of LINE-1 elements in serum cell-free DNA differs between relapsing remitting multiple sclerosis (RRMS) patients and healthy control subjects (CTR). Serum DNA samples of 6 patients and 6 controls were subjected to bisulfite sequencing. The results showed that the methylation level varies among distinct CpG sites in the 5'UTR of LINE-1 repeats and revealed differences in the methylation state of specific sites in this element between patients and controls. The latter differences were largely due to CpG sites in the L1PA2 subfamily, which were more frequently methylated in the RRMS patients than in the CTR group, whereas such differences were not observed in the L1HS subfamily. These data were verified by quantitative PCR using material from 18 patients and 18 control subjects. The results confirmed that the methylation level of a subset of the CpG sites within the LINE-1 promoter is elevated in DNA from RRMS patients in comparison with CTR. The present data suggest that the methylation status of CpG sites of LINE repeats could be a basis for development of diagnostic or prognostic tests.
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Affiliation(s)
- Marina Dunaeva
- Department of Biomolecular Chemistry, Institute for Molecules and Materials and Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands.
| | - Merel Derksen
- Department of Biomolecular Chemistry, Institute for Molecules and Materials and Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials and Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands
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32
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Zander J, Rothe J, Dapprich J, Nagy M. New application for haplotype-specific extraction: Separation of mitochondrial DNA mixtures. Forensic Sci Int Genet 2017; 29:242-249. [DOI: 10.1016/j.fsigen.2017.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/10/2017] [Accepted: 05/01/2017] [Indexed: 10/19/2022]
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33
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Lyozin GT, Kosaka Y, Bhattacharje G, Yost HJ, Brunelli L. Direct Isolation of Seamless Mutant Bacterial Artificial Chromosomes. ACTA ACUST UNITED AC 2017; 118:8.6.1-8.6.29. [PMID: 28369677 DOI: 10.1002/cpmb.34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Seamless (i.e., without unwanted DNA sequences) mutant bacterial artificial chromosomes (BACs) generated via recombination-mediated genetic engineering (recombineering) are better suited to study gene function compared to complementary DNA (cDNA) because they contain only the specific mutation and provide all the regulatory sequences required for in vivo gene expression. However, precisely mutated BACs are typically rare (∼1:1,000 to 1:100,000), making their isolation quite challenging. Although these BACs have been classically isolated by linking the mutation to additional genes, i.e., selectable markers, this approach is prone to false positives and is labor-intensive because it requires the subsequent removal of the selectable marker. We created Founder Principle-driven Enrichment (FPE), a method based on the population genetics "founder principle," to directly isolate rare mutant BACs, without any selectable marker, from liquid cultures via the polymerase chain reaction (PCR). Here, we provide a detailed description of FPE, including protocols for BAC recombineering and PCR screening. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- George T Lyozin
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah.,University of Nebraska and Children's Hospital Medical Center, Omaha, Nebraska
| | - Yasuhiro Kosaka
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Gourab Bhattacharje
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - H Joseph Yost
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Luca Brunelli
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah.,Department of Pediatrics (Neonatology), The University of Utah School of Medicine, Salt Lake City, Utah
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34
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Long YM, Chao WS, Ma GJ, Xu SS, Qi LL. An innovative SNP genotyping method adapting to multiple platforms and throughputs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:597-607. [PMID: 27942775 DOI: 10.1007/s00122-016-2838-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/26/2016] [Indexed: 05/18/2023]
Abstract
An innovative genotyping method designated as semi-thermal asymmetric reverse PCR (STARP) was developed for genotyping individual SNPs with improved accuracy, flexible throughputs, low operational costs, and high platform compatibility. Multiplex chip-based technology for genome-scale genotyping of single nucleotide polymorphisms (SNPs) has made great progress in the past two decades. However, PCR-based genotyping of individual SNPs still remains problematic in accuracy, throughput, simplicity, and/or operational costs as well as the compatibility with multiple platforms. Here, we report a novel SNP genotyping method designated semi-thermal asymmetric reverse PCR (STARP). In this method, genotyping assay was performed under unique PCR conditions using two universal priming element-adjustable primers (PEA-primers) and one group of three locus-specific primers: two asymmetrically modified allele-specific primers (AMAS-primers) and their common reverse primer. The two AMAS-primers each were substituted one base in different positions at their 3' regions to significantly increase the amplification specificity of the two alleles and tailed at 5' ends to provide priming sites for PEA-primers. The two PEA-primers were developed for common use in all genotyping assays to stringently target the PCR fragments generated by the two AMAS-primers with similar PCR efficiencies and for flexible detection using either gel-free fluorescence signals or gel-based size separation. The state-of-the-art primer design and unique PCR conditions endowed STARP with all the major advantages of high accuracy, flexible throughputs, simple assay design, low operational costs, and platform compatibility. In addition to SNPs, STARP can also be employed in genotyping of indels (insertion-deletion polymorphisms). As vast variations in DNA sequences are being unearthed by many genome sequencing projects and genotyping by sequencing, STARP will have wide applications across all biological organisms in agriculture, medicine, and forensics.
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Affiliation(s)
- Y M Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - W S Chao
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
| | - G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - S S Xu
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
| | - L L Qi
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA.
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35
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Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, Gould TJ, Clayton JB, Johnson TJ, Hunter R, Knights D, Beckman KB. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat Biotechnol 2016; 34:942-9. [DOI: 10.1038/nbt.3601] [Citation(s) in RCA: 422] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/11/2016] [Indexed: 12/26/2022]
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36
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Marmesat E, Soriano L, Mazzoni CJ, Sommer S, Godoy JA. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches. PLoS One 2016; 11:e0157402. [PMID: 27294261 PMCID: PMC4905633 DOI: 10.1371/journal.pone.0157402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications.
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Affiliation(s)
- Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - José A. Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
- * E-mail:
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37
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Beckers B, Op De Beeck M, Thijs S, Truyens S, Weyens N, Boerjan W, Vangronsveld J. Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies. Front Microbiol 2016; 7:650. [PMID: 27242686 PMCID: PMC4865482 DOI: 10.3389/fmicb.2016.00650] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/18/2016] [Indexed: 12/29/2022] Open
Abstract
Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high-resolution community profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant-associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non-target DNA and retrieval of bacterial OTUs.
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Affiliation(s)
- Bram Beckers
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | | | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Sascha Truyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGent, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
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38
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Wang D. Effect of internal primer–template mismatches on loop-mediated isothermal amplification. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1125765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Baek IC, Jang JP, Choi EJ, Kim TG. MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. PLoS One 2015; 10:e0142467. [PMID: 26569110 PMCID: PMC4646348 DOI: 10.1371/journal.pone.0142467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/22/2015] [Indexed: 11/25/2022] Open
Abstract
Major histocompatibility complex (MHC) class I chain-related gene B (MICB) encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8+ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE) on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI), whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024) present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations.
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Affiliation(s)
- In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Ho TH, Dang KX, Lintula S, Hotakainen K, Feng L, Olkkonen VM, Verschuren EW, Tenkanen T, Haglund C, Kolho KL, Stenman UH, Stenman J. Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity. Nucleic Acids Res 2015; 43:e4. [PMID: 25378315 PMCID: PMC4288146 DOI: 10.1093/nar/gku1048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022] Open
Abstract
Here we provide the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly similar RNA variants, a reverse-transcriptase primer whose sequence matches a specific variant selectively primes only that variant, whereas mismatch priming to the alternative variant is suppressed by virtue of hybridization and subsequent extension of the perfectly matched ExBP on that alternative variant template to form a cDNA-RNA hybrid. This hybrid will render the alternative RNA template unavailable for mismatch priming initiated by the specific primer in a hot-start protocol of reverse transcription when the temperature decreases to a level where such mismatch priming could occur. The ExBP-based reverse transcription assay detected BRAF and KRAS mutations in at least 1000-fold excess of wild-type RNA and detection was linear over a 4-log dynamic range. This novel strategy not only reveals the presence or absence of rare mutations with an exceptionally high selectivity, but also provides a convenient tool for accurate determination of RNA variants in different settings, such as quantification of allele-specific expression.
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Affiliation(s)
- Tho H Ho
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Kien X Dang
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Susanna Lintula
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Kristina Hotakainen
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland Helsinki University Central Hospital, HUSLAB, Helsinki, 00029 HUS, Finland
| | - Lin Feng
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland
| | | | - Caj Haglund
- Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland Research Program Unit, Translational Cancer Biology, University of Helsinki, Helsinki, FI-00014, Finland Haartman Institute, Department of Pathology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, University of Helsinki, Helsinki, FI-00014, Finland
| | - Ulf-Hakan Stenman
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland Department of Women's and Children's Health, Karolinska Institutet, Stockholm, SE-17176, Sweden
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41
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Mathematical tools to optimize the design of oligonucleotide probes and primers. Appl Microbiol Biotechnol 2014; 98:9595-608. [PMID: 25359473 DOI: 10.1007/s00253-014-6165-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022]
Abstract
The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose.
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PRISE2: software for designing sequence-selective PCR primers and probes. BMC Bioinformatics 2014; 15:317. [PMID: 25252611 PMCID: PMC4261892 DOI: 10.1186/1471-2105-15-317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/20/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. RESULTS PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. CONCLUSIONS PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.
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43
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Jiang C, Kan YY, Jiang JH, Yu RQ. A simple and highly sensitive DNAzyme-based assay for nicotinamide adenine dinucleotide by ligase-mediated inhibition of strand displacement amplification. Anal Chim Acta 2014; 844:70-4. [PMID: 25172818 DOI: 10.1016/j.aca.2014.06.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/14/2014] [Accepted: 06/25/2014] [Indexed: 12/27/2022]
Abstract
Existing strategies for detecting nicotinamide adenine dinucleotide (NAD(+)) or other cofactors are commonly cumbersome and moderate sensitive. We report a novel DNAzyme-based visual assay strategy for NAD(+) based on ligase-mediated inhibition of the strand displacement amplification (SDA). In the presence of NAD(+), the SDA can be inhibited by the ligase reaction of two primers, which can initiate the SDA reaction in the case of no ligation, resulting in a dramatically decreasing yield of the SDA product, a G-quadruplex DNAzyme that can quantitatively catalyze the formation of a colored product. Therefore, the quantitative analysis for NAD(+) can be achieved visually with high sensitivity. The developed strategy provides a simple colorimetric approach with high selectivity against most interferences and a detection limit as low as 50 pM. It also provides a universal platform for investigating cofactors or other related small molecules as well as quantifying the activity of DNA ligases.
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Affiliation(s)
- Cheng Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Ying-Ya Kan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Byrom M, Bhadra S, Jiang YS, Ellington AD. Exquisite allele discrimination by toehold hairpin primers. Nucleic Acids Res 2014; 42:e120. [PMID: 24990378 PMCID: PMC4150758 DOI: 10.1093/nar/gku558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer.
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Affiliation(s)
- Michelle Byrom
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Sanchita Bhadra
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Sherry Jiang
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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Hou J, Liu X, Liu J. Detection of Single Nucleotide Polymorphism by RNase H-Cleavage Mediated Allele-Specific Extension Method. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Samant S, Amann RI, Hahn D. Evaluation of the 23S rRNA gene as target for qPCR based quantification of Frankia in soils. Syst Appl Microbiol 2013; 37:229-34. [PMID: 24315016 DOI: 10.1016/j.syapm.2013.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/08/2013] [Indexed: 12/30/2022]
Abstract
The 23S rRNA gene was evaluated as target for the development of Sybr Green-based quantitative PCR (qPCR) for the analysis of nitrogen-fixing members of the genus Frankia or subgroups of these in soil. A qPCR with a primer combination targeting all nitrogen-fixing frankiae (clusters 1, 2 and 3) resulted in numbers similar to those obtained with a previously developed qPCR using nifH gene sequences, both with respect to introduced and indigenous Frankia populations. Primer combinations more specifically targeting three subgroups of the Alnus host infection group (cluster 1) or members of the Elaeagnus host infection group (cluster 3) were specific for introduced strains of the target group, with numbers corresponding to those obtained by quantification of nitrogen-fixing frankiae with both the 23S rRNA and nifH genes as target. Method verification on indigenous Frankia populations in soils, i.e. in depth profiles from four sites at an Alnus glutinosa stand, revealed declining numbers in the depth profiles, with similar abundance of all nitrogen-fixing frankiae independent of 23S rRNA or nifH gene targets, and corresponding numbers of one group of frankiae of the Alnus host infection only, with no detections of frankiae representing the Elaeagnus, Casuarina, or a second subgroup of the Alnus host infection groups.
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Affiliation(s)
- Suvidha Samant
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA.
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47
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Little DP. A DNA mini-barcode for land plants. Mol Ecol Resour 2013; 14:437-46. [PMID: 24286499 DOI: 10.1111/1755-0998.12194] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/11/2013] [Accepted: 10/18/2013] [Indexed: 11/27/2022]
Abstract
Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).
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Affiliation(s)
- Damon P Little
- Cullman Program for Molecular Systematics, The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA
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48
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Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR. Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates. Environ Microbiol 2013; 16:1354-65. [PMID: 24750536 DOI: 10.1111/1462-2920.12259] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 11/29/2022]
Abstract
We describe a semi-empirical framework that combines thermodynamic models of primer hybridization with experimentally determined elongation biases introduced by 3'-end mismatches for improving polymerase chain reaction (PCR)-based sequence discrimination. The framework enables rational and automatic design of primers for optimal targeting of one or more sequences in ensembles of nearly identical DNA templates. In situations where optimal targeting is not feasible, the framework accurately predicts non-target sequences that are difficult to distinguish with PCR alone. Based on the synergistic effects of disparate sources of PCR bias, we used our framework to robustly distinguish between two alleles that differ by a single base pair. To demonstrate the applicability to environmental microbiology, we designed primers specific to all recognized archaeal and bacterial genera in the Ribosomal Database Project, and have made these primers available online. We applied these primers experimentally to obtain genus-specific amplification of 16S rRNA genes representing minor constituents of an environmental DNA sample. Our results demonstrate that inherent PCR biases can be reliably employed in an automatic fashion to maximize sequence discrimination and accurately identify potential cross-amplifications. We have made our framework accessible online as a programme for designing primers targeting one group of sequences in a set with many other sequences (http://DECIPHER.cee.wisc.edu).
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Affiliation(s)
- Erik S Wright
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin - Madison, Madison, WI, USA
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Lefever S, Pattyn F, Hellemans J, Vandesompele J. Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays. Clin Chem 2013; 59:1470-80. [PMID: 24014836 DOI: 10.1373/clinchem.2013.203653] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genome-sequencing studies have led to an immense increase in the number of known single-nucleotide polymorphisms (SNPs). Designing primers that anneal to regions devoid of SNPs has therefore become challenging. We studied the impact of one or more mismatches in primer-annealing sites on different quantitative PCR (qPCR)-related parameters, such as quantitative cycle (Cq), amplification efficiency, and reproducibility. METHODS We used synthetic templates and primers to assess the effect of mismatches at primer-annealing sites on qPCR assay performance. Reactions were performed with 5 commercially available master mixes. We studied the effects of the number, type, and position of priming mismatches on Cq value, PCR efficiency, reproducibility, and yield. RESULTS The impact of mismatches was most pronounced for the number of mismatched nucleotides and for their distance from the 3' end of the primer. In addition, having ≥4 mismatches in a single primer or having 3 mismatches in one primer and 2 in the other was required to block a reaction completely. Finally, the degree of the mismatch effect was concentration independent for single mismatches, whereas concentration independence failed at higher template concentrations as the number of mismatches increased. CONCLUSIONS Single mismatches located >5 bp from the 3' end have a moderate effect on qPCR amplification and can be tolerated. This finding, together with the concentration independence for single mismatches and the complete blocking of the PCR reaction for ≥4 mismatches, can help to chart mismatch behavior in qPCR reactions and increase the rate of successful primer design for sequences with a high SNP density or for homologous regions of sequence.
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Affiliation(s)
- Steve Lefever
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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STAT3 mutations indicate the presence of subclinical T-cell clones in a subset of aplastic anemia and myelodysplastic syndrome patients. Blood 2013; 122:2453-9. [PMID: 23926297 DOI: 10.1182/blood-2013-04-494930] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Large granular lymphocyte leukemia (LGL) is often associated with immune cytopenias and can cooccur in the context of aplastic anemia (AA) and myelodysplastic syndromes (MDS). We took advantage of the recent description of signal transducer and activator of transcription 3 (STAT3) mutations in LGL clonal expansions to test, using sensitive methods, for the presence of these mutations in a large cohort of 367 MDS and 140 AA cases. STAT3 clones can be found not only in known LGL concomitant cases, but in a small proportion of unsuspected ones (7% AA and 2.5% MDS). In STAT3-mutated AA patients, an interesting trend toward better responses of immunosuppressive therapy and an association with the presence of human leukocyte antigen-DR15 were found. MDSs harboring a STAT3 mutant clone showed a lower degree of bone marrow cellularity and a higher frequency of developing chromosome 7 abnormalities. STAT3-mutant LGL clones may facilitate a persistently dysregulated autoimmune activation, responsible for the primary induction of bone marrow failure in a subset of AA and MDS patients.
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