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Pablo-Fontecha V, Hernández-Illán E, Reparaz A, Asensio E, Morata J, Tonda R, Lahoz S, Parra C, Lozano JJ, García-Heredia A, Martínez-Roca A, Beltran S, Balaguer F, Jover R, Castells A, Trullàs R, Podlesniy P, Camps J. Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers. Sci Rep 2023; 13:18997. [PMID: 37923774 PMCID: PMC10624686 DOI: 10.1038/s41598-023-39874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/01/2023] [Indexed: 11/06/2023] Open
Abstract
Somatic single-nucleotide variants (SNVs) occur every time a cell divides, appearing even in healthy tissues at low frequencies. These mutations may accumulate as neutral variants during aging, or eventually, promote the development of neoplasia. Here, we present the SP-ddPCR, a droplet digital PCR (ddPCR) based approach that utilizes customized SuperSelective primers aiming at quantifying the proportion of rare SNVs. For that purpose, we selected five potentially pathogenic variants identified by whole-exome sequencing (WES) occurring at low variant allele frequency (VAF) in at-risk colon healthy mucosa of patients diagnosed with colorectal cancer or advanced adenoma. Additionally, two APC SNVs detected in two cancer lesions were added to the study for WES-VAF validation. SuperSelective primers were designed to quantify SNVs at low VAFs both in silico and in clinical samples. In addition to the two APC SNVs in colonic lesions, SP-ddPCR confirmed the presence of three out of five selected SNVs in the normal colonic mucosa with allelic frequencies ≤ 5%. Moreover, SP-ddPCR showed the presence of two potentially pathogenic variants in the distal normal mucosa of patients with colorectal carcinoma. In summary, SP-ddPCR offers a rapid and feasible methodology to validate next-generation sequencing data and accurately quantify rare SNVs, thus providing a potential tool for diagnosis and stratification of at-risk patients based on their mutational profiling.
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Affiliation(s)
- Verónica Pablo-Fontecha
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - Eva Hernández-Illán
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Andrea Reparaz
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Elena Asensio
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Jordi Morata
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Raúl Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Carolina Parra
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
| | - Juan José Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Anabel García-Heredia
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Alejandro Martínez-Roca
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Francesc Balaguer
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010, Alicante, Spain
| | - Antoni Castells
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain
| | - Ramon Trullàs
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Petar Podlesniy
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Rosselló 149-153, 4th Floor, 08036, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029, Madrid, Spain.
- Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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2
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Oh C, Kim K, Araud E, Wang L, Shisler JL, Nguyen TH. A novel approach to concentrate human and animal viruses from wastewater using receptors-conjugated magnetic beads. WATER RESEARCH 2022; 212:118112. [PMID: 35091223 DOI: 10.1016/j.watres.2022.118112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
Viruses are present at low concentrations in wastewater; therefore, an effective method for concentrating virus particles is necessary for accurate wastewater-based epidemiology (WBE). We designed a novel approach to concentrate human and animal viruses from wastewater using porcine gastric mucin-conjugated magnetic beads (PGM-MBs). We systematically evaluated the performances of the PGM-MBs method (sensitivity, specificity, and robustness to environmental inhibitors) with six viral species, including Tulane virus (a surrogate for human norovirus), rotavirus, adenovirus, porcine coronavirus (transmissible gastroenteritis virus or TGEV), and two human coronaviruses (NL63 and SARS-CoV-2) in influent wastewater and raw sewage samples. We determined the multiplication factor (the ratio of genome concentration of the final solution to that of the initial solution) for the PGM-MBs method, which ranged from 1.3 to 64.0 depending on the viral species. Because the recovery efficiency was significantly higher when calculated with virus titers than it was with genome concentration, the PGM-MBs method could be an appropriate tool for assessing the risk to humans who are inadvertently exposed to wastewater contaminated with infectious viruses. Furthermore, PCR inhibitors were not concentrated by PGM-MBs, suggesting that this tool will be successful for use with environmental samples. In addition, the PGM-MBs method is cost-effective (0.5 USD/sample) and has a fast turnaround time (3 h from virus concentration to genome quantification). Thus, this method can be implemented in high throughput facilities. Because of its strong performance, intrinsic characteristics of targeting the infectious virus, robustness to wastewater, and adaptability to high throughput systems, the PGM-MBs method can be successfully applied to WBE and ultimately provides valuable public health information.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States.
| | - Kyukyoung Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, United States
| | - Elbashir Araud
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana-Champaign
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, United States
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3
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Iqbal F, Shabbir MI. Genetic analysis with pyrosequencing using loop pipetting and a light dependent resistor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5035-5047. [PMID: 34647115 DOI: 10.1039/d1ay01123e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA sequencing is among the most important techniques in biology to decipher the key genetic players of health and disease. The existing laboratory instruments for DNA sequencing are well established and reliable. However, these instruments are still out of reach of most laboratories in the world due to very high equipment and running costs and require trained personnel to keep them running. These instruments are also large and bulky making them unsuitable for analysis in remote settings away from laboratories. Here we describe a proof-of-concept of a DNA sequencing device LoopSeeq using a simple approach to address the said problems without minimizing the quality of results. The device was designed to perform pyrosequencing by iterative addition of dNTPs by contact dispensing through a loop pipette (loopette) and detection of chemiluminiscence with the cheapest sensor in the market, a light dependent resistor (LDR). Two small geared motors drive the moving parts in a controlled and coordinated manner with the help of a motor driver circuit, an Arduino Nano microcontroller and two small neodymium magnets. The real-time light intensity data from the LDR were transferred to a laptop computer for further analysis. Pyrosequencing was optimized using 55 nt self-primed oligo. In order to demonstrate the DNA sequencing ability with real samples, molecular genetic analysis was performed for a previously identified novel mutation from our lab in exon4 of the OCA2 gene. LoopSeeq successfully identified the homozygous normal (c.408-409_AA), homozygous mutant (c.408-409_delAA) and heterozygous carrier (c.408-409_AA/delAA) alleles in three individuals of a family affected with oculocutaneous albinism (OCA). Further, this can be implemented for molecular diagnostic applications for bacterial, viral or other pathogen detection and genotyping among different subtypes following some reports described earlier. A few drawbacks in the current implementation including the evaporation of liquid reagents, possible loopette contamination, etc. associated with use for longer times are also described along with suggestions to rectify these problems in future designs. With the described capabilities, the LoopSeeq device can be implemented in routine labs as well as in several real-world situations where conventional DNA sequencing instruments are unfeasible, for example, diagnostic testing at remote settings or at the point-of-care.
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Affiliation(s)
- Faisal Iqbal
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
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4
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Lee HH, Kalhor R, Goela N, Bolot J, Church GM. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat Commun 2019; 10:2383. [PMID: 31160595 PMCID: PMC6546792 DOI: 10.1038/s41467-019-10258-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
DNA is an emerging medium for digital data and its adoption can be accelerated by synthesis processes specialized for storage applications. Here, we describe a de novo enzymatic synthesis strategy designed for data storage which harnesses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) in kinetically controlled conditions. Information is stored in transitions between non-identical nucleotides of DNA strands. To produce strands representing user-defined content, nucleotide substrates are added iteratively, yielding short homopolymeric extensions whose lengths are controlled by apyrase-mediated substrate degradation. With this scheme, we synthesize DNA strands carrying 144 bits, including addressing, and demonstrate retrieval with streaming nanopore sequencing. We further devise a digital codec to reduce requirements for synthesis accuracy and sequencing coverage, and experimentally show robust data retrieval from imperfectly synthesized strands. This work provides distributive enzymatic synthesis and information-theoretic approaches to advance digital information storage in DNA. Adoption of DNA as a data storage medium could be accelerated with specialized synthesis processes and codecs. The authors describe TdT-mediated DNA synthesis in which data is stored in transitions between non-identical nucleotides and the use of synchronization markers to provide error tolerance.
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Affiliation(s)
- Henry H Lee
- Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA. .,Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, 02115, MA, USA.
| | - Reza Kalhor
- Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA.,Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, 02115, MA, USA
| | - Naveen Goela
- Technicolor Research & Innovation Lab, Palo Alto, 94306, CA, USA
| | - Jean Bolot
- Technicolor Research & Innovation Lab, Palo Alto, 94306, CA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA. .,Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, 02115, MA, USA.
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5
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Pandey A, Yadav V, Sharma A, Khurana JP, Pandey GK. The unc-53 gene negatively regulates rac GTPases to inhibit unc-5 activity during Distal tip cell migrations in C. elegans. Cell Adh Migr 2017; 12:195-203. [PMID: 28678595 DOI: 10.1080/19336918.2017.1345413] [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: 10/18/2022] Open
Abstract
The unc-53/NAV2 gene encodes for an adaptor protein required for cell migrations along the anteroposterior (AP) axes of C. elegans. This study identifies unc-53 as a novel component of signaling pathways regulating Distal tip cell (DTC) migrations along the AP and dorsoventral (DV) axes. unc-53 negatively regulates and functions downstream of ced-10/Rac pathway genes; ced-10/Rac and mig-2/RhoG, which are required for proper DTC migration. Moreover, unc-53 exhibits genetic interaction with abl-1 and unc-5, the 2 known negative regulators of ced-10/Rac signaling. Our genetic analysis supports the model, where abl-1 negatively regulates unc-53 during DTC migrations and requirement of unc-53 function during both AP and DV DTC migrations could be due to unc-53 mediated regulation of unc-5 activity.
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Affiliation(s)
- Amita Pandey
- a Department of Plant Molecular Biology , University of Delhi South Campus , New Delhi , India
| | - Vipul Yadav
- b Department of Genetics , University of Delhi South Campus , New Delhi , India
| | - Aditi Sharma
- a Department of Plant Molecular Biology , University of Delhi South Campus , New Delhi , India
| | - Jitendra P Khurana
- a Department of Plant Molecular Biology , University of Delhi South Campus , New Delhi , India
| | - Girdhar K Pandey
- a Department of Plant Molecular Biology , University of Delhi South Campus , New Delhi , India
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6
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Du W, Lv M, Li J, Yu R, Jiang J. A ligation-based loop-mediated isothermal amplification (ligation-LAMP) strategy for highly selective microRNA detection. Chem Commun (Camb) 2016; 52:12721-12724. [DOI: 10.1039/c6cc06160e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel ligation-based loop-mediated isothermal amplification (ligation-LAMP) method has been developed for sensitive and selective detection of microRNA.
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Affiliation(s)
- Wenfang Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Mengmei Lv
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Junjie Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
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7
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Abstract
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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Affiliation(s)
- Max Käller
- AlbaNova University Center, School of Biotechnology, Department of Gene Technology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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8
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Abstract
CONTEXT DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined. OBJECTIVE To demonstrate the fundamental principles of pyrosequencing. DATA SOURCES Salient features of pyrosequencing are demonstrated using the free software program Pyromaker ( http://pyromaker.pathology.jhmi.edu ), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results. CONCLUSIONS We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.
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Affiliation(s)
- Colleen T Harrington
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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9
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Liu XP, Hou JL, Liu JH. A novel single nucleotide polymorphism detection of a double-stranded DNA target by a ribonucleotide-carrying molecular beacon and thermostable RNase HII. Anal Biochem 2009; 398:83-92. [PMID: 19891952 DOI: 10.1016/j.ab.2009.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/26/2009] [Accepted: 10/29/2009] [Indexed: 12/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation. SNPs are important markers that link sequence variations to phenotypic changes. Because of the importance of SNPs in the life and medical sciences, a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. In this article, we describe a novel method for SNP genotyping based on differential fluorescence emission due to cleavage by Thermus thermophilus RNase HII (TthRNase HII) of DNA heteroduplexes containing an SNP site-specific chimeric DNA-rN(1)-DNA molecular beacon (cMB). We constructed a loop sequence for a cMB that contains a single SNP-specific ribonucleotide at the central site. When the cMB probe is hybridized to a target double-stranded DNA (dsDNA), a perfect match of the cMB/DNA duplex permits efficient cleavage with TthRNase HII, whereas a mismatch in the duplex due to an SNP greatly reduces efficiency. Cleavage efficiency is measured by the incremental difference of fluorescence emission of the beacon. We show that the genotypes of 10 individuals at 12 SNP sites across a series of human leukocyte antigen (HLA) can be determined correctly with respect to conventional DNA sequencing. This novel TthRNase HII-based method offers a platform for easy and accurate SNP analysis.
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Affiliation(s)
- Xi-Peng Liu
- College of Life Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Abstract
The increasing need for large-scale genotyping applications of single nucleotide polymorphisms (SNPs) in model and nonmodel organisms requires the development of low-cost technologies accessible to minimally equipped laboratories. The method presented here allows efficient discrimination of SNPs by allele-specific PCR in a single reaction with standard PCR conditions. A common reverse primer and two forward allele-specific primers with different tails amplify two allele-specific PCR products of different lengths, which are further separated by agarose gel electrophoresis. PCR specificity is improved by the introduction of a destabilizing mismatch within the 30 end of the allele-specific primers. This is a simple and inexpensive method for SNP detection that does not require PCR optimization.
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Affiliation(s)
- Muriel Gaudet
- Department of Forest Resources and Environment (DiSAFRi), University of Tuscia, Viterbo, Italy
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11
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Toubanaki DK, Christopoulos TK, Ioannou PC, Gravanis A. Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis. Hum Mutat 2008; 29:1071-8. [DOI: 10.1002/humu.20774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Hou J, Liu X, Zheng Y, Liu J. A method for HLA genotyping using the specific cleavage of DNA-rN1-DNA/DNA with RNase HII from Chlamydia pneumoniae. Oligonucleotides 2008; 17:433-43. [PMID: 18154453 DOI: 10.1089/oli.2007.0090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single nucleotide polymorphisms (SNPs) provide a great opportunity for the study of human disease and bacterial drug resistance. However, many SNP typing techniques require dedicated instruments and high cost. Here, we develop a novel method for SNP genotyping based on specific cleavage properties of RNase HII from Chlamydia pneumoniae (CpRNase HII), termed the "CpRNase HII-based method." CpRNase HII cleaves the DNA-rN(1)-DNA/DNA duplex at the 5'-side of the ribonucleotide (rN(1) = one ribonucleotide). Moreover, the cleavage efficiencies of the perfectly matched DNA-rN(1)-DNA/DNA duplexes are higher than those carrying a mismatched ribonucleotide. DNA-rN(1)-DNA fragments are modified with a fluorophore at the 5'-end and a quencher at the 3'-end to generate molecular beacons (MBs), which hybridize with single-stranded DNA (analyte) to be cleaved by CpRNase HII. As perfectly matched duplexes can be cleaved efficiently and mismatched duplexes cannot, CpRNase HII-catalyzed reactions can differentiate between one-nucleotide variations on the DNA-rN(1)-DNA/DNA duplexes. We have validated this method with nine SNPs of the HLA gene, which were successfully determined by endpoint measurements of fluorescence intensity. The new method is simple and effective, because the design of MBs is easy, and all steps of the genotyping consist of simple additions of solutions and incubation. This method will be suitable for large-scale genotyping.
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Affiliation(s)
- Jingli Hou
- College of Life Science & Technology, Shanghai Jiaotong University, Shanghai, People's Republic of China
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13
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Wu Z, Luo J, Ge Q, Zhang D, Wang Y, Jia C, Lu Z. Allele-specific extension on microarray for DNA methylation analysis. Anal Chim Acta 2007; 603:199-204. [DOI: 10.1016/j.aca.2007.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 09/04/2007] [Accepted: 09/05/2007] [Indexed: 11/30/2022]
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14
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Yu X, Susa M, Weile J, Knabbe C, Schmid RD, Bachmann TT. Rapid and sensitive detection of fluoroquinolone-resistant Escherichia coli from urine samples using a genotyping DNA microarray. Int J Med Microbiol 2007; 297:417-29. [PMID: 17482874 DOI: 10.1016/j.ijmm.2007.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/26/2007] [Accepted: 03/13/2007] [Indexed: 11/28/2022] Open
Abstract
Urinary tract infections (UTI) are among the most common bacterial infections in humans, with Escherichia coli being the major cause of infection. Fluoroquinolone resistance of uropathogenic E. coli has increased significantly over the last decade. In this study a microarray-based assay was developed and applied, which provides a rapid, sensitive and specific detection of fluoroquinolone-resistant E. coli in urine. The capture probes were designed against previously identified and described hotspots for quinolone resistance (codons 83 and 87 of gyrA). The key goals of this development were to reduce assay time while increasing the sensitivity and specificity as compared with a pilot version of a gyrA genotyping DNA microarray. The performance of the assay was demonstrated with pure cultures of 30 E. coli isolates as well as with urine samples spiked with 6 E. coli isolates. The microarray results were confirmed by standard DNA sequencing and were in full agreement with the phenotypic antimicrobial susceptibility testing using standard methods. The DNA microarray test displayed an assay time of 3.5h, a sensitivity of 100CFU/ml, and the ability to detect fluoroquinolone-resistant E. coli in the presence of a 10-fold excess of fluoroquinolone-susceptible E. coli cells. As a consequence, we believe that this microarray-based determination of antibiotics resistance has a true potential for the application in clinical routine laboratories in the future.
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Affiliation(s)
- Xiaolei Yu
- Institute of Technical Biochemistry, University of Stuttgart, Germany
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15
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Nussenzveig RH, Swierczek SI, Jelinek J, Gaikwad A, Liu E, Verstovsek S, Prchal JF, Prchal JT. Polycythemia vera is not initiated by JAK2V617F mutation. Exp Hematol 2007; 35:32-8. [PMID: 17198871 DOI: 10.1016/j.exphem.2006.11.012] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 11/27/2006] [Accepted: 11/29/2006] [Indexed: 01/31/2023]
Abstract
OBJECTIVE The somatic JAK2(V617F) mutation is seen in most polycythemia vera (PV) patients; however, it is not clear if JAK2(V617F) is the PV-initiating mutation. METHODS In order to examine this issue, we developed a novel real-time quantitative allele-specific PCR, in which allelic discrimination is enhanced by the synergistic effect of a mismatch in the -1 position, and a locked nucleic acid (LNA) nucleoside at the -2 position. RESULTS Determination of allelic frequencies was reproducible (SD = 1.5%) and sensitive--0.1% mutant allele detected in 40 ng of DNA. The JAK2(V617F) frequency in clonal granulocytes from 3 PV females was less than 50% (27.5 +/- 11) and in 7 females greater than 50% (75 +/- 10.5). We also found that wild-type JAK2 BFU-E colonies from PV patients can grow without erythropoietin. The identification of the primary genetic lesion resulting in PV is essential for the development of novel therapeutic strategies. CONCLUSION Our studies correlating the frequency of JAK2(V617F) mutant allele and clonality, as well as the presence of homozygous wild-type JAK2 erythropoietin-independent erythroid colonies, provide compelling evidence that the JAK2(V617F) is not the PV-initiating mutation. This supports a model wherein the JAK2(V617F) mutation arises as a secondary genetic event. Furthermore, our results indicate that an undefined molecular lesion, preceding JAK2(V617F), is responsible for clonal hematopoiesis in PV. We conclude that development of therapeutic strategies that target the JAK2(V617F) clonal cells may not be sufficient for eradication of PV.
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Affiliation(s)
- Roberto H Nussenzveig
- Department of Leukemia, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
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16
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Apostolidis AP, Apostolou PK, Georgiadis A, Sandaltzopoulos R. Rapid identification of Salmo trutta lineages by multiplex PCR utilizing primers tailored to discriminate single nucleotide polymorphisms (SNPs) of the mitochondrial control region. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9239-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Käller M, Hultin E, Holmberg K, Persson ML, Odeberg J, Lundeberg J, Ahmadian A. Comparison of PrASE and Pyrosequencing for SNP Genotyping. BMC Genomics 2006; 7:291. [PMID: 17107626 PMCID: PMC1657021 DOI: 10.1186/1471-2164-7-291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 11/16/2006] [Indexed: 11/10/2022] Open
Abstract
Background There is an imperative need for SNP genotyping technologies that are cost-effective per sample with retained high accuracy, throughput and flexibility. We have developed a microarray-based technique and compared it to Pyrosequencing. In the protease-mediated allele-specific extension (PrASE), the protease constrains the elongation reaction and thus prevents incorrect nucleotide incorporation to mismatched 3'-termini primers. Results The assay is automated for 48 genotyping reactions in parallel followed by a tag-microarray detection system. A script automatically visualizes the results in cluster diagrams and assigns the genotypes. Ten polymorphic positions suggested as prothrombotic genetic variations were analyzed with Pyrosequencing and PrASE technologies in 442 samples and 99.8 % concordance was achieved. In addition to accuracy, the robustness and reproducibility of the technique has been investigated. Conclusion The results of this study strongly indicate that the PrASE technology can offer significant improvements in terms of accuracy and robustness and thereof increased number of typeable SNPs.
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Affiliation(s)
- Max Käller
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Emilie Hultin
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
| | - Kristina Holmberg
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
| | | | - Jacob Odeberg
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
- Department of Medicine, Atherosclerosis Research Unit, King Gustaf V Research Institute, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
| | - Afshin Ahmadian
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden
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18
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Tintle NL, Ahn K, Mendell NR, Gordon D, Finch SJ. Characteristics of replicated single-nucleotide polymorphism genotypes from COGA: Affymetrix and Center for Inherited Disease Research. BMC Genet 2005; 6 Suppl 1:S154. [PMID: 16451615 PMCID: PMC1866780 DOI: 10.1186/1471-2156-6-s1-s154] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Genetic Analysis Workshop 14 provided re-genotyped single-nucleotide polymorphism (SNP) data. Specifically, both Center for Inherited Disease Research (CIDR) and Affymetrix genotyped the same 11,560 SNPs from the Affymetrix GeneChip Mapping 10K Array marker set on the same 184 individuals from the Collaborative Study on the Genetics of Alcoholism database. While the inconsistency rate between CIDR and Affymetrix (two different genotypes for the same subject) was low (0.2%), the non-replication rate (two different genotypes for the same subject or one identified genotype and one missing genotype) was substantial (9.5%). The missing data could be from no-call regions, which is inconsistent with recent recommendations about the use of no-call regions in association tests. In addition, no-call regions would suggest that the actual inconsistency rate is higher than reported. A high inconsistency rate has significant impact on power in related hypothesis tests. In addition, the data are consistent with assumptions made in a recently proposed likelihood ratio test of association for re-genotyped data.
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Affiliation(s)
- Nathan L Tintle
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794 USA
| | - Kwangmi Ahn
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794 USA
| | - Nancy Role Mendell
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794 USA
| | - Derek Gordon
- Laboratory of Statistical Genetics, Rockefeller University, New York, New York, 10021 USA
| | - Stephen J Finch
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794 USA
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19
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Käller M, Hultin E, Zheng B, Gharizadeh B, Wallin KL, Lundeberg J, Ahmadian A. Tag-array based HPV genotyping by competitive hybridization and extension. J Virol Methods 2005; 129:102-12. [PMID: 15979736 DOI: 10.1016/j.jviromet.2005.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 05/03/2005] [Accepted: 05/04/2005] [Indexed: 01/09/2023]
Abstract
A method is described for HPV genotyping based on multiplex competitive hybridization (MUCH) combined with apyrase mediated allele-specific extension (AMASE). Two type-specific oligonucleotides were designed for each of the 23 investigated HPV types and directed towards two highly inter-type heterogeneous regions. The type-specific oligonucleotides were allowed to compete in the hybridization to an immobilized template resulting in a highly specific hybridization process. To increase further the specificity, a second step of type discrimination was used in which specific extension of 3'-termini matched oligonucleotides was performed. The 46 type-specific oligonucleotides each had a unique tag sequence to allow detection via an array of oligonucleotides complementary to the tags. To evaluate the genotyping assay, a total of 92 HPV positive samples were tested in this study. Twelve had double infections and five had three to five coexisting HPV types. The results show that MUCH-AMASE can readily detect multiple infections, whereas conventional dideoxy sequencing resulted in ambiguous sequence. Four samples with three to five genotypes detected were cloned and individual clones were sequenced. The cloning procedure verified the MUCH-AMASE results with indications that we can find minor infections (<2% relative amounts). We can thus conclude that the developed assay is highly sensitive, with improved throughput and with excellent possibility to detect multiple infections.
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Affiliation(s)
- Max Käller
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm, Sweden
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20
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Ahmadian A, Ehn M, Hober S. Pyrosequencing: history, biochemistry and future. Clin Chim Acta 2005; 363:83-94. [PMID: 16165119 DOI: 10.1016/j.cccn.2005.04.038] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Accepted: 04/27/2005] [Indexed: 01/21/2023]
Abstract
BACKGROUND Pyrosequencing is a DNA sequencing technology based on the sequencing-by-synthesis principle. METHODS The technique is built on a 4-enzyme real-time monitoring of DNA synthesis by bioluminescence using a cascade that upon nucleotide incorporation ends in a detectable light signal (bioluminescence). The detection system is based on the pyrophosphate released when a nucleotide is introduced in the DNA-strand. Thereby, the signal can be quantitatively connected to the number of bases added. Currently, the technique is limited to analysis of short DNA sequences exemplified by single-nucleotide polymorphism analysis and genotyping. Mutation detection and single-nucleotide polymorphism genotyping require screening of large samples of materials and therefore the importance of high-throughput DNA analysis techniques is significant. In order to expand the field for pyrosequencing, the read length needs to be improved. CONCLUSIONS Th pyrosequencing system is based on an enzymatic system. There are different current and future applications of this technique.
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Affiliation(s)
- Afshin Ahmadian
- Department of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
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21
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Hultin E, Käller M, Ahmadian A, Lundeberg J. Competitive enzymatic reaction to control allele-specific extensions. Nucleic Acids Res 2005; 33:e48. [PMID: 15767273 PMCID: PMC1065263 DOI: 10.1093/nar/gni048] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here, we present a novel method for SNP genotyping based on protease-mediated allele-specific primer extension (PrASE), where the two allele-specific extension primers only differ in their 3′-positions. As reported previously [Ahmadian,A., Gharizadeh,B., O'Meara,D., Odeberg,J. and Lundeberg,J. (2001), Nucleic Acids Res., 29, e121], the kinetics of perfectly matched primer extension is faster than mismatched primer extension. In this study, we have utilized this difference in kinetics by adding protease, a protein-degrading enzyme, to discriminate between the extension reactions. The competition between the polymerase activity and the enzymatic degradation yields extension of the perfectly matched primer, while the slower extension of mismatched primer is eliminated. To allow multiplex and simultaneous detection of the investigated single nucleotide polymorphisms (SNPs), each extension primer was given a unique signature tag sequence on its 5′ end, complementary to a tag on a generic array. A multiplex nested PCR with 13 SNPs was performed in a total of 36 individuals and their alleles were scored. To demonstrate the improvements in scoring SNPs by PrASE, we also genotyped the individuals without inclusion of protease in the extension. We conclude that the developed assay is highly allele-specific, with excellent multiplex SNP capabilities.
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Affiliation(s)
| | | | - Afshin Ahmadian
- To whom correspondence should be addressed. Tel: +46 8 5537 8333; Fax: +46 8 5537 8481;
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22
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Wang D, Zhu L, Jiang D, Ma X, Zhou Y, Cheng J. Direct detection of 16S rRNA using oligonucleotide microarrays assisted by base stacking hybridization and tyramide signal amplification. ACTA ACUST UNITED AC 2005; 59:109-20. [PMID: 15163522 DOI: 10.1016/j.jbbm.2003.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Accepted: 10/23/2003] [Indexed: 11/18/2022]
Abstract
A simple method has been developed and validated for direct, sensitive detection and specific identification of 16S rRNA. We first report our direct investigation of discrimination efficiency for sequence variations in RNA using oligonucleotide microarrays assisted by base stacking hybridization, and demonstrate that the sequence variations of double base substitution, single base substitution and single base deletion in RNA could be directly identified. With the help of tyramide signal amplification (TSA), the detection sensitivity of this method for four clinically important bacterial species was below 0.5, 5, 1 and 1 ng of total RNA, which are 100-1000 fold more sensitive than the published methods.
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Affiliation(s)
- Dong Wang
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, PR China
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23
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Yu X, Susa M, Knabbe C, Schmid RD, Bachmann TT. Development and validation of a diagnostic DNA microarray to detect quinolone-resistant Escherichia coli among clinical isolates. J Clin Microbiol 2004; 42:4083-91. [PMID: 15364994 PMCID: PMC516282 DOI: 10.1128/jcm.42.9.4083-4091.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The incidence of resistance against fluoroquinolones among pathogenic bacteria has been increasing in accordance with the worldwide use of this drug. Escherichia coli is one of the most relevant species for quinolone resistance. In this study, a diagnostic microarray for single-base-mutation detection was developed, which can readily identify the most prevalent E. coli genotypes leading to quinolone resistance. Based on genomic sequence analysis using public databases and our own DNA sequencing results, two amino acid positions (83 and 87) on the A subunit of the DNA gyrase, encoded by the gyrA gene, have been identified as mutation hot spots and were selected for DNA microarray detection. Oligonucleotide probes directed against these two positions were designed so that they could cover the most important resistance-causing and silent mutations. The performance of the array was validated with 30 clinical isolates of E. coli from four different hospitals in Germany. The microarray results were confirmed by standard DNA sequencing and were in full agreement with phenotypic antimicrobial susceptibility testing.
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Affiliation(s)
- Xiaolei Yu
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
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24
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Käller M, Ahmadian A, Lundeberg J. Microarray-based AMASE as a novel approach for mutation detection. Mutat Res 2004; 554:77-88. [PMID: 15450406 DOI: 10.1016/j.mrfmmm.2004.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 03/16/2004] [Accepted: 03/26/2004] [Indexed: 11/26/2022]
Abstract
Alterations in the p53 tumor suppressor gene are important events in many cases of human cancers. We have developed a novel microarray based approach for re-sequencing and mutation detection of the p53 gene. The method facilitates rapid and simple scanning of the target gene sequence and could be expanded to include other candidate cancer genes. The methodology employs the previously described apyrase-mediated allele-specific extension reaction (AMASE). In order to re-sequence the selected region, four extension oligonucleotides with different 3'-termini were used for each base position and they were covalently attached to the glass slide's surface. The amplified single-stranded DNA templates were then hybridized to the array followed by in situ extension with fluorescently labeled dNTPs in the presence of apyrase. The model system used was based on analysis of a 15 bp stretch in exon 5 of the p53 gene. Mutations were scored as allelic fractions calculated as (wt)/(wt + mut) signals. When apyrase was included in the extension reactions of wild type templates, the mean allelic fraction was 0.96. When apyrase was excluded with the same wild type templates, significantly lower allelic fractions were obtained. Two 60-mer synthetic oligonucleotides were used to establish the detectable amount of mutations with AMASE and a clear distinction between all the points could be made. Several samples from different stages of skin malignancies were also analyzed. The results from this study imply the possibility to efficiently and accurately re-sequence the entire p53 gene with AMASE technology.
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Affiliation(s)
- Max Käller
- Department of Biotechnology, The Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
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25
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Russom A, Tooke N, Andersson H, Stemme G. Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device. J Chromatogr A 2004; 1014:37-45. [PMID: 14558610 DOI: 10.1016/s0021-9673(03)01033-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.
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Affiliation(s)
- Aman Russom
- Department of Signals, Sensors and Systems, Microsystem Technology, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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26
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Gharizadeh B, Käller M, Nyrén P, Andersson A, Uhlén M, Lundeberg J, Ahmadian A. Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays. Nucleic Acids Res 2004; 31:e146. [PMID: 14602939 PMCID: PMC275583 DOI: 10.1093/nar/gng147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Detection and identification of microbial pathogens are important for disease diagnosis, treatment and prophylaxis measurements. By introducing an innovative technique, we show a robust, reliable and accurate microarray-based method for identification of microbial pathogens. The technique utilizes a unique combination of multiplex competitive hybridization, which enhances hybridization accuracy of oligonucleotides to the specific target, and apyrase-mediated allele-specific extension, which improves specific extension. As a model system, different clinically relevant human papillomaviruses were selected for this study. The method generated accurate results and proves to be promising for specific and correct microbial and viral typing.
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Affiliation(s)
- Baback Gharizadeh
- Department of Biotechnology, Stockholm Center for Physics, Astronomy and Biotechnology, Royal Institute of Technology (KTH), Roslagstullbacken 21, SE-106 91 Stockholm, Sweden
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27
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Latorra D, Campbell K, Wolter A, Hurley JM. Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers. Hum Mutat 2003; 22:79-85. [PMID: 12815597 DOI: 10.1002/humu.10228] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The specificity and reliability of locked nucleic acid (LNA) substitution at the 3' position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3' LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3' LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3' LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3' LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP genotyping applications.
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28
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Affiliation(s)
- Sambasivarao Damaraju
- Polyomx Program (www.polyomx.org), Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
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29
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Mouritzen P, Nielsen AT, Pfundheller HM, Choleva Y, Kongsbak L, Møller S. Single nucleotide polymorphism genotyping using locked nucleic acid (LNA). Expert Rev Mol Diagn 2003; 3:27-38. [PMID: 12528362 DOI: 10.1586/14737159.3.1.27] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Locked nucleic acid (LNA) is a new class of bicyclic high affinity DNA analogs. LNA-containing oligonucleotides confer significantly increased affinity against their complementary DNA targets, increased mismatch discrimination (delta Tm) and allow full control of the melting point of the hybridization reaction. LNA chemistry is completely compatible with the traditional DNA phosphoramidite chemistry and therefore LNA-DNA mixmer oligonucleotides can be designed with complete freedom for optimal performance. These properties render LNA oligonucleotides very well suited for SNP genotyping and have enabled several approaches for enzyme-independent SNP genotyping based on allele-specific hybridization. In addition, allele-specific PCR assays relying on enzymatically-enhanced discrimination can be improved using LNA-modified oligonucleotides. The use of LNA transforms enzyme-independent genotyping approaches into experimentally simple, robust and cost-effective assays, which are highly suited for genotyping in clinical and industrial settings.
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30
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O'Meara D, Ahmadian A, Odeberg J, Lundeberg J. SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays. Nucleic Acids Res 2002; 30:e75. [PMID: 12140337 PMCID: PMC137093 DOI: 10.1093/nar/gnf074] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This study reports the development of a microarray-based allele-specific extension method for typing of single nucleotide polymorphisms (SNPs). The use of allele-specific primers has been employed previously to identify single base variations but it is acknowledged that certain mismatches are not refractory to extension. Here we have overcome this limitation by introducing apyrase, a nucleotide-degrading enzyme, to the extension reaction. We have shown previously that DNA polymerases exhibit slower reaction kinetics when extending a mismatched primer compared with a matched primer. This kinetic difference is exploited in the apyrase-mediated allele-specific extension (AMASE) assay, allowing incorporation of nucleotides when the reaction kinetics are fast but degrading the nucleotides before extension when the reaction kinetics are slow. Here we show that five homozygous variants (14% of the total number of variants) that were incorrectly scored in the absence of apyrase were correctly typed when apyrase was included in the extension reaction. AMASE was performed in situ on the oligonucleotide microarrays using fluorescent nucleotides to type 10 SNPs and two indels in 17 individuals generating approximately 200 genotypes. Cluster analysis of these data shows three distinct clusters with clear-cut boundaries. We conclude that SNP typing on oligonucleotide microarrays by AMASE is an efficient, rapid and accurate technique for large-scale genotyping.
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Affiliation(s)
- Deirdre O'Meara
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
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