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A simple and sensitive direct mRNA multiplexed detection strategy for amoA-targeted monitoring of ammonia-oxidizing activity in water environment. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Microarray technology is a multiplex analytical technique for the detection of many different analytes in a mixture of biomolecules. The detection limits for each of the analytes for which the array is designed depend on a multiplicity of reaction parameters, the array itself, and profoundly on the label and detection technology employed. Significant improvements in assay sensitivity have been achieved by optimizing all steps that affect the generation of signal and noise. Nanoparticle technology brings a new dimension to this technology by providing not only higher sensitivity but also improved specificity for hybridization-based microarray assay systems.
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Poulsen L, Søe MJ, Møller LB, Dufva M. Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays. PLoS One 2011; 6:e14777. [PMID: 21445337 PMCID: PMC3062541 DOI: 10.1371/journal.pone.0014777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/21/2010] [Indexed: 11/21/2022] Open
Abstract
Background The development of microarray-based genetic tests for diseases that are caused by known mutations is becoming increasingly important. The key obstacle to developing functional genotyping assays is that such mutations need to be genotyped regardless of their location in genomic regions. These regions include large variations in G+C content, and structural features like hairpins. Methods/Findings We describe a rational, stable method for screening and combining assay conditions for the genetic analysis of 42 Phenylketonuria-associated mutations in the phenylalanine hydroxylase gene. The mutations are located in regions with large variations in G+C content (20–75%). Custom-made microarrays with different lengths of complementary probe sequences and spacers were hybridized with pooled PCR products of 12 exons from each of 38 individual patient DNA samples. The arrays were washed with eight buffers with different stringencies in a custom-made microfluidic system. The data were used to assess which parameters play significant roles in assay development. Conclusions Several assay development methods found suitable probes and assay conditions for a functional test for all investigated mutation sites. Probe length, probe spacer length, and assay stringency sufficed as variable parameters in the search for a functional multiplex assay. We discuss the optimal assay development methods for several different scenarios.
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Affiliation(s)
- Lena Poulsen
- Department of Micro and Nanotechnology, DTU Nanotech, Technical University of Denmark, Lyngby, Denmark
| | - Martin Jensen Søe
- Department of Micro and Nanotechnology, DTU Nanotech, Technical University of Denmark, Lyngby, Denmark
| | - Lisbeth Birk Møller
- Department of Applied Human Molecular Genetics, Kennedy Center, Glostrup, Denmark
| | - Martin Dufva
- Department of Micro and Nanotechnology, DTU Nanotech, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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Høvik H, Chen T. Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. BMC Bioinformatics 2010; 11:82. [PMID: 20144223 PMCID: PMC2836303 DOI: 10.1186/1471-2105-11-82] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/09/2010] [Indexed: 12/27/2022] Open
Abstract
Background Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles. Results The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position. Conclusions The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.
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Affiliation(s)
- Hedda Høvik
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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5
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Petersen J, Poulsen L, Birgens H, Dufva M. Microfludic device for creating ionic strength gradients over DNA microarrays for efficient DNA melting studies and assay development. PLoS One 2009; 4:e4808. [PMID: 19277213 PMCID: PMC2653225 DOI: 10.1371/journal.pone.0004808] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 01/07/2009] [Indexed: 11/20/2022] Open
Abstract
The development of DNA microarray assays is hampered by two important aspects: processing of the microarrays is done under a single stringency condition, and characteristics such as melting temperature are difficult to predict for immobilized probes. A technical solution to these limitations is to use a thermal gradient and information from melting curves, for instance to score genotypes. However, application of temperature gradients normally requires complicated equipment, and the size of the arrays that can be investigated is restricted due to heat dissipation. Here we present a simple microfluidic device that creates a gradient comprising zones of defined ionic strength over a glass slide, in which each zone corresponds to a subarray. Using this device, we demonstrated that ionic strength gradients function in a similar fashion as corresponding thermal gradients in assay development. More specifically, we noted that (i) the two stringency modulators generated melting curves that could be compared, (ii) both led to increased assay robustness, and (iii) both were associated with difficulties in genotyping the same mutation. These findings demonstrate that ionic strength stringency buffers can be used instead of thermal gradients. Given the flexibility of design of ionic gradients, these can be created over all types of arrays, and encompass an attractive alternative to temperature gradients, avoiding curtailment of the size or spacing of subarrays on slides associated with temperature gradients.
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Affiliation(s)
- Jesper Petersen
- Department of Haematology, Copenhagen University Hospital, Herlev, Denmark
| | - Lena Poulsen
- Department of Micro and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Henrik Birgens
- Department of Haematology, Copenhagen University Hospital, Herlev, Denmark
| | - Martin Dufva
- Department of Micro and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
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6
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Microarray-based assay for the detection of genetic variations of structural genes of West Nile virus. J Virol Methods 2008; 154:27-40. [DOI: 10.1016/j.jviromet.2008.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/09/2008] [Accepted: 09/11/2008] [Indexed: 12/11/2022]
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den Dunnen JT, White SJ. MLPA and MAPH: sensitive detection of deletions and duplications. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.14. [PMID: 18428396 DOI: 10.1002/0471142905.hg0714s51] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The detection of quantitative changes in genomic DNA, i.e., deletions and duplications or so called Copy Number Variants (CNV), is an important element of a complete mutation screening strategy. However, because of practical difficulties, screening for quantitative changes in genomic DNA is often ignored. Hitherto, the techniques available were technically challenging and laborious and thus too costly to be applied on a routine basis. The development of MAPH (Multiplex Amplifiable Probe Hybridization) and more recently MLPA (Multiplex Ligation-dependent Probe Amplification) have revived interest in the detection of deletions and duplications, primarily due to the simplicity and flexibility of these two approaches. Compared to previous technologies, e.g., Southern blotting, fluorescence in situ hybridization (FISH), quantitative PCR (qPCR), and breakpoint PCR, they have some clear advantages, including high resolution, high throughput, amenability to multiplexing, and simplicity.
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Affiliation(s)
- Johan T den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R. A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res 2008; 36:2926-38. [PMID: 18385155 PMCID: PMC2396435 DOI: 10.1093/nar/gkn133] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Well-defined relationships between oligonucleotide properties and hybridization signal intensities (HSI) can aid chip design, data normalization and true biological knowledge discovery. We clarify these relationships using the data from two microarray experiments containing over three million probes from 48 high-density chips. We find that melting temperature (Tm) has the most significant effect on HSI while length for the long oligonucleotides studied has very little effect. Analysis of positional effect using a linear model provides evidence that the protruding ends of probes contribute more than tethered ends to HSI, which is further validated by specifically designed match fragment sliding and extension experiments. The impact of sequence similarity (SeqS) on HSI is not significant in comparison with other oligonucleotide properties. Using regression and regression tree analysis, we prioritize these oligonucleotide properties based on their effects on HSI. The implications of our discoveries for the design of unbiased oligonucleotides are discussed. We propose that isothermal probes designed by varying the length is a viable strategy to reduce sequence bias, though imposing selection constraints on other oligonucleotide properties is also essential.
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Affiliation(s)
- Hairong Wei
- WiCell Research Institute, PO Box 7365, Madison, WI 53707-7365, USA
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Petersen J, Poulsen L, Petronis S, Birgens H, Dufva M. Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays. Nucleic Acids Res 2007; 36:e10. [PMID: 18063568 PMCID: PMC2241873 DOI: 10.1093/nar/gkm1081] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
DNA microarrays are generally operated at a single condition, which severely limits the freedom of designing probes for allele-specific hybridization assays. Here, we demonstrate a fluidic device for multi-stringency posthybridization washing of microarrays on microscope slides. This device is called a multi-thermal array washer (MTAW), and it has eight individually controlled heating zones, each of which corresponds to the location of a subarray on a slide. Allele-specific oligonucleotide probes for nine mutations in the beta-globin gene were spotted in eight identical subarrays at positions corresponding to the temperature zones of the MTAW. After hybridization with amplified patient material, the slides were mounted in the MTAW, and each subarray was exposed to different temperatures ranging from 22 to 40°C. When processed in the MTAW, probes selected without considering melting temperature resulted in improved genotyping compared with probes selected according to theoretical melting temperature and run under one condition. In conclusion, the MTAW is a versatile tool that can facilitate screening of a large number of probes for genotyping assays and can also enhance the performance of diagnostic arrays.
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Affiliation(s)
- Jesper Petersen
- Department of Haematology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
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Laassri M, Meseda CA, Williams O, Merchlinsky M, Weir JP, Chumakov K. Microarray assay for evaluation of the genetic stability of modified vaccinia virus Ankara B5R gene. J Med Virol 2007; 79:791-802. [PMID: 17457926 DOI: 10.1002/jmv.20889] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Adverse events associated with the use of live smallpox vaccines have led to the development of a new generation of attenuated smallpox vaccines that are prepared in cultured cells as alternatives. The inability to conduct direct clinical evaluation of their efficacy in humans demands that licensure be based on animal studies and exhaustive evaluation of their in vitro properties. One of the most important characteristics of live viral vaccines is their genetic stability, including reversion of the vaccine strain to more virulent forms, recombination with other viral sequences to produce potentially pathogenic viruses, and genetic drift that can result in decrease of immunogenicity and efficacy. To study genetic stability of an immunoessential vaccinia virus gene in a new generation smallpox vaccine, an advanced oligonucleotide microchip was developed and used to assay for mutations that could emerge in B5R gene, a vaccinia virus gene encoding for a protein that contains very important neutralizing epitopes. This microarray contained overlapping oligonucleotides covering the B5R gene of modified vaccinia virus Ankara (MVA), a well-studied candidate smallpox vaccine. The microarray assay was shown to be able to detect even a single point mutation, and to differentiate between vaccinia strains. At the same time, it could detect newly emerged mutations in clones of vaccinia strains. In the work described here, it was shown that MVA B5R gene was stable after 34 passages in Vero and MRC-5 cells that were proposed for use as cell substrates for vaccine manufacture. Potentially, the proposed method could be used as an identity test and could be extended for the entire viral genome and used to monitor consistency of vaccine production.
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Affiliation(s)
- Majid Laassri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1401 Rockville Pike, HFM 470, Rockville, Maryland 20852, USA.
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Pasternak A, Kierzek E, Pasternak K, Turner DH, Kierzek R. A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 2007; 35:4055-63. [PMID: 17567607 PMCID: PMC1919511 DOI: 10.1093/nar/gkm421] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 03/28/2007] [Accepted: 05/08/2007] [Indexed: 11/14/2022] Open
Abstract
Modified nucleotides are useful tools to study the structures, biological functions and chemical and thermodynamic stabilities of nucleic acids. Derivatives of 2,6-diaminopurine riboside (D) are one type of modified nucleotide. The presence of an additional amino group at position 2 relative to adenine results in formation of a third hydrogen bond when interacting with uridine. New method for chemical synthesis of protected 3'-O-phosphoramidite of LNA-2,6-diaminopurine riboside is described. The derivatives of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides were used to prepare complete 2'-O-methyl RNA and LNA-2'-O-methyl RNA chimeric oligonucleotides to pair with RNA oligonucleotides. Thermodynamic stabilities of these duplexes demonstrated that replacement of a single internal 2'-O-methyladenosine with 2'-O-methyl-2,6-diaminopurine riboside (D(M)) or LNA-2,6-diaminopurine riboside (D(L)) increases the thermodynamic stability (DeltaDeltaG degrees 37) on average by 0.9 and 2.3 kcal/mol, respectively. Moreover, the results fit a nearest neighbor model for predicting duplex stability at 37 degrees C. D-A and D-G but not D-C mismatches formed by D(M) or D(L) generally destabilize 2'-O-methyl RNA/RNA and LNA-2'-O-methyl RNA/RNA duplexes relative to the same type of mismatches formed by 2'-O-methyladenosine and LNA-adenosine, respectively. The enhanced thermodynamic stability of fully complementary duplexes and decreased thermodynamic stability of some mismatched duplexes are useful for many RNA studies, including those involving microarrays.
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Affiliation(s)
- Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland and Department of Chemistry and Department of Pediatrics, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland and Department of Chemistry and Department of Pediatrics, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland and Department of Chemistry and Department of Pediatrics, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
| | - Douglas H. Turner
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland and Department of Chemistry and Department of Pediatrics, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland and Department of Chemistry and Department of Pediatrics, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
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Gharaibeh RZ, Fodor AA, Gibas CJ. Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates. Comput Biol Chem 2007; 31:92-8. [PMID: 17387043 PMCID: PMC2043163 DOI: 10.1016/j.compbiolchem.2007.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 02/14/2007] [Indexed: 12/27/2022]
Abstract
High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays.
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Affiliation(s)
| | | | - Cynthia J. Gibas
- Corresponding author. Tel.: +1 704 687 8378; fax: +1 704 687 6610. E-mail address: .
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Salvado C, Cram D. Microarray Technology for Mutation Analysis of Low-Template DNA Samples. METHODS IN MOLECULAR MEDICINE™ 2007; 132:153-73. [PMID: 17876083 DOI: 10.1007/978-1-59745-298-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Microarrays containing oligonucleotide mutation probes are emerging as useful platforms for the diagnosis of genetic disease. Herein, we describe the development and validation of an in-house microarray suitable for the diagnosis of common cystic fibrosis (CF) mutations in low-template DNA samples such as those taken for preimplantation genetic diagnosis and prenatal diagnosis. The success of the CF microarray was based on the ability to generate sufficient target DNA for hybridization to the array probes using either direct polymerase chain reaction (PCR) amplification or whole-genome amplification followed by PCR. From replicate experiments using target DNA carrying known CF mutations, it was possible to define strict diagnostic parameters for the accurate diagnosis of CF. This protocol serves as a general guide for DNA-testing laboratories to develop other microarray platforms that may eventually replace traditional PCR-based genetic testing in the near future.
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Affiliation(s)
- Chelsea Salvado
- Monash Immunology and Stem Cell Laboraotires, Monash University, Melbourne, Australia
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14
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Gibbons B, Datta P, Wu Y, Chan A, AL Armour J. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA. BMC Genomics 2006; 7:163. [PMID: 16813644 PMCID: PMC1533824 DOI: 10.1186/1471-2164-7-163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 06/30/2006] [Indexed: 01/29/2023] Open
Abstract
Background Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A). Conclusion Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.
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Affiliation(s)
- Brian Gibbons
- Institute of Genetics, University of Nottingham, QMC, Nottingham NG7 2UH, UK
| | - Parikkhit Datta
- Institute of Genetics, University of Nottingham, QMC, Nottingham NG7 2UH, UK
| | - Ying Wu
- PamGene International B.V., P.O. Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands
| | - Alan Chan
- PamGene International B.V., P.O. Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands
| | - John AL Armour
- Institute of Genetics, University of Nottingham, QMC, Nottingham NG7 2UH, UK
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Anderson N, Szemes M, O'Brien P, de Weerdt M, Schoen C, Boender P, Bonants P. Use of hybridization melting kinetics for detecting Phytophthora species using three-dimensional microarrays: demonstration of a novel concept for the differentiation of detection targets. ACTA ACUST UNITED AC 2006; 110:664-71. [PMID: 16769210 DOI: 10.1016/j.mycres.2006.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
Microarray-based detection is limited by variable and inconsistent hybridization intensities across the diversity of probes used in each array. In this paper, we introduce a novel concept for the differentiation of detection targets using duplex melting kinetics. A microarray assay was developed on a PamChip microarray enabling the differentiation of target Phytophthora species using the melting kinetics of probe-target duplexes. In the majority of cases the hybridization kinetics of target and non-target duplexes differed significantly. Analysis of the melting kinetics of duplexes formed by probes with target and non-target DNA was found to be an effective method for determining specific hybridization and was independent of fluctuations in hybridization signal intensity. This form of analysis was more robust than the traditional approach based on hybridization intensity, and enabled the detection of individual Phytophthora species and mixtures thereof.
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Affiliation(s)
- Nari Anderson
- Murdoch University, South Street, Murdoch 6150, Perth Australia
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16
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Brown TJ, Herrera-Leon L, Anthony RM, Drobniewski FA. The use of macroarrays for the identification of MDR Mycobacterium tuberculosis. J Microbiol Methods 2006; 65:294-300. [PMID: 16153726 DOI: 10.1016/j.mimet.2005.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 08/05/2005] [Accepted: 08/15/2005] [Indexed: 10/25/2022]
Abstract
The emergence of Mycobacterium tuberculosis (Mtb), resistant to both isoniazid (INH) and rifampicin (RIF) (MDR-TB), is an increasing threat to tuberculosis control programs. Susceptibility testing of Mtb complex isolates by phenotypic methods requires a minimum of 14 days from a primary specimen. This can be reduced significantly if molecular analysis is used. Low density oligonucleotide arrays (macroarrays) have been used successfully for the detection of RIF resistance in Mtb. We describe the use of macroarray technology to identify Mtb complex isolates resistant to INH and/or RIF. The macroarray MDR-Mtb screen has been designed to detect mutations in the RIF resistance determining region (RRDR) of Mtb rpoB and loci in katG and mabA-inhA associated with INH resistance. A panel of Mtb isolates containing 38 different RRDR genotypes, 4 different genotypes within codon 315 of katG and 2 genotypes at mabA-inhA was used to validate the macroarray. The wild type (WT) genotype was correctly identified at all three loci. Of the 37 mutant rpoB genotypes, 36 were correctly detected; the single mutant not detected contained a 9 base insertion. All mutations within katG and mabA-inhA were correctly identified. We conclude that this low cost, rapid system can usefully detect the mutations associated with the vast majority of MDR-Mtb.
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Affiliation(s)
- T J Brown
- Health Protection Agency Mycobacterium Reference Unit, Kings College Hospital (Dulwich), East Dulwich Grove, London SE22 8QF, UK.
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17
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Savelkoul PHM, Catsburg A, Mulder S, Oostendorp L, Schirm J, Wilke H, van der Zanden AGM, Noordhoek GT. Detection of Mycobacterium tuberculosis complex with Real Time PCR: comparison of different primer-probe sets based on the IS6110 element. J Microbiol Methods 2006; 66:177-80. [PMID: 16427712 DOI: 10.1016/j.mimet.2005.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2005] [Revised: 12/12/2005] [Accepted: 12/16/2005] [Indexed: 11/25/2022]
Abstract
The sensitivity and specificity to detect Mycobacterium tuberculosis complex of four Real Time PCR primer-probe sets was compared. Three sets targeted nearly the same location on the IS6110 sequence and set 4 targeted a location 200 bp downstream on IS6110. Real Time PCR's with sets 1, 2 and 3 were carried out with co-amplification of a modified target as an internal amplification control. By testing identical DNA samples it was shown that small changes in primer and probe sequences result in differences in the performance of the assays, regarding analytical sensitivity and specificity.
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Affiliation(s)
- Paul H M Savelkoul
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
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18
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Koehler RT, Peyret N. Effects of DNA secondary structure on oligonucleotide probe binding efficiency. Comput Biol Chem 2005; 29:393-7. [PMID: 16290040 DOI: 10.1016/j.compbiolchem.2005.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Revised: 09/13/2005] [Accepted: 09/13/2005] [Indexed: 11/23/2022]
Abstract
Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable "window size" around target sites that is as small as possible without compromising folding algorithm prediction accuracy.
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Affiliation(s)
- Ryan T Koehler
- Applied Biosystems, Department of Bioinformatics, 850 Lincoln Centre Drive, Foster City, CA 94404, USA.
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Gibbs MJ, Armstrong JS, Gibbs AJ. Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences. BMC Bioinformatics 2005; 6:90. [PMID: 15817134 PMCID: PMC1090557 DOI: 10.1186/1471-2105-6-90] [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: 12/09/2004] [Accepted: 04/08/2005] [Indexed: 11/20/2022] Open
Abstract
Background Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, in traditional taxonomy, specimens are usually identified by 'dichotomous keys' that use combinations of characters shared by different members of the target set. Using one specific character for each target is the least efficient strategy for identification. Using combinations of shared bisectionally-distributed characters is much more efficient, and this strategy is most efficient when they separate the targets in a progressively binary way. Results We have developed a practical method for finding minimal sets of sub-sequences that identify individual sequences, and could be targeted by combinations of probes, so that the efficient strategy of traditional taxonomic identification could be used in DNA diagnosis. The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters. We found that 201 distinct cytochrome oxidase subunit-1 (CO1) genes from moths (Lepidoptera) were distinguished using only 15 sub-sequences 20 nucleotides long, whereas only 8–10 sub-sequences 6–10 nucleotides long were required to distinguish the CO1 genes of 92 species from the 9 largest orders of insects. Conclusion The presence/absence of sub-sequences in a set of gene sequences can be used like the questions in a traditional dichotomous taxonomic key; hybridisation probes complementary to such sub-sequences should provide a very efficient means for identifying individual species, subtypes or genotypes. Sequence diversity and sub-sequence length are the major factors that determine the numbers of distinguishing sub-sequences in any set of sequences.
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Affiliation(s)
- Mark J Gibbs
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
| | - John S Armstrong
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
| | - Adrian J Gibbs
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
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Lu SE, Wang N, Wang J, Chen ZJ, Gross DC. Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:324-333. [PMID: 15828684 DOI: 10.1094/mpmi-18-0324] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The salA gene is a key regulatory element for syringomycin production by Pseudomonas syringae pv. syringae and encodes a member of the LuxR regulatory protein family. Previous studies revealed that salA, a member of the GacS/GacA signal transduction system, was required for bacterial virulence, syringomycin production, and expression of the syrB1 synthetase gene. To define the SalA regulon, the spotted oligonucleotide microarray was constructed using gene-specific 70-mer oligonucleotides of all open reading frames (ORFs) predicted in the syringomycin (syr) and syringopeptin (syp) gene clusters along with representative genes important to bacterial virulence, growth, and survival. The microarray containing 95 oligos was used to analyze transcriptional changes in a salA mutant (B301DSL07) and its wild-type strain, B301D. Expression of 16 genes was significantly higher (> twofold) in B301D than in the salA mutant; the maximum change in expression was 15-fold for some toxin biosynthesis genes. Except for the sylD synthetase gene for syringolin production, all ORFs controlled by SalA were located in the syr-syp genomic island and were associated with biosynthesis, secretion, and regulation of syringomycin and syringopeptin. The positive regulatory effect of SalA on transcription of sypA, syrB1, syrC, and sylD was verified by reporter fusions or real-time polymerase chain reaction analysis. None of the genes or ORFs was significantly down-regulated by the salA gene. These results demonstrated that a subgenomic oligonucleotide microarray is a powerful tool for defining the SalA regulon and its relationship to other genes important to plant pathogenesis.
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Affiliation(s)
- Shi-En Lu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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Blaskovic D, Barák I. Oligo-chip based detection of tick-borne bacteria. FEMS Microbiol Lett 2005; 243:473-8. [PMID: 15686852 DOI: 10.1016/j.femsle.2005.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Revised: 12/16/2004] [Accepted: 01/07/2005] [Indexed: 11/24/2022] Open
Abstract
We have developed an oligonucleotide-chip based assay for detection of 16S ribosomal PCR products from tick-borne bacteria. This chip contains 14 specific probes, which target variable regions of 16S rDNA of tick-borne bacteria including Borrellia spp., Rickettsia spp., Anaplasma spp., Coxiella burnetii and Francisella tularensis. The specificity of these probes was tested by hybridization of the chip with fluorescently labeled PCR products amplified from the genomic DNA of selected tick-borne bacteria. The assay was also tested for detection of tick-borne bacteria in single ticks.
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Affiliation(s)
- Dusan Blaskovic
- Institute of Molecular Biology, Centre of Excellence for Molecular Medicine, Slovak Academy of Sciences, 845 51 Bratislava 45, Slovak Republic
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Wade MM, Volokhov D, Peredelchuk M, Chizhikov V, Zhang Y. Accurate mapping of mutations of pyrazinamide-resistant Mycobacterium tuberculosis strains with a scanning-frame oligonucleotide microarray. Diagn Microbiol Infect Dis 2004; 49:89-97. [PMID: 15183857 DOI: 10.1016/j.diagmicrobio.2004.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 01/08/2004] [Indexed: 12/22/2022]
Abstract
The increasing emergence of drug-resistant Mycobacterium tuberculosis poses significant threat to the treatment of tuberculosis. Conventional susceptibility testing for the front-line tuberculosis drug pyrazinamide (PZA) is difficult, because of the requirement for acid pH for the drug to show activity. Resistance to PZA in M. tuberculosis is caused by mutations in the pncA gene, and detection of pncA mutations can be an indicator of PZA resistance. In this study, we examined the feasibility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect pncA mutations (substitutions, deletions, and insertions) in multiple strains of PZA-resistant M. tuberculosis. The genetic mapping of these mutations is necessary to link the gene sequence to the protein function defined by mutant phenotype. Microarray analysis was performed in a blind manner using 57 isolates of M. tuberculosis for which the sequence of the pncA gene was previously determined. Our results showed that all mutations could be unambiguously detected, suggesting that microarray can be a routine and valuable tool for rapid identification of drug-resistant M. tuberculosis isolates. We expect that mutation mapping with a sliding-frame microarray will accelerate the molecular analysis of drug-resistant M. tuberculosis bacteria and the microorganism populations.
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Affiliation(s)
- Mary Margaret Wade
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Li ES, Liu WT. DNA Microarray Technology in Microbial Ecology Studies-Principle, Applications and Current Limitations. Microbes Environ 2003. [DOI: 10.1264/jsme2.18.175] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Emily S.Y. Li
- Department of Civil Engineering, National University of Singapore
| | - Wen-Tso Liu
- Department of Civil Engineering, National University of Singapore
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