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Combinatorial Chemistry & High... Jun 2006Microarrays are a sensitive, specific, miniaturized devices that may be used to detect selected DNA sequences and proteins, or mutated genes associated with human... (Review)
Review
Microarrays are a sensitive, specific, miniaturized devices that may be used to detect selected DNA sequences and proteins, or mutated genes associated with human diseases. Several methods have been developed to detect the binding of complementary molecules to microarrays by generating an optical signal. One of the most commonly used molecular labeling methods at present is fluorescence, but its application is expensive due to sophisticated equipment required to design the platform, hybridize it, and interpret the images derived from microarray-based studies. This is a drawback for its use in laboratories and clinical services. Another less expensive procedure having similar sensitivity and specificity is DNA and protein functional nanoparticles (FNP). Nanoparticles are sphere-like biocompatible materials made of inert silica, metal or crystals of a nanometer in size, which are generally coated with a thin gold layer. They may be used as hybridization probes in single nucleotide polymorphism (SNP) screening and to detect biological markers for cancer, infection, and cardiovascular diseases.
Topics: Biomarkers; Biosensing Techniques; Cardiovascular Diseases; Fluorescence; Humans; Infections; Microarray Analysis; Nanostructures; Nanotechnology; Neoplasms; Nucleic Acid Hybridization; Polymorphism, Single Nucleotide; Quantum Dots; Sensitivity and Specificity
PubMed: 16787152
DOI: 10.2174/138620706777452438 -
Pediatric Neurology Dec 2009The chromosomal microarray now plays a central role in the evaluation of children with neurologic developmental disorders, including global developmental delay, mental... (Review)
Review
The chromosomal microarray now plays a central role in the evaluation of children with neurologic developmental disorders, including global developmental delay, mental retardation, and increasingly also autistic spectrum disorders. As arrays become more sophisticated and their use more widespread, the child neurologist is likely to encounter abnormal chromosomal microarray results. The interpretation of such data is not always straightforward. This review article discusses in a practical manner the nature of chromosomal microarray results, describes an algorithm to help the child neurologist navigate a variety of testing scenarios, and proposes a standardized system for ranking array data based on levels of evidence of genotype-phenotype correlation.
Topics: Child; Chromosomes; DNA Copy Number Variations; Developmental Disabilities; Humans; Microarray Analysis; Nervous System Diseases; Practice Guidelines as Topic
PubMed: 19931159
DOI: 10.1016/j.pediatrneurol.2009.05.003 -
European Journal of Obstetrics,... May 2017This study aimed to evaluate the detection rate of chromosomal microarray analysis (CMA) in prenatal fetuses compared with conventional karyotype and to assess the...
OBJECTIVES
This study aimed to evaluate the detection rate of chromosomal microarray analysis (CMA) in prenatal fetuses compared with conventional karyotype and to assess the additional diagnostic yields of CMA in groups of different indications.
STUDY DESIGN
A total of 217 fetuses were divided into seven groups according to different indications. All cases were tested by both CMA and karyotype. The detection rates of CMA and karyotype were evaluated. The increased value of CMA in each group was also calculated.
RESULTS
A total of 35 cases were detected to have a pathogenic result by CMA, indicating the overall detection rate of 16.1%. Nine more cases were detected only by CMA, indicating an incremental diagnostic yield of 4.2%. The highest incremental value was observed in fetuses with structural defects (6.6%). In 11 cases with known abnormal chromosome anomalies, CMA revealed additional information over conventional karyotyping in 4 fetuses.
CONCLUSIONS
The present study convincingly demonstrated the efficiency of CMA in detecting feal chromosomal rearrangements. CMA significantly improves the detection rate in fetuses with structural defects and provides helpful information for fetuses with known abnormal chromosomes but without clear diagnosis.
Topics: China; Chromosome Aberrations; Chromosome Disorders; Female; Humans; Karyotyping; Microarray Analysis; Pregnancy; Prenatal Diagnosis; Retrospective Studies
PubMed: 28340467
DOI: 10.1016/j.ejogrb.2017.03.007 -
Chemical Society Reviews Mar 2007This tutorial review introduces the uninitiated to the world of microarrays (or so-called chips) and covers a number of basic concepts such as substrates and surfaces,... (Review)
Review
This tutorial review introduces the uninitiated to the world of microarrays (or so-called chips) and covers a number of basic concepts such as substrates and surfaces, printing and analysis. It then moves on to look at some newer applications of microarray technology, which include enzyme analysis (notably kinases and proteases) as well as the growing enchantment with so-called cell-based microarrays that offer a unique approach to high-throughput cellular analysis. Finally, it looks forwards and highlights future possible trends and directions in the microarray arena.
Topics: Animals; Cells, Cultured; Enzymes, Immobilized; Humans; Microarray Analysis
PubMed: 17325784
DOI: 10.1039/b511848b -
BMC Bioinformatics Dec 2015Microarray analysis represents a powerful way to test scientific hypotheses on the functionality of cells. The measurements consider the whole genome, and the large...
BACKGROUND
Microarray analysis represents a powerful way to test scientific hypotheses on the functionality of cells. The measurements consider the whole genome, and the large number of generated data requires sophisticated analysis. To date, no gold-standard for the analysis of microarray images has been established. Due to the lack of a standard approach there is a strong need to identify new processing algorithms.
METHODS
We propose a novel approach based on hyperbolic partial differential equations (PDEs) for unsupervised spot segmentation. Prior to segmentation, morphological operations were applied for the identification of co-localized groups of spots. A grid alignment was performed to determine the borderlines between rows and columns of spots. PDEs were applied to detect the inflection points within each column and row; vertical and horizontal luminance profiles were evolved respectively. The inflection points of the profiles determined borderlines that confined a spot within adapted rectangular areas. A subsequent k-means clustering determined the pixels of each individual spot and its local background.
RESULTS
We evaluated the approach for a data set of microarray images taken from the Stanford Microarray Database (SMD). The data set is based on two studies on global gene expression profiles of Arabidopsis Thaliana. We computed values for spot intensity, regression ratio, and coefficient of determination. For spots with irregular contours and inner holes, we found intensity values that were significantly different from those determined by the GenePix Pro microarray analysis software. We determined the set of differentially expressed genes from our intensities and identified more activated genes than were predicted by the GenePix software.
CONCLUSIONS
Our method represents a worthwhile alternative and complement to standard approaches used in industry and academy. We highlight the importance of our spot segmentation approach, which identified supplementary important genes, to better explains the molecular mechanisms that are activated in a defense responses to virus and pathogen infection.
Topics: Algorithms; Cluster Analysis; Gene Expression; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Software
PubMed: 26698293
DOI: 10.1186/s12859-015-0842-3 -
Chemical Society Reviews Jan 2010This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical... (Review)
Review
This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.
Topics: Animals; Humans; Microarray Analysis; Molecular Imaging; Oligonucleotide Array Sequence Analysis; Optical Fibers; Protein Array Analysis; Tissue Array Analysis
PubMed: 20023835
DOI: 10.1039/b809339n -
BMC Bioinformatics Sep 2008Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in...
BACKGROUND
Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.
RESULTS
A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.
CONCLUSION
The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.
Topics: Database Management Systems; Information Dissemination; Information Storage and Retrieval; Internet; Microarray Analysis; Research Design; User-Computer Interface
PubMed: 18801157
DOI: 10.1186/1471-2105-9-379 -
The Analyst Mar 2007Microarray techniques use a combinatorial approach to assess complex biochemical interactions. The fundamental goal is simultaneous, large-scale experimentation... (Review)
Review
Microarray techniques use a combinatorial approach to assess complex biochemical interactions. The fundamental goal is simultaneous, large-scale experimentation analogous to the automation achieved in the semiconductor industry. However, microarray deposition inherently involves liquids contacting solid substrates. Liquid droplet shapes are determined by surface and interfacial tension forces, and flows during drying. This article looks at how surface free energy and wetting considerations may influence the accuracy and reliability of spotted microarray experiments.
Topics: Chemical Phenomena; Chemistry, Physical; Dust; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Pressure; Surface Properties; Water; Wettability
PubMed: 17325750
DOI: 10.1039/b617339j -
Methods in Molecular Biology (Clifton,... 2017Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening... (Review)
Review
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
Topics: Microarray Analysis; Small Molecule Libraries
PubMed: 27873196
DOI: 10.1007/978-1-4939-6584-7_1 -
Annual Review of Analytical Chemistry... 2015DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by... (Review)
Review
DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by which molecular recognition assays can be performed and analyzed. Cell microarrays (CMAs) make use of similar construction principles. They are applied to profile a given cell population with respect to the expression of specific molecular markers and also to measure functional cell responses to drugs and chemicals. This review focuses on the use of cell-based microarrays for assessing the cytotoxicity of drugs, toxins, or chemicals in general. It also summarizes CMA construction principles with respect to the cell types that are used for such microarrays, the readout parameters to assess toxicity, and the various formats that have been established and applied. The review ends with a critical comparison of CMAs and well-established microtiter plate (MTP) approaches.
Topics: Animals; Biomarkers; Cell Physiological Phenomena; Dose-Response Relationship, Drug; Humans; Microarray Analysis; Toxicology
PubMed: 26077916
DOI: 10.1146/annurev-anchem-071213-020051