Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Oligonucleotide Array Sequence Analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54Linked to original sources
PubMed2006

Genetically distinct and clinically relevant subtypes of glioblastoma defined by array-based comparative genomic hybridization (array-CGH).

To optimize treatment strategies for patients with glioblastoma, a more precise understanding of the molecular basis of this disease clearly is necessary. Therefore, numerous studies have focused on the molecular biology of glioblastoma and its linkage to clinical behavior. Here we investigated 70 glioblastomas using the array-based comparative genomic hybridization (array-CGH) with GenoSensor Array 300 to identify recurrent DNA copy number imbalances associated with patient outcomes. Univariate log-rank analysis of array-CGH data revealed 46 copy number aberrations (CNAs) associated with outcome. Among them, 26 CNAs were associated with shortened survival whereas the remaining 20 CNAs correlated with good prognosis. A hierarchical cluster analysis disclosed two genetically distinct groups of glioblastomas (1 and 2; 56 and 14 tumors, respectively). Univariate log-rank test discerned significant difference in survival between both genetic subsets while the 5-year survival rate consisted of 0 for group 1 and 63% for group 2. Multivariate analysis revealed that unfavorable genetic signature is an independent prognostic factor increasing a risk of patient death (hazard ratio, 4.38; P=0.00001). In conclusion, our current study suggests that glioblastomas can be subdivided into clinically relevant genetic subsets. Therefore, array-CGH screening of glioblastomas could provide clinically useful information and, perhaps, potentially improve the quality of treatment.

Adult↗
PubMed2000

Constraint structure analysis of gene expression.

A microarray experiment gives a snapshot of the state of an organism in terms of the relative abundances of its mRNA transcripts, locating the organism at a point in a high dimensional state space where each axis represents the relative expression level of a single gene. Multiple experiments generate a cloud of points in this gene expression space. We present a geometric approach to analyzing the covariational properties of such a cloud and use a dataset from Saccharomyces cerevisiae as an illustration. In particular, we use singular value decomposition to identify significant linear sub-structures in the data and analyze the contributions of both individual genes and functional classes of genes to these major directions of variation. Analyzing the publicly available yeast expression data, we show that under all experimental conditions the variation in expression is limited to a small number of linear dimensions. Projections of individual gene axes onto the significant dimensions can order the contribution of individual genes to variation in expression within an experiment. We show that no particular groups of genes characterize particular experimental conditions. Instead, the particular structure of the coordinated expression of the entire genome characterizes a particular experiment.

Gene Expression↗
PubMed2006

The early dark-response in Arabidopsis thaliana revealed by cDNA microarray analysis.

Despite intense research on light responses in plants, the consequences of a simple shift from light to darkness remain poorly characterized. We have examined the transcriptome of Arabidopsis thaliana seedling leaves upon a shift from constant light to darkness for between 1 and 8 h, while excluding most effects associated with circadian oscillation. Expression clustering and gene ontology analyses identified about 790 responsive genes implicated in diverse cellular processes. Compared to the better-studied long-term dark adaptation response, the early response to darkness is partially overlapping yet clearly distinct, encompassing early transient, early sustained, and late response clusters. The repressor of photomorphogenesis, COP1 (constitutive photomorphogenic 1), is not a chief regulator of the early response to darkness, in contrast to its well-established role during long-term dark adaptation and etiolation. Only part of the early dark response can be understood as the opposite of the response following a dark-to-light transition and as a response to sugar deprivation. Bioinformatic comparisons with published microarray datasets further suggest that abscisic acid (ABA) signaling plays a prominent role in the early response to darkness, although this effect is not mediated by an increase in the ABA level. The potential basis for the co-regulation by darkness and ABA is discussed in light of sugar and redox signaling.

Abscisic Acid↗
PubMed2002

DNA microarrays in prostate cancer.

DNA microarray technology provides a means to examine large numbers of molecular changes related to a biological process in a high throughput manner. This review discusses plausible utilities of this technology in prostate cancer research, including definition of prostate cancer predisposition, global profiling of gene expression patterns associated with cancer initiation and progression, identification of new diagnostic and prognostic markers, and discovery of novel patient classification schemes. The technology, at present, has only been explored in a limited fashion in prostate cancer research. Some hurdles to be overcome are the high cost of the technology, insufficient sample size and repeated experiments, and the inadequate use of bioinformatics. With the completion of the Human Genome Project and the advance of several highly complementary technologies, such as laser capture microdissection, unbiased RNA amplification, customized functional arrays (eg, single-nucleotide polymorphism chips), and amenable bioinformatics software, this technology will become widely used by investigators in the field. The large amount of novel, unbiased hypotheses and insights generated by this technology is expected to have a significant impact on the diagnosis, treatment, and prevention of prostate cancer. Finally, this review emphasizes existing, but currently underutilized, data-mining tools, such as multivariate statistical analyses, neural networking, and machine learning techniques, to stimulate wider usage.

Algorithms↗
PubMed2004

Electrochemical study of the XNA on Gold microarray.

A novel electrode array was developed based on the XNA on Gold trade mark microarray platform. The platform combines self-assembling monolayers, thick film patterning and streptavidin based immobilization to provide a robust, versatile platform capable of analysing virtually any biomolecule including nucleic acids, proteins, carbohydrates and lipids. Electrochemical analysis of the self-assembling monolayer/streptavidin (SAMS) XNA on Gold coating revealed that the ferrocene redox current for the SAMS modified electrode was greater than that with a bare Gold electrode. The electrochemical reaction of K4Fe(CN)6 was inhibited by the SAMS coating, but was reactivated upon addition of ferrocene. These results indicate that ferrocene is involved as a mediator in the electron transfer of K4Fe(CN)6 to the SAMS modified electrode. Addition of DNA to the SAMS resulted in only a minor change in the electrochemical signal, indicating that XNA on Gold can be used for electrochemical based bioanalysis. After cycling a SAMS electrode 50 times, no signs of deterioration were detected showing that coating has excellent stability. In addition to the biosensing applications, the scheme provides a non-invasive method for accessing the quality of the SAMS coatings which is of industrial interest. These studies show that the XNA on Gold microarray platform can be used for electrochemical studies, thus providing an additional alternative for developing multianalyte biosensors as well as expanding the range of detection methods available for microarray analysis.

DNA↗
PubMed2005

Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe.

A high-resolution scanning Kelvin nanoprobe is introduced as an alternative technique to the conventional fluorescence and mass spectrometric detection methods currently employed in nucleic acid and protein microarray technology. The new instrument is capable of the highly sensitive discernment of surface biochemical events taking place at molecular level such as nucleic acid hybridization and antibody-antigen interaction. The method involves measurement of changes in work function and surface potential instigated by such interactions. Being a label-free and non-contact technique, the structure, spatial configuration, local properties or function of the molecular system under study are not affected, nor perturbed by intercalating dyes, a strong electric field or ionizing beam. Subsequent to scanning, the microarray can be examined by other alternative approaches. Nucleic acids and proteins have been printed in microarray format on slides with a gold film in place using gold-sulphur interactive chemistry. Hybridization of nucleic acids for complementary and mismatched configurations shows consistent and reproducible values of work function. Differentiation of single internal mismatches is demonstrated. Protein concentration and formation of antibody-antigen pairs can be visualized and examined with high sensitivity and good inter-spot reproducibility.

Amplifiers, Electronic↗
PubMed2005

Opto-electronic DNA chip: high performance chip reading with an all-electric interface.

Reading of DNA chips is usually based on fluorescence labeling of hybridised target molecules. Combined with the use of confocal fluorescence scanners, this approach shows very high performances in terms of accuracy and sensitivity. However, fluorescence readers remain costly and cumbersome. This prevents the use of DNA chips as a decentralised testing tool. Electrical monitoring of hybridisation is one way to reduce the cost and size of the reader. However, the multiplexing of electric detection-based systems in a miniaturised form remains challenging. Here, we present a system based on the use of a low cost CMOS photodetector array as a solid support for a DNA chip, coupled with revelation by enzyme-catalysed chemiluminescence. This system is shown to allow the detection of low pM target concentrations with a 3 logs dynamic range on dense DNA microarrays, with excellent inter-spot reproducibility. Combining electric interface and high analytical performances, this opto-electronic DNA chip is one attractive solution for nucleic acids detection and analysis in disposable, fully automatised, total analysis systems developed for decentralised testing.

Biosensing Techniques↗
PubMed2005

Enzyme-based impedimetric detection of PCR products using oligonucleotide-modified screen-printed gold electrodes.

This paper describes the optimisation and the analytical performances of an enzyme-based electrochemical genosensor, developed using disposable oligonucleotide-modified screen-printed gold electrodes. The immobilisation of a thiol-tethered probe was qualitatively investigated by means of faradic impedance spectroscopy. Impedance spectra confirmed that the thiol moiety unambiguously drives the immobilisation of the oligonucleotide probe. Furthermore, both probe surface densities and hybridisation efficiencies were quantified through chronocoulometric measurements. Electrochemical transduction of the hybridisation process was also performed by means of faradic impedance spectroscopy, after coupling of a streptavidin-alkaline phosphatase conjugate and bio-catalysed precipitation of an insoluble and insulating product onto the sensing interface. Chronocoulometric results allowed discussion of the magnitude of hybridisation signals in terms of probe surface densities and their corresponding hybridisation efficiency. The genosensor response varied linearly (r2 = 0.9998) with the oligonucleotide target concentration over three orders of magnitude, between 12 pmol/L and 12 nmol/L. The estimated detection limit was 1.2 pmol/L (i.e., 7.2 x 10(6) target molecules in 10 microL of sample solution). The analytical usefulness of the impedimetric genosensor was finally demonstrated analysing amplified samples obtained from the pBI121 plasmid and soy and maize powders containing 1 and 5% of genetically modified product. Sensing of such unmodified amplicons was achieved via sandwich hybridisation with a biotinylated signaling probe. The electrochemical enzyme-amplified assay allowed unambiguous identification of all genetically modified samples, while no significant non-specific signal was detected in the case of all negative controls.

Biosensing Techniques↗
PubMed2005

Detection of DNA recognition events using multi-well field effect devices.

We proposed the multi-well field effect device for detection of charged biomolecules and demonstrated the detection principle for DNA recognition events using quasi-static capacitance-voltage (QSCV) measurement. The multi-well field effect device is based on the electrostatic interaction between molecular charges induced by DNA recognition and surface electrons in silicon through the Si(3)N(4)/SiO(2) thin double-layer. Since DNA molecules and DNA binders such as Hoechst 33258 have intrinsic charges in aqueous solutions, respectively, the charge density changes due to DNA recognition events at the Si(3)N(4) surface were directly translated into electrical signal such as a flat band voltage change in the QSCV measurement. The average flat band shifts were 20.7 mV for hybridization and -13.5 mV for binding of Hoechst 33258. From the results of flat band voltage shifts due to hybridization and binding of Hoechst 33258, the immobilization density of oligonucleotide probes at the Si(3)N(4) surface was estimated to be 10(8) cm(-2). The platform based on the multi-well field effect device is suitable for a simple and arrayed detection system for DNA recognition events.

DNA↗
PubMed2006

Electrochemical detection of 17beta-estradiol using DNA aptamer immobilized gold electrode chip.

An electrochemical detection method for chemical sensing has been developed using a DNA aptamer immobilized gold electrode chip. DNA aptamers specifically binding to 17beta-estradiol were selected by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random ssDNA library, composed of approximately 7.2 x 10(14) DNA molecules. Gold electrode chips were employed to evaluate the electrochemical signals generated from interactions between the aptamers and the target molecules. The DNA aptamer immobilization on the gold electrode was based on the avidin-biotin interaction. The cyclic voltametry (CV) and square wave voltametry (SWV) values were measured to evaluate the chemical binding to aptamer. When 17beta-estradiol interacted with the DNA aptamer, the current decreased due to the interference of bound 17beta-estradiol with the electron flow produced by a redox reaction between ferrocyanide and ferricyanide. In the negative control experiments, the current decreased only mildly due to the presence of other chemicals.

Aptamers, Nucleotide↗
PubMed2006

A dimensionless number analysis of the hybridization process in diffusion- and convection-driven DNA microarray systems.

The present theoretical analysis aims at providing a general understanding of the combined effect the many different process variables have on the hybridization rate in diffusion- and convection-driven DNA microarray systems. It is shown that all process variables can be grouped into only four different dimensionless numbers (the Damkohler number Da, the dimensionless association constant kappa(A), the dimensionless initial concentration C'(0) and a geometrical ratio alpha). These four numbers have a straightforward physical meaning and only contain easily measurable parameters. Reducing the solution space from 7D to 4D, the dimensionless number representation greatly facilitates the insight in the conditions leading to the occurrence of diffusion-limited hybridization rates in both diffusion- and convection-driven DNA microarray systems. This in turn simplifies their design and the interpretation of the experimental results that are obtained with these systems.

Diffusion↗
PubMed2006

Analysis of polysomal mRNA populations of mouse oocytes and zygotes: dynamic changes in maternal mRNA utilization and function.

Transcriptional activation in mammalian embryos occurs in a stepwise manner. In mice, it begins at the late one-cell stage, followed by a minor wave of activation at the early two-cell stage, and then the major genome activation event (MGA) at the late two-cell stage. Cellular homeostasis, metabolism, cell cycle, and developmental events are orchestrated before MGA by time-dependent changes in the array of maternal transcripts being translated. Many elegant studies have documented the importance of maternal mRNA (MmRNA) and its correct recruitment for development. Many other studies have illuminated some of the molecular mechanisms regulating MmRNA utilization. However, neither the complete array of recruited mRNAs nor the regulatory mechanisms responsible for temporally different patterns of recruitment have been well characterized. We present a comprehensive analysis of changes in the maternal component of the zygotic polysomal mRNA population during the transition from oocyte to late one-cell stage embryo. We observe global transitions in the functional classes of translated MmRNAs and apparent changes in the underlying cis-regulatory mechanisms.

Animals↗
PubMed2004

E4F1, a novel estrogen-responsive gene in possible atheroprotection, revealed by microarray analysis.

Estrogen has been postulated to be involved in inhibition of vascular smooth muscle cell (VSMC) proliferation mainly via estrogen receptor (ER), but the detailed mechanism has remained primarily unknown. Therefore, in this study, microarray analysis was used in two types of cultured human VSMCs: one positive for ER alpha, and the other for ER beta, which were treated by estrogens to detect the estrogen-responsive genes. We also used quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) to evaluate mRNA levels of selective target gene (TG) in these cells. We further studied whether the TG product was involved in inhibition of proliferation using small interfering RNA (siRNA) of the TG transfection. We subsequently used quantitative RT-PCR and in situ hybridization analysis to evaluate the expression of these gene products in human aorta. E4F1, a possible inducer of cell growth arrest, was markedly increased only in ER alpha-positive VSMCs by estrogens in both microarray and RT-PCR analyses. Blocking of E4F1 using siRNA suppressed estrogenic inhibition of ER alpha-positive VSMC proliferation. E4F1 mRNA was abundant in premenopausal female aorta with mild atherosclerotic changes. E4F1 is therefore considered one of the estrogen-responsive genes involving ER alpha-mediated inhibition of VSMC proliferation and may play an important role in estrogen-related atheroprotection of human aorta.

Adenovirus E4 Proteins↗
PubMed2001

Basic microarray analysis: grouping and feature reduction.

DNA microarray technologies are useful for addressing a broad range of biological problems - including the measurement of mRNA expression levels in target cells. These studies typically produce large data sets that contain measurements on thousands of genes under hundreds of conditions. There is a critical need to summarize this data and to pick out the important details. The most common activities, therefore, are to group together microarray data and to reduce the number of features. Both of these activities can be done using only the raw microarray data (unsupervised methods) or using external information that provides labels for the microarray data (supervised methods). We briefly review supervised and unsupervised methods for grouping and reducing data in the context of a publicly available suite of tools called CLEAVER, and illustrate their application on a representative data set collected to study lymphoma.

Algorithms↗
PubMed2003

Directed immobilization of nucleic acids at ultramicroelectrodes using a novel electro-deposited polymer.

A two-step method for the directed immobilization of nucleic acids at ultramicroelectrodes with micron-size dimensions is described. The approach is based on the immobilization of streptavidin at the surface of carbon or noble metal electrodes within a novel electro-deposited polymer, formed by electropolymerization of the natural compound scopoletin (7-hydroxy-6-methoxy-coumarin) at potentials between 0.4 and 0.7 V vs. Ag/AgCl. Biotin-tagged nucleic acids or proteins are immobilized on top of the modified electrodes in a second step. The new method has some advantages compared to classical electropolymerization approaches (e.g. polypyrrole, polyphenol), because the growing polymer is highly hydrophilic, resulting in efficient incorporation of streptavidin and a high biotin binding capacity of 6 pmol cm(-2). The polymer film seems to be non-conductive but shows good swelling properties in aqueous solutions. The feasibility of the method for the electro-directed biochemical modification of individual microelectrodes has been demonstrated by sequential immobilization of two different single strand oligonucleotides onto interdigitated ultramicroelectrodes. The resulting miniature DNA probe was used for single base mutation detection with two synthetic targets (fluorescence-labeled 17-mer oligomers) by evaluating the fluorescence patterns after hybridisation with the immobilised DNA probes. The new method is useful for the production of microelectrode based DNA chips and for the electro-directed immobilisation of biomolecules at microelectrode structures with high spatial resolution and yield.

Adsorption↗
PubMed2004

DNA detection by integrable electronics.

This paper presents a new electronic methodology to detect DNA hybridization for rapid identification of diseases, as well as food and environmental monitoring on a genetic base. The proposed solution exploits a new (electrical) capacitive measurement circuit, not requiring any prior labeling of the DNA (as it is often the case with the commonly employed optical detection). The sensitivity, the reliability, and the reproducibility of this device have been evaluated by experiments performed with a (non-integrated) prototype implementation, easily integrable in IC and/or micro-fabricated lab-on-a-chip.

Adsorption↗