Mutational analysis using oligonucleotide microarrays

Hacia, Joseph G.; Collins, Francis S.

doi:10.1136/jmg.36.10.730

Cited by 116 publications

(62 citation statements)

References 54 publications

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“…Hybridizationbased assays and the microarray format provide an extremely versatile technology. There is an increasingly broad range of applications to which microarrays have been applied, including genotyping of polymorphisms and mutations (39 ), determining the binding sites of DNA-binding proteins (40 ), and identifying structural alterations by use of arrayed comparative genome hybridization approaches (41 ). The most widespread use of this technology to date has been the analysis of gene expression.…”

Section: Urinary Tumor Biomarkers In Bladder Cancermentioning

confidence: 99%

Use of High-Throughput DNA Microarrays to Identify Biomarkers for Bladder Cancer

Sänchez‐Carbayo

2003

Clinical Chemistry

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Background: Numerous markers have been described to correlate to some extent with tumor stage and prognosis of patients with bladder cancer. The power of many of these biomarkers in detecting superficial disease or predicting the clinical outcome of individual tumors is limited, and alternative markers are still in demand. High-throughput microarrays represent novel means for cancer research and tumor marker discovery. Approach: The aim of this report was to discuss the application of DNA technologies to provide novel biomarkers for bladder cancer. Content: Specific bladder tumor subtypes have distinct gene expression profiles. The use of high-throughput DNA microarrays allows identification of the most prevalent and relevant alterations within bladder tumors. Clusters of differentially expressed genes will become biomarkers to discriminate subgroups of patients with different histopathology or clinical outcome. Additionally, the identified individual molecular targets might be further validated and developed into novel serum or urinary biomarkers for the diagnosis and/or as prognostic factors to be applied in clinical practice. The diagnosis and prognosis of bladder cancer would be enhanced by the use of such markers, and the marker itself may constitute a therapeutic target when studied in appropriate patients and control groups. Summary: Expression profiling with high-throughput DNA microarrays has the potential of providing critical clues for the management of bladder cancer patients. As the quality, standardization, and ease of use of the technology increase and the costs decrease, DNA microarrays will move from being a technology restricted to research to clinical laboratories in the near future.

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Section: Urinary Tumor Biomarkers In Bladder Cancermentioning

confidence: 99%

Use of High-Throughput DNA Microarrays to Identify Biomarkers for Bladder Cancer

Sänchez‐Carbayo

2003

Clinical Chemistry

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“…DNA microarrays are currently used for gene expression profiling (18,25), DNA sequencing (24), disease screening (17), diagnostics (9,29), and genotyping (14), usually within the context of clinical applications. The extension of microarray technology to the detection and analysis of 16S rRNAs in mixed microbial communities likewise holds tremendous potential for microbial community analysis, pathogen detection, and process monitoring in both basic and applied environmental sciences (7,12,27).…”

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confidence: 99%

Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays

Chandler

Newton²,

Small³

et al. 2003

Appl Environ Microbiol

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A two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rRNAs from environmental samples on oligonucleotide arrays. In this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16S rRNA detection for the dissimilatory metal and sulfate reducer 16S rRNAs. Microarray specificity was deduced by analyzing signal intensities across replicate microarrays with a statistical analysis-of-variance model that accommodates well-to-well and slide-to-slide variations in microarray signal intensity. Chaperone detector probes located in immediate proximity to the capture probe resulted in detectable, nonspecific binding of nontarget rRNA, presumably due to base-stacking effects. Species-specific rRNA detection was achieved by using a 22-nt capture probe and a 15-nt detector probe separated by 10 to 14 nt along the primary sequence. Chaperone detector probes with up to three mismatched nucleotides still resulted in species-specific capture of 16S rRNAs. There was no obvious relationship between position or number of mismatches and within-or between-genus hybridization specificity. From these results, we conclude that relieving secondary structure is of principal concern for the successful capture and detection of 16S rRNAs on planar surfaces but that the sequence of the capture probe is more important than relieving secondary structure for achieving specific hybridization.DNA microarrays are currently used for gene expression profiling (18, 25), DNA sequencing (24), disease screening (17), diagnostics (9, 29), and genotyping (14), usually within the context of clinical applications. The extension of microarray technology to the detection and analysis of 16S rRNAs in mixed microbial communities likewise holds tremendous potential for microbial community analysis, pathogen detection, and process monitoring in both basic and applied environmental sciences (7,12,27). The application of microarrays for unattended in-field or point-of-use environmental applications, however, frequently involves requirements to (i) detect many different microorganisms simultaneously, (ii) utilize a bioanalytical detection method that is conducive to automation and/or field deployment, (iii) monitor RNA as a qualitative indicator of microbial activity, and (iv) quantify RNA levels and/or the extent of microbial activity. Such requirements are especially pertinent for monitoring changes in microbial community composition and activity through time and space. Thus, continued use of microarray protocols that rely on PCR amplification represents a significant bottleneck for the routine application and deployment of microarrays in the field and highlights the need to develop sensitive and specific direct RNA detection methods for environmental samples.There are several rep...

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“…Oligonucleotide biochips are promising tools for molecular biology-based diagnosis due to their ability to perform a multitude of tests simultaneously (3-5, 9, 11, 12, 22, 26, 28). Biochips enable the rapid identification of mutations in thousands of genes as well as gene products with desired properties, such that much information about biomolecules can be collected on various scales in a short time (13)(14)(15). Although biochip technologies present their own challenges, they have been used extensively in surveys of gene expression (4,20,28), for the detection of genetic polymorphisms (9), and for the serological detection of pathogens (10) and have been broadly used to screen clinical samples for microorganisms and to characterize microorganisms (3,4,12).…”

mentioning

confidence: 99%

Detection of gyrA and parC Mutations Associated with Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of Oligonucleotide Biochip Technology

Zhou

Cao

et al. 2004

J Clin Microbiol

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An oligonucleotide biochip that specifically detects point mutations in the gyrA and parC genes of Neisseria gonorrhoeae was designed and subsequently evaluated with 87 untreated clinical specimens. The susceptibilities of the N. gonorrhoeae strains were tested to determine the prevalence of ciprofloxacin-resistant strains in Anhui Province, People's Republic of China. Conventional DNA sequencing was also performed to identify mutations in gyrA and parC and to confirm the biochip data. The study demonstrates that all of the point mutations in the gyrA and parC genes of N. gonorrhoeae were easily discriminated by use of the oligonucleotide biochip. Fifteen different alteration patterns involved in the formation of ciprofloxacin resistance were identified by the biochip assay. Double mutations in both Ser91 and Asp95 of the GyrA protein were seen in all nonsensitive isolates. Double mutations in Ser91 and Asp95 of GyrA plus mutation of Glu91 or Ser87 of the ParC protein lead to significant high-level resistance to ciprofloxacin in N. gonorrhoeae isolates. The results obtained by use of the oligonucleotide biochip were identical to those obtained by use of DNA sequencing. In conclusion, the oligonucleotide biochip technology has potential utility for the rapid and reliable identification of point mutations in the drug resistance genes of N. gonorrhoeae.

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Mutational analysis using oligonucleotide microarrays

Cited by 116 publications

References 54 publications

Use of High-Throughput DNA Microarrays to Identify Biomarkers for Bladder Cancer

Use of High-Throughput DNA Microarrays to Identify Biomarkers for Bladder Cancer

Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays

Detection of gyrA and parC Mutations Associated with Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of Oligonucleotide Biochip Technology

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