A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences

Coelho, Valéria de Mello; Hess, Krista L.

doi:10.1590/s0100-879x2005001000011

“…Target cDNA sequences, radioactively or fluorescently labeled during RNA reverse transcription, are hybridized on the solid matrix. Hybridization signals are acquired and processed by computational programs [4,5]. The gene expression profiles obtained are used to perform class comparison or class predictioncontrol-disease, tissue-tissue, cancer grades, pretreatment-treated, drug response, survival, cross-species, age-dependant changes, etc-.…”

Section: Cdna Microarraysmentioning

confidence: 99%

Microarray Gene Expression Profiling in Meningiomas and Schwannomas

Martinez-Glez¹,

Franco-Hernandez²,

Rey

³

2008

CMC

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Microarray gene expression profiling is a high throughput system recently used in basic and applied research. It provides a large amount of data -at molecular level- that once acquired, must be functionally integrated in order to find common patterns within a defined group of biological samples. In addition to identification of differentially expressed genes and the establishment of gene regulation patterns, microarrays may also allow us to discover new tumor markers that could have a great impact on the improvement of clinical practice and therapeutics for cancer. The classification method used for cancer is currently based on the morphological characteristics of the biological samples. The information obtained with this method is limited, omitting many important tumor characteristics like the proliferation rate, the capacity of invasion and metastases, as well as the possible development of mechanisms of cellular resistance to treatment. Microarrays can be used in combination with conventional diagnostics as a helpful complement. In this review we focus on how this technology has contributed to our knowledge of the molecular pathogenesis of meningiomas and schwannomas, its potential role as a useful tool for tumor classification and its application in clinical practice.

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“…There is also a high degree of interrelations among tested genes (Li & Luan, 2005; Mello-Coelho & Hess, 2005). In our previous study, after initial filtering with paired t -tests, we applied an alternative strategy of examining the genes passing this filter in the context of underlying biological processes based on prior knowledge in the database of the Gene Ontology (GO) consortium (Ashburner et al, 2000).…”

mentioning

confidence: 99%

Prospective Study of Metal Fume-Induced Responses of Global Gene Expression Profiling in Whole Blood

Wang¹,

Neuberg

²

,

Li³

et al. 2008

Inhalation Toxicology

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Metal particulate inhalation causes pulmonary and cardiovascular diseases. Our previous results showed that systemic responses to short-term occupational welding-fume exposure could be assessed by microarray analyses in whole-blood total RNA sampled before and after exposure. To expand our understanding of the duration of particulate-induced gene expression changes, we conducted a study using a similar population 1 yr after the original study and extended our observations in the postexposure period. We recruited 15 individuals with welding fume exposure and 7 nonexposed individuals. Thirteen of the 22 individuals (9 in exposed group and 4 in nonexposed group) had been monitored in the previous study. Whole-blood total RNA was analyzed at 3 time points, including baseline, immediately following exposure (approximately 5 h after baseline), and 24 h after baseline, using cDNA microarray technology. We replicated the patterns of Gene Ontology (GO) terms associated with response to stimulus, cell death, phosphorus metabolism, localization, and regulation of biological processes significantly enriched with altered genes in the nonsmoking exposed group. Most of the identified genes had opposite expression changes between the exposure and postexposure periods in nonsmoking welders. In addition, we found dose-dependent patterns that were affected by smoking status. In conclusion, short-term occupational exposure to metal particulates causes systemic responses in the peripheral blood. Furthermore, the acute particulate-induced effects on gene expression profiling were transient in nonsmoking welders, with most effects diminishing within 19 h following exposure.Copyright © Informa UK Ltd.Address correspondence to Zhaoxi Wang, MD, PhD, 665 Huntington Avenue, I-1404B, Boston, MA 02115, USA. E-mail: mikewang@hsph.harvard.edu. NIH Public Access Author ManuscriptInhal Toxicol. Author manuscript; available in PMC 2009 November 1. Published in final edited form as:Inhal Toxicol. 2008 November ; 20(14): 1233-1244. doi:10.1080/08958370802192874. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptAmbient particulate exposure increases morbidity and mortality from respiratory and cardiovascular diseases (Samet et al., 2000; Peters et al., 2001a). The welding process generates high levels of respirable metal particulate, and is associated with increased prevalence of inflammatory lung diseases and adverse cardiovascular effects (El-Zein et al., 2003;Antonini, 2003;Donaldson et al., 2005). A cohort study demonstrated that occupational exposure to welding fumes significantly increased the risk of myocardial infarction (Sjogren et al., 2002). It has been proposed that inhaled particulates from air pollution may cause systemic alterations, in addition to effects on the autonomic nervous system, by releasing inflammatory cytokines subsequent to pulmonary inflammation (Magari et al., 2001;Liao et al., 2005). Systemic inflammation, in turn, plays an important role in the pathogenesis of atherosclerosis and coron...

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Biochips as Novel Bioassays

Rudolph

¹

,

Weber

²

,

Möller

³

2012

Handbook of Biophotonics

1

0

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The sections in this article are Introduction Types of Microarrays DNA Microarrays Protein Microarrays Tissue Microarrays Cell‐Based Microarrays (Transfection Microarrays) Principle Steps of an Experimental Microarray Process Basics Surface Biofunctionalization Preparation of Biomolecules (Sample Preparation) DNA RNA Proteins Target Amplification and Labeling PCR – Polymerase Chain Reaction In Vitro Transcription – c DNA / IVT Bio‐Barcode Amplification of Nucleic Acids and Proteins Radioactive and Fluorophore Labeling Enzymes Nanoparticles Readout/Detection Radioactivity Fluorescence/Absorbance Surface Plasmon Resonance Examples of Biochip Applications in Biology and Medicine Genomic Research SNP Detection Gene Expression Profile Analysis Pharmacogenomics and Toxicogenomics Pathogen Detection and Clinical Diagnosis Pathogen Detection Clinical Diagnosis Trends in Biochip Research Metal Nanoparticles Quantum Dots Enzymes Conclusion

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A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences

Cited by 9 publications

References 57 publications

Microarray Gene Expression Profiling in Meningiomas and Schwannomas

Microarray Gene Expression Profiling in Meningiomas and Schwannomas

Prospective Study of Metal Fume-Induced Responses of Global Gene Expression Profiling in Whole Blood

Biochips as Novel Bioassays

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