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oligonucleotide microarray expression analysis of genes whose expression is correlated with tumorigenic and non-tumorigenic phenotype of HeLa X human fibroblast hybrid cells

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CANCER LETTERS 2001年第2期165卷 201-209页

作者： Nishizuka, S Winokur, ST Simon, M Martin, J Tsujimoto, H Stanbridge, EJ Univ Calif Irvine Dept Biol Chem Irvine CA 92697 USA Kyoto Prefectural Univ Med Dept Surg Gastroenterol Kamigyo Ku Kyoto 6020841 Japan Univ Calif Irvine Dept Mol Genet & Microbiol Irvine CA 92697 USA

In order to understand the differences and similarities between tumorigenic and non-tumorigenic HeLa x human fibroblast hybrids, gene expression profiles were examined with synthetic oligonucleotide arrays containing nearly 7000 gene probe sets. We used two pairs of genetically related hybrids, each pair representing individual clones of non-tumorigenic and tumorigenic segregant hybrids, respectively. Analysis of six possible comparisons, utilizing two algorithms, identified 204 genes with differential expression. The greater number of differentially expressed genes was observed when non-tumorigenic hybrids were compared with tumorigenic segregants. Fifteen and 14 genes, respectively, were consistently found to be differentially expressed in non-tumorigenic and tumorigenic cells. Among those 29 differentially expressed genes, three (intestinal alkaline phosphatase, caveolin-1, and solute carrier family2, member3) have been reported previously to be associated with the tumorigenic phenotype, using the same hybrid pairs. In addition, among the genes previously detected by differential display, 78% of them exhibited more than 5-fold change, demonstrating a high consistency between the two methods of differential gene expression. These findings suggest that synthetic oligonucleotide arrays are a powerful and highly reproducible tool to identify those genes whose expression is associated with certain phenotypes. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved.

关键词： oligonucleotide microarray HeLa x fibroblast hybrid cell tumorigenicity differential gene expression gene expression profiling

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oligonucleotide microarray for HLA-DRB1 genotyping: preparation and clinical evaluation

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TISSUE ANTIGENS 2005年第5期65卷 467-473页

作者： Zhang, F Hu, SW Huang, J Wang, H Zhang, W Geng, YY Wang, SQ Beijing Inst Radiat Med Beijing 100850 Peoples R China Shenzhen YiShengTang Biol Med Ltd Shenzhen Peoples R China

In this study, HLA-DRB1 gene was genotyped by using the microarray technique. oligonucleotide probes were designed based on partial sequences of various genotypes of HLA-DRB1, and were fixed on a silylated slide to form a microarray. The second exon of HLA-DRB1 gene in the extracted genomic DNA samples was amplified and labelled by means of polymerase chain reaction (PCR);then it was hybridized to the microarray. The microarray was scanned, and the result was analysed in order to determine the genotypes of HLA-DRB1 of the tested sample. A total of 1574 of 1592 clinical samples had accordant results of genotypes in either microarray assay or PCR-SSP assay;8 of 10 samples that had inconsistent results of genotypes were proved to be microarray-assay reliable by confirmation of DNA sequencing. It is concluded that microarray is an alternative reliable method for HLA-DRB1 genotyping.

关键词： clinical evaluation genotyping HLA-DRB1 oligonucleotide microarray

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Patient-based cross-platform comparison of oligonucleotide microarray expression profiles

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LABORATORY INVESTIGATION 2005年第8期85卷 1024-1039页

作者： Schlingemann, J Habtemichael, N Ittrich, C Toedt, G Kramer, H Hambek, M Knecht, R Lichter, P Stauber, R Hahn, M Deutsch Krebsforschungszentrum Div Mol Genet D-69120 Heidelberg Germany Chemotherapeut Forschungsinst Georg Speyer Haus D-60596 Frankfurt Germany Deutsch Krebsforschungszentrum Cent Unit Biostat D-6900 Heidelberg Germany Goethe Univ Frankfurt Univ Klin Dept Otorhinolaryngol D-6000 Frankfurt Germany

The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether interplatform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when using the 70-mer probes. Real-time quantitative reverse transcription PCR measurements were conducted to verify expression ratios for a subset of genes and achieved good agreement regarding both array platforms. In conclusion, similar profiles of relative gene expression were obtained using arrays of either single 70-mer or multiple short 25-mer oligonucleotide probes per gene. Although qualitative assessments of the expression of individual genes have to be made with caution, our results indicate that the comparison of gene expression profiles generated on these platforms will help to discover disease-related gene signatures in general.

关键词： comparative study expression profiling head and neck cancer oligonucleotide microarray oligonucleotide probes reproducibility of results statistics and numerical data

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oligonucleotide microarray analysis of genes regulating apoptosis in chronically ischemic and postinfarction myocardium

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BIOCHEMICAL GENETICS 2008年第5-6期46卷 241-247页

作者： Dabek, Jozefa Owczarek, Aleksander Gasior, Zbigniew Ulczok, Rafal Skowerski, Mariusz Kulach, Andrzej Mazurek, Urszula Bochenek, Andrzej Med Univ Silesia Dept Cardiol Katowice Poland Med Univ Silesia Dept Mol Biol Sosnowiec Poland Med Univ Silesia Dept Cardiac Surg 1 Katowice Poland

The pathology of cardiomyocyte death during and after myocardial infarction involves both necrosis and apoptosis. Although both mechanisms lead to cell death, participation of apoptosis in this process carries the potential of developing therapies influencing at least part of the population of dying cells. Therefore the aim of this study was to determine (using oligonucleotide microarrays) expression profiles of apoptosis-regulating genes in postinfarction myocardium, comparing chronically ischemic and healthy heart muscle. Tissue samples were obtained during elective surgery from the right cardiac auricles of three patients. The expression of 141 genes involved in fibrosis was assessed using the Affymetrix HG_U133A microarray. The patients' transcriptomes were compared using hierarchical clusterization. Differentiating genes were determined using regression analysis and Bland-Altman graph analysis. Hierarchical clusterization demonstrated that the profile of gene expression in postinfarction myocardium was different from that in the remaining specimens. Further statistical analysis showed two important differentiating genes: FOXO3A (underexpressed in post-MI sample) and CFLAR (overexpressed in post-MI sample). The expression of apoptosis-regulating genes is significantly different in post-MI myocardium from chronically ischemic and a nonischemic myocardium. Our results suggest that CFLAR is important in the induction of apoptosis in postinfarction cardiac tissue.

关键词： oligonucleotide microarray apoptosis regulation myocardial infarction

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oligonucleotide microarray data mining: search for age-dependent gene expression

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2002年第5期298卷 772-778页

作者： Kirschner, M Pujol, G Radu, A Mt Sinai Sch Med Carl C Icahn Inst Gene Therapy & Mol Med New York NY 10029 USA

Information on gene expression in colon tumors versus normal human colon was recently generated by an oligonucleotide microarray study [1]. We used the associated database to search for genes that display age-dependent variations in expression. Statistically significant evidence was obtained that such genes are present in both the tumor and normal tissue databases. Besides the analysis of all genes included in the database, three subsets of genes were analyzed separately: genes controlled by p53, and genes coding for ribosomal proteins and for nuclear-encoded mitochondrial proteins. Among the genes controlled by p53 some show an age-dependent change in expression in tumor tissues, in the sense compatible with an activation of p53 at higher age. A decreased expression of some ribosomal genes at advanced age was detected both in tumor and normal tissues. No significant age-dependent expression could be detected for genes encoding mitochondrial proteins. (C) 2002 Elsevier Science (USA). All rights reserved.

关键词： oligonucleotide microarray aging colon tumors p53 ribosomal proteins

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oligonucleotide microarray based detection of repetitive sequence changes

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HUMAN MUTATION 2000年第4期16卷 354-363页

作者： Hacia, JG Edgemon, K Fang, N Mayer, RA Sudano, D Hunt, N Collins, FS NHGRI NIH Bethesda MD 20892 USA

Prior studies of oligonucleotide microarray-based mutational analysis have demonstrated excellent sensitivity and specificity except in circumstances where a frameshift mutation occurs in the context of a short repeated sequence. To further evaluate this circumstance, a series of nucleic acid samples having heterozygous mutations within repetitive BRCA1 sequence tracts was prepared and evaluated. These mutations included single nucleotide insertions and deletions in homopolymer runs, insertions and deletions of trinucleotide repeats, and duplications. Two-color comparative hybridization experiments were used wherein wild type reference and test targets are co-hybridized to microarrays designed to screen the entire BRCA1 coding sequence for all possible sequence changes. Mutations in simulated heterozygote samples were detected by observing relative losses of test target hybridization signal to select perfect match oligonucleotide probes. While heterozygous mutations could be readily distinguished above background noise in 9/19 cases, it was not possible to detect alterations in a poly dA/dT tract, small tripler repeat expansions, and a 10 bp direct repeat. Unexpectedly, samples containing (GAT)(3) tripler repeat expansions showed significantly higher affinity toward specific perfect match probes relative to their wild type counterparts. Therefore, markedly increased as well as decreased test sample hybridization to perfect march probes should be used to raise a suspicion of repetitive sequence changes. Hum Mutat 16:354-363, 2000. (C) 2000 Wiley-Liss, Inc.

关键词： oligonucleotide microarray DNA chip mutation detection double labeling repetitive sequences loss of hybridization signal analysis BRCA1 tripler repeat expansion

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Establishment and preliminary application of oligonucleotide microarray assay for detection of food-borne toxigenic microorganisms

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EUROPEAN FOOD RESEARCH AND TECHNOLOGY 2013年第6期236卷 1073-1083页

作者： Feng, Jiawang Wang, Xiaoyu Cao, Guiyun Hu, Songnan Kuang, Xiaoshan Tang, Shiming You, Shuzhu Liu, Lideng Zhuhai Entry Exit Inspect & Quarantine Bur Zhuhai 519015 Peoples R China Zhuhai Water Grp Co Ltd Water Qual Res Ctr Zhuhai 519000 Peoples R China

Rapid, high-throughput and accurate detection and identification of food-borne toxigenic microorganisms is crucial for food safety nowadays. An oligonucleotide microarray was designed and established and was applied to detect common food-borne toxigenic microorganisms in this study. PCR amplification of marker genes and 16S rRNA gene of 14 toxigenic bacteria and fungi using specific primers and oligo probes residing in these genes were employed and designed to fabricate the microarray. Optimization of hybridization conditions was implemented. The optimal conditions for hybridization were 51 A degrees C for 30 min. Furthermore, the ratio of biotin labeled to unlabeled primer for PCR amplification was also optimized to enhance specific hybridization of the microarray. Specificity, sensitivity (710 CFU/mL), and reproductivity assessment confirmed the practicability of the microarray. Finally, this microarray was successfully applied to detect 6 common toxigenic microorganisms from 328 food samples. The established microarray may provide potential for rapid detection and identification of toxigenic microorganisms from foods.

关键词： Toxigenic microorganism oligonucleotide microarray Food-borne Detection Optimization

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Quantitative oligonucleotide microarray data analysis with an artificial standard probe strategy

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BIOSENSORS & BIOELECTRONICS 2008年第11期23卷 1738-1744页

作者： Hwang, Byeong Hee Cha, Hyung Joon Pohang Univ Sci & Technol Dept Chem Engn Pohang 790784 South Korea

Quantitative data analysis is an important element in several applications of DNA microarray, including mRNA expression profiling and estimation of infectious doses for pathogens. Here, we introduce an artificial standard probe strategy for quantitative pathogen detection using an oligonucleotide chip as a model system. The standard capture probe sequence was artificially designed to prevent non-specific hybridization with bacterial targets. Based on the fluorescence intensities of artificial standard spots, the raw fluorescence intensity data for specific spots could be corrected to generate linear correlations with target concentrations. Therefore, our novel artificial standard probe may be effectively applied for the correction of chip-to-chip variations and quantitative data analysis of a one-color labeled DNA microarray system. (c) 2008 Elsevier B.V. All rights reserved.

关键词： DNA chip oligonucleotide microarray quantitative data analysis artificial standard probe

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Analysis of interactions of template/primer duplexes with T7 DNA polymerase by oligonucleotide microarray

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SENSORS AND ACTUATORS B-CHEMICAL 2006年第1期115卷 428-433页

作者： Yang, MS Tsoi, PY Li, CW Zhao, HL Chinese Acad Sci Biochip Res Lab Inst Microsyst & Informat Technol Shanghai 200050 Peoples R China

Recent advances in DNA microarray technology have contributed significantly to assessing massive quantities of genetic data, especially for gene expression monitoring, mutation detection and polymorphism analysis. However, fewer studies have been reported on the use of such novel technique for molecular recognition events, involving the protein-DNA interactions. In this study, DNA microarray technology was employed to study the binding interactions between a series of template/primer DNA duplexes (dsDNA) and single-stranded DNA (ssDNA) and T7 DNA polymerase enzymes containing both polymerase and exonuclease activities. Various DNA targets were printed on the streptavidin-modified gold surface based on the biotin-streptavidin chemistry. The effects of mismatches on the overall binding affinities of T7 DNA polymerase were estimated after introduction of a number of different mismatches at/near the 3'-end of the primer strand. The overall binding affinities of the enzyme towards the mismatched DNAs were one to four times less than with the fully matched DNA. The results have demonstrated the feasibility of using the microarray technique to study molecular recognition events such as the mismatch base discrimination involved in DNA-polymerase interactions. (c) 2005 Elsevier B.V. All rights reserved.

关键词： oligonucleotide microarray T7 DNA polymerase protein-DNA interaction binding affinity

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Screening genetically modified organisms using multiplex-PCR coupled with oligonucleotide microarray

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BIOSENSORS & BIOELECTRONICS 2006年第1期22卷 71-77页

作者： Xu, Jia Miao, Haizhen Wu, Houfei Huang, Wensheng Tang, Rong Qiu, Minyan Wen, Jianguo Zhu, Shuifang Li, Yao Fudan Univ State Key Lab Genet Engn Inst Genet Sch Life Sci Shanghai 200433 Peoples R China CAIQ Inst Anim & Plant Quarantine Beijing 100029 Peoples R China Shanghai BioStar Genechip Inst Shanghai 200092 Peoples R China

In this research, we developed a multiplex polymerase chain reaction (multiplex-PCR) coupled with a DNA microarray system simultaneously aiming at many targets in a consecutive reaction to detect a genetically modified organism (GMO). There are a total of 20 probes for detecting a GMO in a DNA microarray which can be classified into three categories according to their purpose: the first for screening GMO from un-transgenic plants based on the common elements such as promoter, reporter and terminator genes;the second for specific gene confirmation based on the target gene sequences such as herbicide-resistance or insect-resistance genes;the third for species-specific genes which the sequences are unique for different plant species. To ensure the reliability of this method, different kinds of positive and negative controls were used in DNA microarray. Commercial GM soybean, maize, rapeseed and cotton were identified by means of this method and further confirmed by PCR analysis and sequencing. The results indicate that this method discriminates between the GMOs very quickly and in a cost-saving and more time efficient way. It can detect more than 95% of currently commercial GMO plants and the limits of detection are 0.5% for soybean and 1% for maize. This method is proved to be a new method for routine analysis of GMOs. (c) 2005 Elsevier B.V. All rights reserved.

关键词： oligonucleotide microarray GMO screening multiplex-PCR

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