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17 - Microarrays and quantitative real-time reverse transcriptase–polymerase chain reaction

Published online by Cambridge University Press:  25 January 2011

Stephen A. Bustin
Affiliation:
Queen Mary University of London
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Summary

Since the introduction of gene expression microarray technology, the number of applications and publications based on it has grown enormously. Nowadays, there is almost no institution or university in the field of molecular biology that has no genomic facility helping to apply this technique. Microarrays, an ordered assembly of thousands of probes, have the ability to allow the simultaneous determination of the expression levels of thousands of genes. This technique was used to describe gene programs that underlie various cellular processes, such as immunity and hormone responses, as well as to refine classifications of neoplasias, and to define diagnostic molecular markers for diseases. However, one drawback of the microarray technique is that, the more genes are tested, the higher the risk of identifying false positives as a result of random effects. Furthermore, biological and technical variations, including the microarray design, can affect the precision of microarray results. More difficult situations are found when working with complex multicellular tissue samples as compared to cell line experiments. The outcome of these microarray experiments can result in low fold changes and low signal intensities for differentially expressed genes, which makes it difficult to detect regulated genes reliably. Therefore, the identification of differentially expressed genes requires independent confirmation. Quantitative real-time reverse transcriptase–polymerase chain reaction (qPCR) is the method of choice because of its broad range of linearity, high sensitivity, and reproducibility and because it can be easily adapted to test several hundreds of transcripts.

Type
Chapter
Information
The PCR Revolution
Basic Technologies and Applications
, pp. 262 - 275
Publisher: Cambridge University Press
Print publication year: 2009

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References

Jaluria, P, Konstantopoulos, K, Betenbaugh, M, Shiloach, J (2007) A perspective on microarrays: current applications, pitfalls, and potential uses. Microbial Cell Factories 6: 4.CrossRefGoogle ScholarPubMed
Schena, M, Shalon, D, Davis, RW, Brown, PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.CrossRefGoogle ScholarPubMed
Bakel, H, Holstege, FC (2004) In control: systematic assessment of microarray performance. EMBO Reports 5: 964–969.CrossRefGoogle ScholarPubMed
Boutros, M, Agaisse, H, Perrimon, N (2002) Sequential activation of signaling pathways during innate immune responses in Drosophila. Developmental Cell 3: 711–722.CrossRefGoogle ScholarPubMed
Wurmbach, E, Yuen, T, Ebersole, BJ, Sealfon, SC (2001) Gonadotropin releasing hormone receptor-coupled gene network organization. Journal of Biological Chemistry 276: 47195–47201.CrossRefGoogle ScholarPubMed
Alizadeh, AA, Eisen, MB, Davis, RE, Ma, C, Lossos, IS, Rosenwald, A, et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503–511.CrossRefGoogle ScholarPubMed
Golub, TR, Slonim, DK, Tamayo, P, Huard, C, Gaasenbeek, M, Mesirov, JP, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531–537.CrossRefGoogle ScholarPubMed
van't Veer, LJ, Dai, H, Vijver, MJ, He, YD, Hart, AA, Mao, M, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530–536.CrossRefGoogle Scholar
Wurmbach, E, Chen, YB, Khitrov, G, Zhang, W, Roayaie, S, Schwartz, M, et al. (2007) Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 45: 938–947.CrossRefGoogle ScholarPubMed
Dudoit, S, Popper Shaffer, J, Boldrick, JC (2002) Multiple hypothesis testing in microarray experiments. UC Berkeley Division of Biostatistics Working Paper Series.
Churchill, GA (2002) Fundamentals of experimental design for cDNA microarrays. Nature Genetics 32 Suppl: 490–495.CrossRefGoogle ScholarPubMed
Bustin, SA, Benes, V, Nolan, T, Pfaffl, MW (2005) Quantitative real-time RTPCR – a perspective. Journal of Molecular Endocrinology 34: 597–601.CrossRefGoogle ScholarPubMed
Wong, ML, Medrano, JF (2005) Real-time PCR for mRNA quantitation. BioTechniques 39: 75–85.CrossRefGoogle ScholarPubMed
Cowell, JK, Hawthorn, L (2007) The application of microarray technology to the analysis of the cancer genome. Current Molecular Medicine 7: 103–120.CrossRefGoogle ScholarPubMed
Lee, N, Saeed, A (2007) Microarrays: An Overview. Volume 353, Second edition. Totowa, NJ: Humana Press.Google ScholarPubMed
Rosok, O, Sioud, M (2007) Discovery of differentially expressed genes: technical considerations. Methods in Molecular Biology (Clifton, N.J.) 360: 115–129.Google ScholarPubMed
Wurmbach, E, Yuen, T, Sealfon, SC (2003) Focused microarray analysis. Methods 31: 306–316.CrossRefGoogle ScholarPubMed
Taniguchi, M, Miura, K, Iwao, H, Yamanaka, S (2001) Quantitative assessment of DNA microarrays – comparison with Northern blot analyses. Genomics 71: 34–39.CrossRefGoogle ScholarPubMed
Quackenbush, J (2002) Microarray data normalization and transformation. Nature Genetics 32 Suppl: 496–501.CrossRefGoogle Scholar
Auburn, RP, Kreil, DP, Meadows, , Fischer, B, Matilla, SS, Russell, S (2005) Robotic spotting of cDNA and oligonucleotide microarrays. Trends in Biotechnology 23: 374–379.CrossRefGoogle ScholarPubMed
Wang, Y, Li, Y, Liu, S, Shen, W, Jiang, B, Xu, X, et al. (2005) Study on the dynamic behavior of a DNA microarray. Journal of Nanoscience and Nanotechnology 5: 1249–1255.CrossRefGoogle ScholarPubMed
Peterson, AW, Heaton, RJ, Georgiadis, RM (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Research 29: 5163–5168.CrossRefGoogle ScholarPubMed
Yuen, T, Wurmbach, E, Pfeffer, RL, Ebersole, BJ, Sealfon, SC (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Research 30: e48.CrossRefGoogle ScholarPubMed
Chee, M, Yang, R, Hubbell, E, Berno, A, Huang, XC, Stern, D, et al. (1996) Accessing genetic information with high-density DNA arrays. Science 274: 610–614.CrossRefGoogle ScholarPubMed
Lockhart, DJ, Dong, H, Byrne, MC, Follettie, MT, Gallo, MV, Chee, MS, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14: 1675–1680.CrossRefGoogle ScholarPubMed
Ramakrishnan, R, Dorris, D, Lublinsky, A, Nguyen, A, Domanus, M, Prokhorova, A, et al. (2002) An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Research 30: e30.CrossRefGoogle ScholarPubMed
Tan, PK, Downey, TJ, Spitznagel, EL Jr, Xu, P, Fu, D, Dimitrov, DS, et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Research 31: 5676–5684.CrossRefGoogle ScholarPubMed
Järvinen, AK, Hautaniemi, S, Edgren, H, Auvinen, P, Saarela, J, Kallioniemi, OP, et al. (2004) Are data from different gene expression microarray platforms comparable?Genomics 83: 1164–1168.CrossRefGoogle ScholarPubMed
Petersen, D, Chandramouli, GV, Geoghegan, J, Hilburn, J, Paarlberg, J, Kim, CH, et al. (2005) Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6: 63.CrossRefGoogle ScholarPubMed
Shi, L, Reid, LH, Jones, WD, Shippy, R, Warrington, JA, Baker, SC, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 24: 1151–1161.Google ScholarPubMed
Schmittgen, TD, Zakrajsek, BA (2000) Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. Journal of Biochemical and Biophysical Methods 46: 69–81.CrossRefGoogle ScholarPubMed
Waxman, S, Wurmbach, E (2007) De-regulation of common housekeeping genes in hepatocellular carcinoma. BMC Genomics 8: 243.CrossRefGoogle ScholarPubMed
Vandesompele, J, Preter, K, Pattyn, F, Poppe, B, Roy, N, Paepe, A, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3: 34.CrossRefGoogle Scholar
Wurmbach, E, Gonzalez-Maeso, J, Yuen, T, Ebersole, BJ, Mastaitis, JW, Mobbs, CV, et al. (2002) Validated genomic approach to study differentially expressed genes in complex tissues. Neurochemical Research 27: 1027–1033.CrossRefGoogle ScholarPubMed
Mastaitis, JW, Wurmbach, E, Cheng, H, Sealfon, SC, Mobbs, CV (2005) Acute induction of gene expression in brain and liver by insulin-induced hypoglycemia. Diabetes 54: 952–958.CrossRefGoogle ScholarPubMed
Gonzalez-Maeso, J, Yuen, T, Ebersole, BJ, Wurmbach, E, Lira, A, Zhou, M, et al. (2003) Transcriptome fingerprints distinguish hallucinogenic and nonhallucinogenic 5-hydroxytryptamine 2A receptor agonist effects in mouse somatosensory cortex. Journal of Neuroscience 23: 8836–8843.CrossRefGoogle ScholarPubMed
Ginsberg, SD (2005) RNA amplification strategies for small sample populations. Methods 37: 229–237.CrossRefGoogle ScholarPubMed
Marko, NF, Frank, B, Quackenbush, J, Lee, NH (2005) A robust method for the amplification of RNA in the sense orientation. BMC Genomics 6: 27.CrossRefGoogle ScholarPubMed

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