Abstract
DNA microarray technology has been used for genome-wide gene expression studies that incorporate molecular genetics and computer science analyses on massive levels. The availability of microarrays permit the simultaneous analysis of tens of thousands of genes for the purposes of gene discovery, disease diagnosis, improved drug development, and therapeutics tailored to specific disease processes. In this chapter, we provide an overview on the current state of common microarray technologies and platforms. Since many genes contribute to normal functioning, research efforts are moving from the search for a disease-specific gene to the understanding of the biochemical and molecular functioning of a variety of genes whose disrupted interaction in complicated networks can lead to a disease state. The field of microarrays has evolved over the past decade and is now standardized with a high level of quality control, while providing a relatively inexpensive and reliable alternative to studying various aspects of gene expression.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80.
Kulesh DA, Clive DR, Zarlenga DS et al (1987) Identification of interferon-modulated proliferation-related cDNA sequences. Proc Natl Acad Sci U S A 84: 8453–8457.
Kuo WP, Liu F, Trimarchi J et al (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24:832–840.
Fodor SP, Read JL, Pirrung MC et al (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773.
Lausted C, Dahl T, Warren C et al (2004) POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol 5:R58.
Baum M, Bielau S, Rittner N et al (2003) Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res 31:e151.
Ruano JM, Benoit VV, Aitchison JS et al (2000) Flame hydrolysis deposition of glass on silicon for the integration of optical and microfluidic devices. Anal Chem 72: 1093–1097.
Benoit V, Steel A, Torres M et al (2001) Evaluation of three-dimensional microchannel glass biochips for multiplexed nucleic acid fluorescence hybridization assays. Anal Chem 73:2412–2420.
Hokaiwado N, Asamoto M, Tsujimura K et al (2004) Rapid analysis of gene expression changes caused by liver carcinogens and chemopreventive agents using a newly developed three-dimensional microarray system. Cancer Sci 95: 123–130.
Fare TL, Coffey EM, Dai H, et al (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75:4672–4675.
Quinn MC, Wilson DJ, Young F et al (2009) The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles. J Transl Med 7:55.
Gunderson KL, Kruglyak S, Graige MS et al (2004) Decoding randomly ordered DNA arrays. Genome Res 14:870–877.
Bond GL, Hu W, Levine A (2005) A single nucleotide polymorphism in the MDM2 gene: from a molecular and cellular explanation to clinical effect. Cancer Res 65:5481–5484.
Guilford P, Hopkins J, Harraway J et al (1998) E-cadherin germline mutations in familial gastric cancer. Nature 392:402–405.
Imyanitov EN (2009) Gene polymorphisms, apoptotic capacity and cancer risk. Hum Genet 125:239–246.
Lindblad-Toh K, Tanenbaum DM, Daly MJ et al (2000) Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 18:1001–1005.
Reddy EP (1983) Nucleotide sequence analysis of the T24 human bladder carcinoma oncogene. Science 220:1061–1063.
Tuna M, Knuutila S, Mills GB (2009) Uniparental disomy in cancer. Trends Mol Med 15:120–128.
Mockler TC, Chan S, Sundaresan A et al (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85:1–15.
Nonne N, Ameyar-Zazoua M, Souidi M et al (2010) Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res 38:e20.
Wheeler DL, Church DM, Lash AE et al (2001) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 29:11–16.
Brazma A, Parkinson H, Sarkans U et al (2003) ArrayExpress – a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31:68–71.
Brooksbank C, Camon E, Harris MA et al (2003) The European Bioinformatics Institute’s data resources. Nucleic Acids Res 31:43–50.
Ball CA, Sherlock G, Parkinson H et al (2002) Standards for microarray data. Science 298:539.
Ikeo K, Ishi-i J, Tamura T et al (2003) CIBEX: center for information biology gene expression database. C R Biol 326:1079–1082.
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat Genet 29:365–371.
Kuo WP, Jenssen TK, Butte AJ et al (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405–412.
Mecham BH, Klus GT, Strovel J et al (2004) Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 32:e74.
Carter SL, Eklund AC, Mecham BH et al (2005) Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6:107.
Bammler T, Beyer RP, Bhattacharya S et al (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2: 351–356.
Larkin JE, Frank BC, Gavras H et al (2005) Independence and reproducibility across microarray platforms. Nat Methods 2:337–344.
Wang H, He X, Band M et al (2005) A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 6:71.
Zhu B, Ping G, Shinohara Y et al (2005) Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. Genomics 85:657–665.
Barnes M, Freudenberg J, Thompson S et al (2005) Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33:5914–5923.
Sherlock G (2005) Of fish and chips. Nat Methods 2:329–330.
Casciano DA, Woodcock J (2006) Empowering microarrays in the regulatory setting. Nat Biotechnol 24:1103.
Shi L, Reid LH, Jones WD et al (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151–1161.
Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26:317–325.
Spurgeon SL, Jones RC, Ramakrishnan R (2008) High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One 3:e1662.
Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651–657.
Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680.
Acknowledgments
This work was conducted with support from Harvard Catalyst – The Harvard Clinical and Translational Science Center (NIH Award #UL1 RR 025758 and financial contributions from Harvard University and its affiliated academic health care centers). The content is solely the responsibility of the authors and does not necessarily represent the official views of Harvard Catalyst, Harvard University and its affiliated academic health care centers, the National Center for Research Resources, or the National Institutes of Health.
Alexander J. Trachtenberg and Jae-Hyung Robert Chang contributed equally to this work.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Trachtenberg, A.J. et al. (2012). A Primer on the Current State of Microarray Technologies. In: Wang, J., Tan, A., Tian, T. (eds) Next Generation Microarray Bioinformatics. Methods in Molecular Biology, vol 802. Humana Press. https://doi.org/10.1007/978-1-61779-400-1_1
Download citation
DOI: https://doi.org/10.1007/978-1-61779-400-1_1
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-399-8
Online ISBN: 978-1-61779-400-1
eBook Packages: Springer Protocols