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Expert Review of Molecular Diagnostics Volume 6, 2006 - Issue 3
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Review

Improving reliability and performance of DNA microarrays

Maria Sievertzon Royal Institute of Technology, AlbaNova University Center, KTH Genome Center, Department of Biotechnology, S-106 91 Stockholm, Sweden. [email protected]
,
Peter Nilsson Royal Institute of Technology, AlbaNova University Center, KTH Genome Center, Department of Biotechnology, S-106 91 Stockholm, Sweden. [email protected]
&
Joakim Lundeberg Royal Institute of Technology, AlbaNova University Center, KTH Genome Center, Department of Biotechnology, S-106 91 Stockholm, Sweden. [email protected]
Pages 481-492 | Published online: 09 Jan 2014

References

  • Pennisi E. Bioinformatics. Gene counters struggle to get the right answer.Science301(5636), 1040–1041 (2003).
  • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature431(7011), 931–945 (2004).
  • Claverie JM. Fewer genes, more noncoding RNA.Science309(5740), 1529–1530 (2005).
  • Yamamoto M, Wakatsuki T, Hada A, Ryo A. Use of serial analysis of gene expression (SAGE) technology.J. Immunol. Methods250(1–2), 45–66 (2001).
  • Jongeneel CV, Iseli C, Stevenson BJ et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing.Proc. Natl Acad. Sci. USA100(8), 4702–4705 (2003).
  • Bishop JO, Morton JG, Rosbash M, Richardson M. Three abundance classes in HeLa cell messenger RNA.Nature250(463), 199–204 (1974).
  • Ekins R, Chu FW. Microarrays: their origins and applications.Trends Biotechnol.17(6), 217–218 (1999).
  • Weeraratna AT, Nagel JE, de Mello-Coelho V, Taub DD. Gene expression profiling: from microarrays to medicine.J. Clin. Immunol.24(3), 213–224 (2004).
  • Ekins R, Chu F, Micallef J. High specific activity chemiluminescent and fluorescent markers: their potential application to high sensitivity and ‘multi-analyte’ immunoassays.J. Biolumin. Chemilumin.4(1), 59–78 (1989).
  • Ekins RP. Multi-analyte immunoassay.J. Pharm. Biomed. Anal.7(2), 155–168 (1989).
  • Augenlicht LH, Wahrman MZ, Halsey H et al. Expression of cloned sequences in biopsies of human colonic tissue and in colonic carcinoma cells induced to differentiate in vitro.Cancer Res.47(22), 6017–6021 (1987).
  • Lennon GG, Lehrach H. Hybridization analyses of arrayed cDNA libraries.Trends Genet.7(10), 314–317 (1991).
  • Southern EM, Case-Green SC, Elder JK et al. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids.Nucleic Acids Res.22(8), 1368–1373 (1994).
  • Zhao N, Hashida H, Takahashi N, Misumi Y, Sakaki Y. High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression.Gene156(2), 207–213 (1995).
  • Lockhart DJ, Dong H, Byrne MC et al. Expression monitoring by hybridization to high-density oligonucleotide arrays.Nature Biotechnol.14(13), 1675–1680 (1996).
  • Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays.Nature Genet.21(1 Suppl.), 20–24 (1999).
  • Fodor SP, Read JL, Pirrung MC et al. Light-directed, spatially addressable parallel chemical synthesis.Science251(4995), 767–773 (1991).
  • Pease AC, Solas D, Sullivan EJ et al. Light-generated oligonucleotide arrays for rapid DNA sequence analysis.Proc. Natl Acad. Sci. USA91(11), 5022–5026 (1994).
  • Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics20(3), 323–331 (2004).
  • Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy–analysis of Affymetrix GeneChip data at the probe level.Bioinformatics20(3), 307–315 (2004).
  • Barrett JC, Kawasaki ES. Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression.Drug Discov. Today8(3), 134–141 (2003).
  • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science270(5235), 467–470 (1995).
  • Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.Genome Res.6(7), 639–645 (1996).
  • DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale.Science278(5338), 680–686 (1997).
  • Chipping forecast I.Nature Genet.21(Suppl.), 1–60 (1999).
  • Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays.Nature405(6788), 827–836 (2000).
  • Schulze A, Downward J. Navigating gene expression using microarrays – a technology review.Nature Cell Biol.3(8), E190–E195 (2001).
  • Chipping forecast I.Nature Genet.32(Suppl.), 461–552 (2002).
  • Beaucage SL. Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications.Curr. Med. Chem.8(10), 1213–1244 (2001).
  • Forster T, Roy D, Ghazal P. Experiments using microarray technology: limitations and standard operating procedures.J. Endocrinol.178(2), 195–204 (2003).
  • Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations.Proc. Natl Acad. Sci. USA97(18), 9834–9839 (2000).
  • Pan W, Lin J, Le CT. How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach.Genome Biol.3(5), RESEARCH0022 (2002).
  • Churchill GA. Fundamentals of experimental design for cDNA microarrays.Nature Genet.32(Suppl.), 490–495 (2002).
  • Dobbin K, Shih JH, Simon R. Questions and answers on design of dual-label microarrays for identifying differentially expressed genes.J. Natl Cancer Inst.95(18), 1362–1369 (2003).
  • Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments.Proc. Natl Acad. Sci. USA102(12), 4252–4257 (2005).
  • Yang YH, Speed T. Design issues for cDNA microarray experiments.Nature Rev. Genet.3(8), 579–588 (2002).
  • Kerr MK, Churchill GA. Experimental design for gene expression microarrays.Biostatistics2(2), 183–201 (2001).
  • Dudley AM, Aach J, Steffen MA, Church GM. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.Proc. Natl Acad. Sci. USA99(11), 7554–7559 (2002).
  • Sterrenburg E, Turk R, Boer JM, van Ommen GB, den Dunnen JT. A common reference for cDNA microarray hybridizations.Nucleic Acids Res.30(21), e116 (2002).
  • Randolph JB, Waggoner AS. Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes.Nucleic Acids Res.25(14), 2923–2929 (1997).
  • Schroeder BG, Peterson LM, Fleischmann RD. Improved quantitation and reproducibility in Mycobacterium tuberculosis DNA microarrays.J. Mol. Microbiol. Biotechnol.4(2), 123–126 (2002).
  • Stears RL, Getts RC, Gullans SR. A novel, sensitive detection system for high-density microarrays using dendrimer technology.Physiol. Genomics3(2), 93–99 (2000).
  • Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis.Nucleic Acids Res.30(2), e4 (2002).
  • Yang YH, Buckley MJ, Dudoit S, Speed TP. Comparison of methods for image analysis on cDNA microarray data.J. Comput. Graph. Stat.11, 108–136 (2002).
  • Yang YH, Dudoit S, Luu P et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.Nucleic Acids Res.30(4), e15 (2002).
  • Glasbey CA, Ghazal P. Combinatorial image analysis of DNA microarray features.Bioinformatics19(2), 194–203 (2003).
  • Brown CS, Goodwin PC, Sorger PK. Image metrics in the statistical analysis of DNA microarray data.Proc. Natl Acad. Sci. USA98(16), 8944–8949 (2001).
  • Wang X, Ghosh S, Guo SW. Quantitative quality control in microarray image processing and data acquisition.Nucleic Acids Res.29(15), e75 (2001).
  • Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.Nucleic Acids Res.29(12), 2549–2557 (2001).
  • Jenssen TK, Langaas M, Kuo WP et al. Analysis of repeatability in spotted cDNA microarrays.Nucleic Acids Res.30(14), 3235–3244 (2002).
  • Yang MC, Ruan QG, Yang JJ et al. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays.Physiol. Genomics7(1), 45–53 (2001).
  • Tran PH, Peiffer DA, Shin Y et al. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals.Nucleic Acids Res.30(12), e54 (2002).
  • Smyth GK, Speed T. Normalization of cDNA microarray data.Methods31(4), 265–273 (2003).
  • Quackenbush J. Microarray data normalization and transformation.Nature Genet.32(Suppl.), 496–501 (2002).
  • Yang YH, Dudoit S, Luu P, Speed TP. Normalization for cDNA microarray data. In:Microarrays: Optical Technologies and Informatics. Bittner ML, Chen Y, Dorsel AN, Dougherty ER et al. (Eds) Proceedings of SPIE, Volume 4266 (2001).
  • Finkelstein DB, Gollub J, Ewing R et al. Iterative linear regression by sector. In:Methods of Microarray Data Analysis. Papers from CAMDA 2000. Lin SM, Johnson KF (Eds), Kluwer Academic, The Netherlands, 57–68 (2001).
  • Xie Y, Jeong KS, Pan W, Khodursky A, Carlin BP. A case study on choosing normalization methods and test statistics for two-channel microarray data.Comp. Funct. Genomics5, 432–444 (2004).
  • Kepler TB, Crosby L, Morgan KT. Normalization and analysis of DNA microarray data by self-consistency and local regression.Genome Biol.3(7), RESEARCH0037 (2002).
  • Kerr MK, Martin M, Churchill GA. Analysis of variance for gene expression microarray data.J. Comput. Biol.7(6), 819–837 (2000).
  • Wolfinger RD, Gibson G, Wolfinger ED et al. Assessing gene significance from cDNA microarray expression data via mixed models.J. Comput. Biol.8(6), 625–637 (2001).
  • Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling.Proc. Natl Acad. Sci. USA97(18), 10101–10106 (2000).
  • Newton MA, Kendziorski CM, Richmond CS, Blattner FR, Tsui KW. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data.J. Comput. Biol.8(1), 37–52 (2001).
  • Gentleman R, Carey V, Bates D et al. Bioconductor: open software development for computational biology and bioinformatics.Genome Biol.5(10), R80 (2004).
  • Smyth G. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments.Statistical Applications in Genetics and Molecular Biology3(1), Article 3 (2004).
  • Yang IV, Chen E, Hasseman JP et al. Within the fold: assessing differential expression measures and reproducibility in microarray assays.Genome Biol.3(11), RESEARCH0062 (2002).
  • Kerr MK, Churchill GA. Statistical design and the analysis of gene expression microarray data.Genet. Res.77(2), 123–128 (2001).
  • Dudoit S, Yang YH, Speed TP, Callow MJ. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.Statistica Sinica12, 111–140 (2002).
  • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response.Proc. Natl Acad. Sci. USA98(9), 5116–5121 (2001).
  • Efron B, Tibshirani R, Storey JD, Tusher V. Empirical Bayes analysis of a micoarray experiment.J. Am. Stat. Assoc.96, 1151–1160 (2001).
  • Lönnstedt I, Speed T. Replicated microarray data.Statistica Sinica12, 31–46 (2002).
  • Smyth GK, Michaud J, Scott H. The use of within-array duplicate spots for assessing differential expression in microarray experiments. 21(9),Bioinformatics2067–2075 (2005).
  • Long AD, Mangalam HJ, Chan BY et al. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12.J. Biol. Chem.276(23), 19937–19944 (2001).
  • Thomas JG, Olson JM, Tapscott SJ, Zhao LP. An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles.Genome Res.11(7), 1227–1236 (2001).
  • Ideker T, Thorsson V, Siegel AF, Hood LE. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.J. Comput. Biol.7(6), 805–787 (2000).
  • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing.J. R. Stat. Soc. Ser. B57, 289–300 (1995).
  • Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures.Bioinformatics19(3), 368–375 (2003).
  • Quackenbush J. Computational analysis of microarray data.Nature Rev. Genet.2(6), 418–427 (2001).
  • Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns.Proc. Natl Acad. Sci. USA95(25), 14863–14868 (1998).
  • Spellman PT, Sherlock G, Zhang MQ et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.Mol. Biol. Cell9(12), 3273–3297 (1998).
  • Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture.Nature Genet.22(3), 281–285 (1999).
  • Tamayo P, Slonim D, Mesirov J et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.Proc. Natl Acad. Sci. USA96(6), 2907–2912 (1999).
  • Toronen P, Kolehmainen M, Wong G, Castren E. Analysis of gene expression data using self-organizing maps.FEBS Lett.451(2), 142–146 (1999).
  • Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to spoulation time series.Pac. Symp. Biocomput.2000, 455–466 (2000).
  • Cho RJ, Campbell MJ, Winzeler EA et al. A genome-wide transcriptional analysis of the mitotic cell cycle.Mol. Cell2(1), 65–73 (1998).
  • Hughes TR, Marton MJ, Jones AR et al. Functional discovery via a compendium of expression profiles.Cell102(1), 109–126 (2000).
  • Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.Nature Biotechnol.16(10), 939–945 (1998).
  • Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression.Nature Genet.27(2), 167–171 (2001).
  • Alizadeh AA, Eisen MB, Davis RE et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.Nature403(6769), 503–511 (2000).
  • Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.Science286(5439), 531–537 (1999).
  • Dudoit S, Fridlyand J, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data.J. Am. Stat. Assoc.97, 77–87 (2002).
  • Brown MP, Grundy WN, Lin D et al. Knowledge-based analysis of microarray gene expression data by using support vector machines.Proc. Natl Acad. Sci. USA97(1), 262–267 (2000).
  • Ashburner M, Ball CA, Blake JA et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.Nature Genet.25(1), 25–29 (2000).
  • Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE.Genome Biol.4(10), R70 (2003).
  • Doniger SW, Salomonis N, Dahlquist KD et al. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data.Genome Biol.4(1), R7 (2003).
  • Zeeberg BR, Feng W, Wang G et al. GoMiner: a resource for biological interpretation of genomic and proteomic data.Genome Biol.4(4), R28 (2003).
  • Ogata H, Goto S, Sato K et al. KEGG: Kyoto Encyclopedia of Genes and Genomes.Nucleic Acids Res.27(1), 29–34 (1999).
  • Irizarry RA, Warren D, Spencer F et al. Multiple-laboratory comparison of microarray platforms.Nature Methods2(5), 345–350 (2005).
  • Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J. Independence and reproducibility across microarray platforms.Nature Methods2(5), 337–344 (2005).
  • Petersen D, Chandramouli GV, Geoghegan J et al. Three microarray platforms: an analysis of their concordance in profiling gene expression.BMC Genomics6(1), 63 (2005).
  • Baker SC, Bauer SR, Beyer RP et al. The External RNA Controls Consortium: a progress report.Nature Methods2(10), 731–734 (2005).
  • Brazma A, Hingamp P, Quackenbush J et al. Minimum information about a microarray experiment (MIAME) – toward standards for microarray data.Nature Genet.29(4), 365–371 (2001).
  • Hu GK, Madore SJ, Moldover B et al. Predicting splice variant from DNA chip expression data.Genome Res.11(7), 1237–1245 (2001).
  • Clark TA, Sugnet CW, Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.Science296(5569), 907–910 (2002).
  • Johnson JM, Castle J, Garrett-Engele P et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.Science302(5653), 2141–2144 (2003).
  • Yeakley JM, Fan JB, Doucet D et al. Profiling alternative splicing on fiber-optic arrays.Nature Biotechnol.20(4), 353–358 (2002).
  • Cawley S, Bekiranov S, Ng HH et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.Cell116(4), 499–509 (2004).
  • Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays.Proc. Natl Acad. Sci. USA99(15), 9697–9702 (2002).
  • Fan J, Yang X, Wang W et al. Global analysis of stress-regulated mRNA turnover by using cDNA arrays.Proc. Natl Acad. Sci. USA99(16), 10611–10616 (2002).
  • Hertzberg M, Sievertzon M, Aspeborg H et al. cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol.Plant J.25(5), 585–591 (2001).
  • Sievertzon M, Agaton C, Nilsson P, Lundeberg J. Amplification of mRNA populations by a cDNA tag strategy.Biotechniques36(2), 253–259 (2004).
  • Shoemaker DD, Schadt EE, Armour CD et al. Experimental annotation of the human genome using microarray technology.Nature409(6822), 922–927 (2001).
  • Kapranov P, Cawley SE, Drenkow J et al. Large-scale transcriptional activity in chromosomes 21 and 22.Science296(5569), 916–919 (2002).
  • Patil N, Berno AJ, Hinds DA et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.Science294(5547), 1719–1723 (2001).
  • O’Meara D, Ahmadian A, Odeberg J, Lundeberg J. SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays.Nucleic Acids Res.30(15), e75 (2002).
  • Kashiwagi H, Uchida K, Genome-wide profiling of gene amplification and deletion in cancer.Hum. Cell13(3), 135–141 (2000).
  • Raghuraman MK, Winzeler EA, Collingwood D et al. Replication dynamics of the yeast genome.Science294(5540), 115–121 (2001).
  • Lundgren M, Andersson A, Chen L, Nilsson P, Bernander R. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination.Proc. Natl Acad. Sci. USA101(18), 7046–7051 (2004).
  • Iyer VR, Horak CE, Scafe CS et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.Nature409(6819), 533–838 (2001).
  • Bulyk ML, Huang X, Choo Y, Church GM. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.Proc. Natl Acad. Sci. USA98(13), 7158–7163 (2001).
  • van Steensel B, Henikoff S. Epigenomic profiling using microarrays.Biotechniques35(2), 346–350, 352–354, 356–357 (2003).
  • Hoheisel JD. Microarray technology: beyond transcript profiling and genotype analysis.Nature Rev. Genet.7(3), 200–210 (2006).

Websites

  • Affymetrix, Inc. www.affymetrix.com
  • The R Project for Statistical Computing www.r-project.org
  • Bengtsson H. aroma – An R Object-oriented Microarray Analysis environment www.maths.lth.se/help/R/aroma
  • Database for Annotation, Visualization and Integrated Discovery and Expression Analysis Systematic Explorer bioinformatic resources http://apps1.niaid.nih.gov/david
  • GenMAPP www.genmapp.org
  • GoMiner http://discover.nci.nih.gov/gominer
  • ArrayExpress at the EBI www.ebi.ac.uk/arrayexpress
  • NCBI’s Gene Expression Omnibus www.ncbi.nlm.nih.gov/geo
  • Human Protein Atlas www.proteinatlas.org

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