In control: systematic assessment of microarray performance

Expression profiling using DNA microarrays is a powerful technique that is widely used in the life sciences. How reliable are microarray-derived measurements? The assessment of performance is challenging because of the complicated nature of microarray experiments and the many different technology platforms. There is a mounting call for standards to be introduced, and this review addresses some of the issues that are involved. Two important characteristics of performance are accuracy and precision. The assessment of these factors can be either for the purpose of technology optimization or for the evaluation of individual microarray hybridizations. Microarray performance has been evaluated by at least four approaches in the past. Here, we argue that external RNA controls offer the most versatile system for determining performance and describe how such standards could be implemented. Other uses of external controls are discussed, along with the importance of probe sequence availability and the quantification of labelled material.

[1]  J. D. den Dunnen,et al.  Fluorescent labelling of cRNA for microarray applications. , 2003, Nucleic acids research.

[2]  E. Hovig,et al.  Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction , 2004, BMC Genomics.

[3]  R. Shippy,et al.  An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. , 2002, Nucleic acids research.

[4]  K. Miura,et al.  Quantitative assessment of DNA microarrays--comparison with Northern blot analyses. , 2001, Genomics.

[5]  P. Kemmeren,et al.  Monitoring global messenger RNA changes in externally controlled microarray experiments , 2003, EMBO reports.

[6]  R. Young,et al.  Biomedical Discovery with DNA Arrays , 2000, Cell.

[7]  John Quackenbush.  Microarray data normalization and transformation , 2002, Nature Genetics.

[8]  B. Korn,et al.  Normalization of array hybridization experiments in differential gene expression analysis. , 1999, Nucleic acids research.

[9]  J. Warrington,et al.  A high-density probe array sample preparation method using 10- to 100-fold fewer cells , 1999, Nature Biotechnology.

[10]  Kevin R Coombes,et al.  Sources of nonlinearity in cDNA microarray expression measurements , 2001, Genome Biology.

[11]  G. Churchill.  Fundamentals of experimental design for cDNA microarrays , 2002, Nature Genetics.

[12]  Stephen M. Hewitt,et al.  Post-analysis follow-up and validation of microarray experiments , 2002, Nature Genetics.

[13]  Hans Geir Eiken,et al.  Evaluation of five different cDNA labeling methods for microarrays using spike controls , 2003, BMC biotechnology.

[14]  Andy L. Johnson,et al.  Directly labeled mRNA produces highly precise and unbiased differential gene expression data. , 2003, Nucleic acids research.

[15]  I. Mian,et al.  Exploratory differential gene expression analysis in microarray experiments with no or limited replication , 2004, Genome Biology.

[16]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[17]  J. Hoheisel,et al.  Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. , 2001, Nucleic acids research.

[18]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[19]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[20]  J. Ohlrogge,et al.  Microarray analysis of developing Arabidopsis seeds. , 2000, Plant physiology.

[21]  Elisabetta Manduchi,et al.  Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. , 2003, Physiological genomics.

[22]  T. Speed,et al.  Design issues for cDNA microarray experiments , 2002, Nature Reviews Genetics.

[23]  V. Beneš,et al.  Standardization of protocols in cDNA microarray analysis. , 2003, Trends in biochemical sciences.

[24]  M. Hergenhahn,et al.  High-accuracy amplification of nanogram total RNA amounts for gene profiling. , 2004, Genomics.

[25]  Kristina Hanspers,et al.  Spotted long oligonucleotide arrays for human gene expression analysis. , 2003, Genome research.

[26]  Christopher J Herbert,et al.  Optimizing spotting solutions for increased reproducibility of cDNA microarrays. , 2003, Nucleic acids research.

[27]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[28]  Ramesh Ramakrishnan,et al.  A highly reproducible, linear, and automated sample preparation method for DNA microarrays. , 2002, Genome research.

[29]  Li Feng,et al.  Expression profiling using a hexamer-based universal microarray , 2004, Nature Biotechnology.

[30]  John D. Storey,et al.  Precision and functional specificity in mRNA decay , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Jian-Bing Fan,et al.  A versatile assay for high-throughput gene expression profiling on universal array matrices. , 2004, Genome research.

[32]  Elisabetta Manduchi,et al.  Comparison of different labeling methods for two-channel high-density microarray experiments. , 2002, Physiological genomics.

[33]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[34]  Van,et al.  A gene-expression signature as a predictor of survival in breast cancer. , 2002, The New England journal of medicine.

[35]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[36]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[37]  S. V. Anisimov,et al.  SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells. , 2002, Genomics.

[38]  Guangshan Li,et al.  Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride. , 2003, Analytical biochemistry.

[39]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[40]  Angela Relógio,et al.  Optimization of oligonucleotide-based DNA microarrays. , 2002, Nucleic acids research.

[41]  John Quackenbush,et al.  Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays , 2003, Genome Biology.

[42]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[43]  R. Nuttall,et al.  An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. , 2001, Nucleic acids research.

[44]  Margaret Werner-Washburne,et al.  Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays. , 2003, Nucleic acids research.

[45]  Thomas Preiss,et al.  Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock , 2003, Nature Structural Biology.

[46]  P. Lichter,et al.  Erratum: Optimization of high-density cDNA-microarray protocols by 'design of experiments' (Nucleic Acids Research (2003) vol. 31 (e67)) , 2003 .

[47]  S. Sealfon,et al.  Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. , 2002, Nucleic acids research.

[48]  Gunnar Wrobel,et al.  Optimization of high-density cDNA-microarray protocols by 'design of experiments'. , 2003, Nucleic acids research.

[49]  Yudong D. He,et al.  Effects of atmospheric ozone on microarray data quality. , 2003, Analytical chemistry.

[50]  R. Lempicki,et al.  Evaluation of gene expression measurements from commercial microarray platforms. , 2003, Nucleic acids research.