Artefacts and reliability of DNA microarray expression profiling data

Current Genomics

Volumn 4, Issue 7, 2003, Pages 615-621

  Drobyshev, Alexei L ^a   de Angelis, Martin Hrabé ^a   Beckers, Johannes ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Cross hybridisation; DNA chip; Expression profiling; Fluorescent labelling; Hybirisation specificity; Hybridisation; Image processing; Microarray artefacts

Indexed keywords

DNA; FLUORESCENT DYE; RNA;

ARTIFACT; DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HYBRIDIZATION; IMAGE PROCESSING; ISOTOPE LABELING; METHODOLOGY; NONHUMAN; QUALITY CONTROL; RELIABILITY; REVIEW; RNA EXTRACTION;

EID: 0141616511     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389202033490204     Document Type: Review

References (46)

1. Schena, M., Shalon, D., Davis, R.W., Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270: 467-470.
2. Li, X., Gu, W., Mohan, S., Baylink, D.J. DNA microarrays: their use and misuse. Microcirculation, 2002, 9: 13-22.
3. Vingron, M., Hoheisel, J. Computational aspects of expression data. J. Mol. Med, 1999, 77: 3-7.
4. Quackenbush, J. Computational analysis of microarray data. Nat. Rev. Genet., 2001, 2: 418-427.
5. Sabatti, C. Statistical Issues in Microarray Analysis. Curr. Genomics, 2002, 3: 7-12.
6. Millican, D.S., Bird, I.M. Extraction of cellular and tissue RNA. Methods Mol. Biol, 1998, 105: 315-324.
7. Krafft, A.E., Duncan, B.W., Bijwaard, K.E., Taubenberger, J.K., Lichy, J.H. Optimization of the Isolation and Amplification of RNA From Formalin-fixed, Paraffin-embedded Tissue: The Armed Forces Institute of Pathology Experience and Literature Review. Mol. Diagn., 1997, 2: 217-230.
8. Hegde, P., Qi, R., Abernathy, K., Gay, C., Dharap, S., Gaspard, R., Hughes, J.E., Snesrud, E., Lee, N., Quackenbush, J. A concise guide to cDNA microarray analysis. Biotechniques, 2000, 29: 548-550, 552-544, 556 passim.
9. Beaucage, S.L. Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications. Curr. Med. Chem., 2001, 8: 1213-1244.
10. Turner, A.P. Tech. Sight. Biochemistry. Biosensors-sense and sensitivity. Science, 2000, 290: 1315-1317.
11. Peterson, A.W., Heaton, R.J., Georgiadis, R.M. The effect of surface probe density on DNA hybridization. Nucleic Acids Res., 2001, 29: 5163-5168.
12. Lipshutz, R.J., Fodor, S.P., Gingeras, T.R., Lockhart, D.J. High density synthetic oligonucleotide arrays. Nat. Genet., 1999, 21: 20-24.
13. Machl, A.W., Schaab, C., Ivanov, I. Improving DNA array data quality by minimising 'neighbourhood' effects. Nucleic Acids Res., 2002, 30: e127.
14. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O., Davis, R.W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA, 1996, 93: 10614-10619.
15. Yu, J., Othman, M.I., Farjo, R., Zareparsi, S., MacNee, S.P., Yoshida, S., Swaroop, A. Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays. Mol. Vis., 2002, 8: 130-137.
16. Stears, R.L., Getts, R.C., Gullans, S.R. A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol. Genomics, 2000, 3: 93-99.
17. Manduchi, E., Scearce, L.M., Brestelli, J.E., Grant, G.R., Kaestner, K.H., Stoeckert, C.J., Jr. Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol. Genomics, 2002, 10: 169-179.
18. Wang, E., Miller, L.D., Ohnmacht, G.A., Liu, E.T., Marincola, F.M. High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol., 2000, 18: 457-459.
19. Baugh, L.R., Hill, A.A., Brown, E.L., Hunter, C.P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res., 2001, 29: E29.
20. Iscove, N.N., Barbara, M., Gu, M., Gibson, M., Modi, C., Winegarden, N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol., 2002, 20: 940-943.
21. Relogio, A., Schwager, C., Richter, A., Ansorge, W., Valcarcel, J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res., 2002, 30: e51.
22. Li, Y., Zon, G., Wilson, W.D. NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex. Proc. Natl. Acad. Sci. USA, 1991, 88: 26-30.
23. Li, Y., Zon, G., Wilson, W.D. Thermodynamics of DNA duplexes with adjacent G.A mismatches. Biochemistry, 1991, 30: 7566-7572.
24. Krause, A., Haas, S.A., Coward, E., Vingron, M. SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. Nucleic Acids Res., 2002, 30: 299-300.
25. Yershov, G., Barsky, V., Belgovskiy, A., Kirillov, E., Kreindlin, E., Ivanov, I., Parinov, S., Guschin, D., Drobishev, A., Dubiley, S., Mirzabekov, A. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. USA, 1996, 93: 4913-4918.
26. Gerry, N.P., Witowski, N.E., Day, J., Hammer, R.P., Barany, G., Barany, F. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol., 1999, 292: 251-262.
27. Broude, N.E., Woodward, K., Cavallo, R., Cantor, C.R., Englert, D. DNA microarrays with stem-loop DNA probes: preparation and applications. Nucleic Acids Res., 2001, 29: E92.
28. Fotin, A.V., Drobyshev, A.L., Proudnikov, D.Y., Perov, A.N., Mirzabekov, A.D. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res., 1998, 26: 1515-1521.
29. Belosludtsev, Y., Iverson, B., Lemeshko, S., Eggers, R., Wiese, R., Lee, S., Powdrill, T., Hogan, M. DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal. Biochem., 2001, 292: 250-256.
30. Lemeshko, S.V., Powdrill, T., Belosludtsev, Y.Y., Hogan, M. Oligonucleotides form a duplex with non-helical properties on a positively charged surface. Nucleic Acids Res., 2001, 29: 3051-3058.
31. Shi, S.J., Scheffer, A., Bjeldanes, E., Reynolds, M.A., Arnold, L.J. DNA exhibits multi-stranded binding recognition on glass microarrays. Nucleic Acids Res., 2001, 29: 4251-4256.
32. Nishinaka, T., Shinohara, A., Ito, Y., Yokoyama, S., Shibata, T. Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination. Proc. Natl. Acad. Sci. USA, 1998, 95: 11071-11076.
33. Martinez, M.J., Aragon, A.D., Rodriguez, A.L., Weber, J.M., Timlin, J.A., Sinclair, M.B., Haaland, D.M., Werner-Washburne, M. Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays. Nucleic Acids Res., 2003, 31: e18.
34. Kane, M.D., Jatkoe, T.A., Stumpf, C.R., Lu, J., Thomas, J.D., Madore, S.J. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res., 2000, 28: 4552-4557.
35. Dai, H., Meyer, M., Stepaniants, S., Ziman, M., Stoughton, R. Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res., 2002, 30: e86.
36. Drobyshev, A.L., Machka, C., Horsch, M., Seltmann, M., Liebscher, V., Hrabe De Angelis, M., Beckers, J. Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies. Nucleic Acids Res., 2003, 31: E1-1.
37. Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., Brown, E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 1996, 14: 1675-1680.
38. Yue, H., Eastman, P.S., Wang, B.B., Minor, J., Doctolero, M.H., Nuttall, R.L., Stack, R., Becker, J.W., Montgomery, J.R., Vainer, M., Johnston, R. An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res., 2001, 29: E41-41.
39. Yuen, T., Wurmbach, E., Pfeffer, R.L., Ebersole, B.J., Sealfon, S.C. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res., 2002, 30: e48.
40. Basarsky, T., Verdnik, D., Zhay, J.Y., and Wellis, D. Overview of a Microarray Scanner: Design Essentials for an Integrated Acquisition and Analysis Platform. In Microarray Biochip Technology, 2000, S. M, ed. (Natick, MA: Eaton Publishing), pp. 265-284.
41. Tran, P.H., Peiffer, D.A., Shin, Y., Meek, L.M., Brody, J.P., Cho, K.W. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals, Nucleic Acids Res., 2002, 30: e54.
42. Zhou, Y.X., Kalocsai, P., Chen, J.Y., and Shams, S. Information Processing Issues and Solutions Associated with Microarray Technology. In Microarray Biochip Technology, 2000, M. Schena, ed. (Natick, MA: Eaton Publishing), pp. 167-200.
43. Wang, X., Ghosh, S., Guo, S.W. Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res., 2001, 29: E75-75.
44. Tseng, G.C., Oh, M.K., Rohlin, L., Liao, J.C., Wong, W.H. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res., 2001, 29: 2549-2557.
45. Lee, M.L., Kuo, F.C., Whitmore, G.A., Sklar, J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA, 2000, 97: 9834-9839.
46. Diehl, F., Grahlmann, S., Beier, M., Hoheisel, J.D. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res., 2001, 29: E38.