Application of the taguchi method to the analysis of the deposition step in microarray production

IEEE Transactions on Nanobioscience

Volumn 5, Issue 3, 2006, Pages 164-171

  Severgnini, Marco ^b   Pattini, Linda ^c   Consolandi, Clarissa ^b   Rizzi, Ermanno ^b   Battaglia, Cristina ^d   De Bellis, Gianluca ^c   Cerutti, Sergio ^a,c  

^a IEEE   (Italy)

^b INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

^c POLITECNICO DI MILANO   (Italy)

^d UNIVERSITY OF MILAN   (Italy)

Author keywords

Design of experiments; Microarray; Optimization; Taguchi methods

Indexed keywords

DESIGN OF EXPERIMENTS; MICROARRAYS; OLIGONUCLEOTIDE SEQUENCES; TAGUCHI METHODS;

ARRAYS; ATMOSPHERIC HUMIDITY; DEPOSITION; GLASS; OPTIMIZATION; ORTHOGONAL FREQUENCY DIVISION MULTIPLEXING; SULFUR COMPOUNDS;

ELECTRIC EQUIPMENT;

ALGORITHM; ARTICLE; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 33748605328     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2006.880851     Document Type: Article

References (34)

1. D. J. Lockhart, H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, and M. S. Chee et al., "Expression monitoring by hybridization to high-density oligonucleotide arrays," Nature Biotechnol., vol. 13, pp. 1675-1680, 1996.
2. R. Ramakrishnan, D. Dorris, A. Lublinsky, A. Nguyen, M. Domanus, and A. Prokhorova et al., "An assessment of motorola codelink microarray performance for gene expression profiling applications," Nucleic Acids Res., vol. 7, p. e30, 2002.
3. T. R. Hughes, M. Mao, A. R. Jones, J. Burchard, M. J. Marton, and K. W. Shannon et al., "Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer," Nature Biotechnol., vol. 4, pp. 342-347, 2001.
4. M. Schena, D. Shalon, R. W. Davis, and P. O. Brown, "Quantitative monitoring of gene expression patterns with a complementary DNA microarray," Science, vol. 270, pp. 467-470, 1995.
5. J. DeRisi, L. Penland, P. O. Brown, M. L. Bittner, P. S. Meltzer, and M. Ray et al., "Use of a cDNA microarray to analyse gene expression patterns in human cancer," Nature Genetics, vol. 4, pp. 457-460, 1996.
6. S. Singh-Gasson, R. D. Green, Y. Yue, C. Nelson, F. Blattner, and M. R. Sussman et al., "Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array," Nature Biotechnol., vol. 10, pp. 974-978, 1999.
7. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, and C. Stoeckert et al., "Minimum information about a microarray experiment (MIAME)-toward standards for microarray data," Nature Genetics, vol. 29, pp. 365-371, 2001.
8. V. Benes and M. Muckenthaler, "Standardization of protocols in cDNA microarray analysis," Trends Biochem. Sci., vol. 28, pp. 244-249, 2003.
9. M. J. Hessner, X. Wang, S. Khan, L. Meyer, M. Schlicht, and J. Tackes et al., "Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility," Nucleic Acids Res., vol. 31, p. e60, 2003.
10. J. E. Korkola, A. L. Estep, S. Pejavar, S. DeVries, R. Jensen, and F. M. Waldman, "Optimizing stringency for expression microarrays," Biotechniques, vol. 35, pp. 828-835, 2003.
11. A. Relogio, C. Schwager, A. Richter, W. Ansorge, and J. Valcarcel, "Optimization of oligonucleotide-based DNA microarrays," Nucleic Acids Res., vol. 30, p. e51, 2002.
12. M. Sartor, J. Schwanekamp, D. Halbleib, I. Mohamed, S. Karyala, and M. Medvedovic et al., "Microarray results improve significantly as hybridization approaches equilibrium," Biotechniques, vol. 36, pp. 790-796, 2004.
13. C. C. Chou, C. H. Chen, T. T. Lee, and K. Peck, "Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression," Nucleic Acids Res., vol. 32, p. e99, 2004.
14. [i4] S. D. Li, L. Tong, S. H. Cheng, Y. Ding, S. B. Li, and S. Q. Wang, "Fabrication and optimization of HLA-DRB1-12 oligonucleotide microarray," Zhongguo Shi Yan Xue Ye Xue Za Zhi, vol. 11, pp. 393-397, 2003.
15. J. Peplies, F. O. Glockner, and R. Amann, "Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes," Appl. Environ. Microbiol, vol. 69, pp. 1397-1407, 2003.
16. H. Zhao, T. Hastie, M. L. Whitfield, A. L. Borresen-Dale, and S. S. Jeffrey, "Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis," BMC Genomics, vol. 3, p. 31, 2002.
17. J. H. Xiao, D. X. Chen, J. W. Liu, Z. L. Liu, W. H. Wan, and N. Fang et al., "Optimization of submerged culture requirements for the production of mycelial growth and exopolysaccharide by Cordyceps jiangxiensis JXPJ 0109," J. Appl. Microbiol, vol. 96, pp. 1105-1116, 2004.
18. Y. L. Loukas, "A computer-based expert system designs and analyzes a 2(k-p) fractional factorial design for the formulation optimization of novel multicomponent liposomes," J. Pharm. Biomed. Anal., vol. 1, pp. 133-140, 1998.
19. S. E. Wildsmith, G. E. Archer, A. J. Winkley, P. W. Lane, and P. J. Bugelski, "Maximization of signal derived from cDNA microarrays," Biotechniques, vol. 30, pp. 202-206, 208, 2001.
20. M. D. Gupte and P. R. Kulkarni, "A study of antifungal antibiotic production by Streptomyces chattanoogensis MTCC 3423 using full factorial design," Lett Appl Microbiol, vol. 35, pp. 22-26, 2002.
21. V. Czitrom, "One-factor-at-a-time versus designed experiment," Amer. Statist., vol. 53, pp. 126-131, 1999.
22. G. Wrobel, J. Schlingemann, L. Hummerich, H. Kramer, P. Lichter, and M. Hahn, "Optimization of high-density cDNA-microarray protocols by 'design of experiments'," Nucleic Acids Res., vol. 31, p. e67, 2003.
23. B. D. Cobb and J. M. Clarkson, "A simple procedure for optimising the polymerase chain reaction (PCR) using modified Taguchi methods," Nucleic Acids Res., vol. 22, pp. 3801-3805, 1994.
24. G. Caetano-Anolles, "DAF optimization using Taguchi methods and the effect of thermal cycling parameters on DNA amplification," Biotechniques, vol. 25, pp. 472-476, 478-480, 1998,.
25. C. Jeney, O. Dobay, A. Lengyel, E. Adam, and I. Nasz, "Taguchi optimisation of ELISA procedures," J. Immunol. Methods, vol. 223, pp. 137-146, 1999.
26. P. J. Ross, Taguchi Techniques for Quality Engineering. New York: McGraw-Hill, 1988.
27. G. Taguchi, Introduction to Quality Engineering: Designing Quality Into Products and Processes. Tokyo, Japan: Asian Productivity Organization, 1986.
28. M. K. McQuain, K. Seale, J. Peek, S. Levy, and F. R. Haselton, "Effects of relative humidity and buffer additives on the contact printing of microarrays by quill pins," Anal. Biochem., vol. 320, pp. 281-291, 2003.
29. F. Diehl, S. Grahlmann, M. Beier, and J. D. Hoheisel, "Manufacturing DNA microarrays of high spot homogeneity and reduced background signal," Nucleic Acids Res., vol. 29, p. E38, 2001.
30. K. Lindroos, U. Liljedahl, M. Raitio, and A. C. Syvanen, "Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries," Nucleic Acids Res., vol. 29, p. E69-9, 2001.
31. S. Taylor, S. Smith, B. Windle, and A. Guiseppi-Elie, "Impact of surface chemistry and blocking strategies on DNA microarrays," Nucleic Acids Res., vol. 31, p. e87, 2003.
32. C. Consolandi, B. Castiglioni, R. Bordoni, E. Busti, C. Battaglia, and L. Rossi Bernardi et al., "Two efficient polymeric chemical platforms for oligonucleotide microarray preparation," Nucleosides Nucleotides Nucleic Acids, vol. 21, pp. 561-580, 2002.
33. C. Consolandi, M. Severgnini, B. Castiglioni, R. Bordoni, A. Frosini, and C. Battaglia et al., "A structured chitosan-based platform for biomolecule attachment to solid surfaces: application to DNA microarray preparation," Bioconjug. Chem., vol. 2, pp. 371-377, 2006.
34. R. K. Roy, A Primer on the Taguchi Method. Dearborn, MI: SME, 1990.