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Comparability of Microarray Experiments from the Instrument and the Sample Site and Approaches Towards Standardization

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Standardization and Quality Assurance in Fluorescence Measurements II

Part of the book series: Springer Series on Fluorescence ((SS FLUOR,volume 6))

Abstract

This chapter will give a short introduction into current technology related and biology related problems in the microarray technology, approaches undertaken to overcome such problems, and, finally, it will present some key features of most commercial platforms which have emerged over the past few years and may help to solve some technical problems at least related to the instrumentation side. Standard operating protocols, guidelines, as well as careful and routine checking of the instrumentation, such as spotting or hybridization devices as well as microarray reader (laser/charge-coupled device (CCD) camera), are necessary for running a microarray platform successfully. Furthermore, standardized reference material, databases, and analysis software will be necessary for generating confidential data across all platforms and laboratories and will additionally support the full power of DNA microarray technology as a research and diagnostic tool.

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References

  1. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467–470

    Article  CAS  Google Scholar 

  2. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680

    Article  CAS  Google Scholar 

  3. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93:10614–10619

    Article  CAS  Google Scholar 

  4. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863–14868

    Article  CAS  Google Scholar 

  5. Eisen MB, Brown PO (1999) DNA arrays for analysis of gene expression. Meth Enzymol 303:179–205

    Article  CAS  Google Scholar 

  6. Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lander ES (1998) Large-scale identification, mapping, genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082

    Article  CAS  Google Scholar 

  7. Taniguchi M, Miura K, Iwao H, Yamanaka S (2001) Quantitative assessment of DNA microarrays-comparison with Northern Blot analyses. Genomics 71:34–39

    Article  CAS  Google Scholar 

  8. Butte A (2002) The use and analysis of microarray data. Nat Rev Drug Discovery 1:951–960

    Article  CAS  Google Scholar 

  9. Hoheisel JD (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 7:200–210

    Article  CAS  Google Scholar 

  10. Anderson MT, Foy CA (2005) The development of microarray standards. Anal Bioanal Chem 381:87–97

    Article  CAS  Google Scholar 

  11. Draghici S, Khatri P, Eklund AC, Szallasi Z (2005) Reliability and reproducibility issues in DNA microarray measurements. Trends Genetics 22:101–1099

    Article  CAS  Google Scholar 

  12. Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M (2004) A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. BMC Genomics 5:2

    Article  Google Scholar 

  13. Holland MJ (2002) Transcript abundance in yeast varies over six orders of magnitude. J Biol Chem 277:14363–14366

    Article  CAS  Google Scholar 

  14. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38:366–379

    Article  CAS  Google Scholar 

  15. Liang RQ, Li W, Li Y, Tan CY, Li JX, Jin YX, Ruan KC (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res 33:e17

    Article  CAS  Google Scholar 

  16. www.psb.rug.ac.be/CAGE/

    Google Scholar 

  17. Hubbell E, Liu WM, Mei R (2002) Robust estimators for expression analysis. Bioinformatics 18:1585–1592

    Article  CAS  Google Scholar 

  18. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30:e48

    Article  Google Scholar 

  19. Bartosiewicz M, Trounstine M, Barker D, Jonston R, Buckpitt A (2000) Development of a toxicological gene array and quantitative assessment of this technology. Arch Biochem Biophys 376:66–73

    Article  CAS  Google Scholar 

  20. Winzeler EA, Schena M, Davis RW (1999) Fluorescence-based expression monitoring using microarrays. Meth Enzymol 306:3–18

    Article  CAS  Google Scholar 

  21. Guo Z, Guilfoylem RA, Thiel AJ, Wang R, Smith LM (1994) Direct fluorescence analysis of genetic polymorphism by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res 22:5456–65

    Article  CAS  Google Scholar 

  22. Randolph JB, Waggoner AS (1997) Stability, specifity and fluorescence brightness of multiply-labeled fluorescent DNA probes. Nucleic Acids Res 25:2923–2929

    Article  CAS  Google Scholar 

  23. Perraut F, Lagrange A, Pouteau P, Peyssonneaux O, Puget P, McGall G, Menou L, Gonzalez R, Labeye P, Ginot F (2002) A new generation of scanners for DNA chips. Biosens Bioelectron 17:803–813

    Article  CAS  Google Scholar 

  24. Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J (2004) Universal Reference RNA as a standard for microarray experiments. BMC Genomics 5:20

    Article  Google Scholar 

  25. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J (2002) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 3:research0062.1-0062.12

    Google Scholar 

  26. Sterrenburg E, Turk R, Boer JM, van Ommen GB, den Dunnen JT (2002) A common reference for cDNA microarray hybridizations. Nucleic Acids Res 30:e116

    Article  Google Scholar 

  27. Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183:545–556

    Article  CAS  Google Scholar 

  28. Williams BA, Gwirtz RM, Wold BJ (2004) Genomic DNA as a cohybridization standard for mammalian microarray measurements. Nucleic Acids Res 32:e81

    Article  CAS  Google Scholar 

  29. Dudley AM, Aach J, Steffen MA, Church GM (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Nat Acad Sci USA 99(11):7554–7559

    Article  CAS  Google Scholar 

  30. Weil MR, Macatee T, Garner HR (2002) Toward a universal standard: comparing two methods for standardizing spotted microarray data. Biotechniques 32:1310–1314

    CAS  Google Scholar 

  31. Cronin M, Ghosh K, Sistare F, Quackenbush J, Vilker V, O'Connell C (2004) Universal RNA reference materials for gene expression. Clin Chem 50:1464–1471

    Article  CAS  Google Scholar 

  32. Forster T, Roy D, Ghazal P (2003) Experiments using microarray technology: limitations and standard operating procedures. J Endocrinol 178(2):195–204

    Article  CAS  Google Scholar 

  33. Tumor Analysis Best Practices Working Group (2004) Expression profiling – best practices for data generation and interpretation in clinical trials. Nat Rev Genet 5:229–237

    Google Scholar 

  34. Leung YF, Cavalieri D (2003) Fundamentals of cDNA microarray data analysis. Trends Genet 19:649–59

    Article  CAS  Google Scholar 

  35. Weeraratna AT, Nagel JE, de Mello-Coelho V, Taub DD (2004) Gene expression profiling: from microarrays to medicine. J Clin Immunol 24(3):213–224

    Article  CAS  Google Scholar 

  36. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371

    Article  CAS  Google Scholar 

  37. Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 3:RESEARCH0046

    Google Scholar 

  38. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA (2003) ArrayExpress – a public repository for microarray gene expression data at the EBI. Nucl Acids Res 31(1):68–71

    Article  CAS  Google Scholar 

  39. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G (2003) The Stanford Microarray Database: data access and quality assessment tools. Nucl Acids Res 31:94–96

    Article  CAS  Google Scholar 

  40. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18:405–412

    Article  CAS  Google Scholar 

  41. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24:227–235

    Article  CAS  Google Scholar 

  42. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676–5684

    Article  CAS  Google Scholar 

  43. Yauk CL, Berndt ML, Williams A, Douglas GR (2004) Comprehensive comparison of six microarray technologies. Nucleic Acids Res 32:e124

    Article  CAS  Google Scholar 

  44. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J (2005) Independence and reproducibility across microarray platforms. Nat Methods 2:337–344

    Article  CAS  Google Scholar 

  45. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345–349

    Article  CAS  Google Scholar 

  46. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'Malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H, Members of the Toxicogenomics Research Consortium (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2:351–356

    Google Scholar 

  47. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342–347

    Article  CAS  Google Scholar 

  48. Dickinson T, Craumer W (2003) RNA profiling with bead-based array platforms (Tutorial): Sentrix arrays for focused gene expression studies across large sample sets. Gen Engin News 23:15

    Google Scholar 

  49. Liu RH, Nguyen T, Schwarzkopf K, Fuji HS, Petrova A, Siuda T, Peyvan K, Bizak M, Danley D, McShea A (2006) Fully integrated miniature device for automated gene expression DNA microarray processing. Anal Chem 78:1980–1986

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Ihnestr. 63–73, 14195, Berlin, Germany

    Wilfried Nietfeld

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  1. Wilfried Nietfeld
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Correspondence to Wilfried Nietfeld .

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Ute Resch-Genger

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Nietfeld, W. (2008). Comparability of Microarray Experiments from the Instrument and the Sample Site and Approaches Towards Standardization . In: Resch-Genger, U. (eds) Standardization and Quality Assurance in Fluorescence Measurements II. Springer Series on Fluorescence, vol 6. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4243_2008_033

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