In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays

Journal of Molecular Diagnostics

Volumn 8, Issue 2, 2006, Pages 183-192

  Ma, Changqing ^a   Lyons Weiler, Maureen ^a   Liang, Wenjing ^a   LaFramboise, William ^a   Gilbertson, John R ^a   Becich, Michael J ^a   Monzon, Federico A ^a  

^a UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA; NUCLEOTIDE; RNA;

ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA HYBRIDIZATION; DNA MICROARRAY; EUKARYOTE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; IN VITRO STUDY; INCUBATION TIME; INTERMETHOD COMPARISON; REPRODUCIBILITY;

EUKARYOTA;

EID: 33744549560     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2006.050077     Document Type: Article

References (27)

1. Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA 2004, 101:811-816
2. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AAM, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET. Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009
3. Johnson K, Lin S: QA/QC as a pressing need for microarray analysis: meeting report from CAMDA'02. BioTechniques 2003, Mar, Suppl:62-63
4. Tan PK, Downey TJ, Spitznagel Jr EL, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31:5676-5684
5. Puskás LG, Zvara Á, Hackler Jr L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. BioTechniques 2002, 32:1330-1340
6. Baugh LR, Hill AA, Brown EL, Hunter CP: Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 2001, 29:e29
7. Gelder RNV, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH: Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 1990, 87:1663-1667
8. Dorris DR, Ramakrishnan R, Trakas D, Dudzik F, Belval R, Zhao C, Nguyen A, Domanus M, Mazumder A: A highly reproducible, linear, and automated sample preparation method for DNA microarrays. Genome Res 2002, 12:976-984
9. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Norton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotech 1996, 14:1675-1680
10. CodeLink Gene Expression System: Manual Labeled cRNA Target Preparation. Edited by GE Healthcare, Piscataway, 2004
11. Affymetrix: Affymetrix GeneChip Expression Analysis Technical Manual. Santa Clara, Affymetrix, 2001
12. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001, 2:research 0032.1-0032.11
13. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98:31-36
14. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868
15. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121
16. Dumur CI, Garrett CT, Archer KJ, Nasim S, Wilkinson DS, Ferreira-Gonzalez A: Evaluation of a linear amplification method for small samples used on high-density oligonucleotide microarray analysis. Anal Biochem 2004, 331:314-321
17. Li Y, Li T, Liu S, Qiu M, Han Z, Jiang Z, Li R, Ying K, Xie Y, Mao Y: Systematic comparison of the fidelity of aRNA, mRNA and T-RNA on gene expression profiling using cDNA microarray. J Biotechnol 2004, 107:19-28
18. Zhao H, Hastie T, Whitfield M, Borresen-Dale A-L, Jeffrey S: Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics 2002, 3:31
19. Daly TM, Dumaual CM, Dotson CA, Farmen MW, Kadam SK, Hockett RD: Precision profiling and components of variability analysis for Affymetrix microarray assays run in a clinical context. J Mol Diagn 2005, 7:404-412
20. Spiess A-N, Mueller N, Ivell R: Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 2003, 4:44
21. Sastry SS, Ross BM: Nuclease activity of T7 RNA polymerase and the heterogeneity of transcription elongation complexes. J Biol Chem 1997, 272:8644-8652
22. Shippy R, Sendera T, Lockner R, Palaniappan C, Kaysser-Kranich T, Watts G, Alsobrook J: Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 2004, 5:61
23. Yauk CL, Berndt ML, Williams A, Douglas GR: Comprehensive comparison of six microarray technologies. Nucleic Acids Res 2004, 32:e124
24. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods 2005, 2:337-344
25. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JGN, Geoghegan J, Germino G, Griffin C, Hilmar 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: Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2:345-350
26. 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: Standardizing global gone expression analysis between laboratories and across platforms. Nat Methods 2005, 2:351-356
27. Dobbin KK, Beer DG, Meyerson M, Yeatman TJ, Gerald WL, Jacobson JW, Conley B, Buetow KH, Heiskanen M, Simon RM, Minna JD, Girard L, Misek DE, Taylor JM, Hanash S, Naoki K, Hayes DN, Ladd-Acosta C, Enkemann SA, Viale A, Giordano TJ: Interlaboratory comparability study of cancer gene expression analysis using oligo-nucleotide microarrays. Clin Cancer Res 2005, 11:565-572