Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays

American Journal of Pathology

Volumn 165, Issue 5, 2004, Pages 1799-1807

  Bibikova, Marina ^a   Talantov, Dimitri ^b   Chudin, Eugene ^a   Yeakley, Joanne M ^a   Chen, Jing ^a   Doucet, Dennis ^a   Wickham, Eliza ^a   Atkins, David ^b   Barker, David ^a   Chee, Mark ^a   Wang, Yixin ^b   Fan, Jian Bing ^a  

^a ILLUMINA INC   (United States)

^b JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; FORMALDEHYDE; PARAFFIN; RNA;

ANALYTIC METHOD; ARTICLE; CANCER; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME; HUMAN; HUMAN TISSUE; PRIORITY JOURNAL; REPRODUCIBILITY; RNA ISOLATION; STORAGE; TISSUE SECTION; VALIDATION PROCESS;

EID: 7244245443     PISSN: 00029440     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0002-9440(10)63435-9     Document Type: Article

References (32)

1. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol 1996, 14:1675-1680
2. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537
3. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D: Molecular portraits of human breast tumours. Nature 2000, 406:747-752
4. Welsh JB, Sapinoso LM, Su AI, Kern SG, Wang-Rodriguez J, Moskaluk CA, Frierson HF, Jr., Hampton GM: Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res 2001, 61:5974-5978
5. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM: Delineation of prognostic biomarkers in prostate cancer. Nature 2001, 412:822-826
6. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536
7. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR: Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci USA 2001, 98:11462-11467
8. Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P: Unlocking the archive - gene expression in paraffin-embedded tissue. J Pathol 2001, 195:66-71
9. Godfrey TE, Kim SH, Chavira M, Ruff DW, Warren RS, Gray JW, Jensen RH: Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5′ nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn 2000, 2:84-91
10. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH: An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 2002, 30:E4
11. Abrahamsen HN, Steiniche T, Nexo E, Hamilton-Dutoit SJ, Sorensen BS: Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: a methodological study on lymph nodes from melanoma patients. J Mol Diagn 2003, 5:34-41
12. Lehmann U, Bock O, Glockner S, Kreipe H: Quantitative molecular analysis of laser-microdissected paraffin-embedded human tissues. Pathobiology 2000, 68:202-208
13. Daigo Y, Chin SF, Gorringe KL, Bobrow LG, Ponder BA, Pharoah PD, Caldas C: Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers: a new approach for the molecular analysis of paraffin-embedded cancer tissue. Am J Pathol 2001, 158:1623-1631
14. Palmieri G, Ascierto PA, Cossu A, Mozzillo N, Motti ML, Satriano SM, Botti G, Caraco C, Celentano E, Satriano RA, Lissia A, Tanda F, Pirastu M, Castello G: Detection of occult melanoma cells in paraffin-embedded histologically negative sentinel lymph nodes using a reverse transcriptase polymerase chain reaction assay. J Clin Oncol 2001, 19:1437-1443
15. Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H: Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 2001, 158: 419-429
16. Lehmann U, Glockner S, Kleeberger W, von Wasielewski HF, Kreipe H: Detection of gene amplification in archival breast cancer speciens by laser-assisted microdissection and quantitative real-time polymerase chain reaction. Am J Pathol 2000, 156:1855-1864
17. Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB: Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol 2004, 164:35-42
18. Fan JB, Yeakley JM, Bibikova M, Chudin E, Wickham E, Chen J, Doucet D, Rigault P, Zhang B, Shen R, McBride C, Li HR, Fu XD, Oliphant A, Barker DL, Chee MS: A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res 2004, 14:878-885
19. Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods 1996, 10:283-288
20. Barker DL, Theriault G, Che D, Dickinson T, Shen R, Kain R: Self-assembled random arrays: high-performance imaging and genomics applications on a high-density microarray platform. Proc SPIE 2003, 4966:1-11
21. Fan JB, Oliphant A, Shen R, Kermani B, Garcia F, Gunderson K, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS: Highly parallel SNP genotyping. Cold Spring Harbor Symposia on Quantitative Biology 2003, 68:69-78
22. Gunderson KL, Kruglyak S, Graige MS, Garcia F, Kermani B, Zhao C, Che D, Dickinson T, Wickham E, Bierle J, Doucet D, Milewski M, Yang R, Siegmund C, Haas J, Zhou L, Oliphant A, Fan JB, Barnard S, Chee MS: Decoding Randomly Ordered DNA Arrays. Genome Res 2004, 14:870-877
23. Galinsky VL: Automatic registration of microarray images. II. Hexagonal grid. Bioinformatics 2003, 19:1832-1836
24. Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3:research0048
25. Weisstein EW: Fisher's Exact Test: From MathWorld-A Wolfram Web Resource: http://mathworld.wolfram.com/FishersExactTest.html., 1999
26. Naimi B, Latil A, Fournier G, Mangin P, Cussenot O, Berthon P: Down-regulation of (IIIb) and (IIIc) isoforms of fibroblast growth factor receptor 2 (FGFR2) is associated with malignant progression in human prostate. Prostate 2002, 52:245-252
27. Lee DH, Yang Y, Lee SJ, Kim KY, Koo TH, Shin SM Song KS, Lee YH, Kim YJ, Lee JJ, Choi I, Lee JH: Macrophage inhibitory cytokine-1 induces the invasiveness of gastric cancer cells by up-regulating the urokinase-type plasminogen activator system. Cancer Res 2003, 63:4648-4655
28. Liu D, Buluwela L, Ali S, Thomson S, Gomm JJ, Coombes RC: Retroviral infection of the FGF2 gene into MCF-7 cells induces branching morphogenesis, retards cell growth and suppresses tumorigenicity in nude mice. Eur J Cancer 2001, 37:268-280
29. Eppler E, Zapf J, Bailer N, Falkmer UG, Falkmer S, Reinecke M: IGF-I in human breast cancer: low differentiation stage is associated with decreased IGF-I content. Eur J Endocrinol 2002, 146:813-821
30. Bieche I, Onody P, Tozlu S, Driouch K, Vidaud M, Lidereau R: Prognostic value of ERBB family mRNA expression in breast carcinomas. Int J Cancer 2003, 106:758-765
31. Deyoung MP, Scheurle D, Damania H, Zylberberg C, Narayanan R: Down's syndrome-associated single minded gene as a novel tumor marker. Anticancer Res 2002, 22:3149-3157
32. DeYoung MP, Tress M, Narayanan R: Identification of Down's syndrome critical locus gene SIM2-S as a drug therapy target for solid tumors. Proc Natl Acad Sci USA 2003, 100:4760-4765