Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  April, Craig ^a   Klotzle, Brandy ^a   Royce, Thomas ^a   Wickham Garcia, Eliza ^a   Boyaniwsky, Tanya ^a   Izzo, John ^a   Cox, Donald ^a   Jones, Wendell ^b   Rubio, Renee ^c   Holton, Kristina ^c   Matulonis, Ursula ^c   Quackenbush, John ^c   Fan, Jian Bing ^a  

^a ILLUMINA INC   (United States)

^b Expression Analysis   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOASSAY; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENOME; HUMAN; HUMAN TISSUE; HYBRIDIZATION; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; SENSITIVITY ANALYSIS; VALIDATION PROCESS; CHEMISTRY; DNA MICROARRAY; FROZEN SECTION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN GENOME; METHODOLOGY; RNA STABILITY; TISSUE FIXATION; TUMOR CELL LINE;

FORMALDEHYDE; PARAFFIN; RNA;

CELL LINE, TUMOR; FORMALDEHYDE; FROZEN SECTIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA STABILITY; RNA, NEOPLASM; TISSUE FIXATION; TRANSCRIPTION, GENETIC;

EID: 77949529725     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008162     Document Type: Article

References (37)

1. Bouchie A (2004) Coming soon: a global grid for cancer research. Nat Biotechnol 22: 1071-1073.
2. Ramaswamy S (2004) Translating cancer genomics into clinical oncology. N Engl J Med 350: 1814-1816.
3. Farragher SM, Tanney A, Kennedy RD, Paul Harkin D (2008) RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol 130: 435-445.
4. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K (1999) Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 27: 4436-4443.
5. Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, et al. (2008) Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer 98: 1403-1414.
6. Coudry RA, Meireles SI, Stoyanova R, Cooper HS, Carpino A, et al. (2007) Successful application of microarray technology to microdissected formalinfixed, paraffin-embedded tissue. J Mol Diagn 9: 70-79.
7. Scicchitano MS, Dalmas DA, Bertiaux MA, Anderson SM, Turner LR, et al. (2006) Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J Histochem Cytochem 54: 1229-1237.
8. Tomlins SA, Mehra R, Rhodes DR, Shah RB, Rubin MA, et al. (2006) Whole transcriptome amplification for gene expression profiling and development of molecular archives. Neoplasia 8: 153-162.
9. Fan JB, Yeakley JM, Bibikova M, Chudin E, Wickham E, et al. (2004) A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res 14: 878-885.
10. Bibikova M, Talantov D, Chudin E, Yeakley JM, Chen J, et al. (2004) Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol 165: 1799-1807.
11. Bibikova M, Yeakley JM, Chudin E, Chen J, Wickham E, et al. (2004) Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis. Clin Chem 50: 2384-2386.
12. Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, et al. (2008) Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst 100: 815-825.
13. Abramovitz M, Ordanic-Kodani M, Wang Y, Li Z, Catzavelos C, et al. (2008) Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. Biotechniques 44: 417-423.
14. Haller AC, Kanakapalli D, Walter R, Alhasan S, Eliason JF, et al. (2006) Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy. BMC Clin Pathol 6: 9.
15. Paik S (2006) Methods for gene expression profiling in clinical trials of adjuvant breast cancer therapy. Clin Cancer Res 12: 1019s-1023s.
16. Ravo M, Mutarelli M, Ferraro L, Grober OM, Paris O, et al. (2008) Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays. Lab Invest 88: 430-440.
17. Bibikova M, Chudin E, Arsanjani A, Zhou L, Garcia EW, et al. (2007) Expression signatures that correlated with Gleason score and relapse in prostate cancer. Genomics 89: 666-672.
18. Li HR, Wang-Rodriguez J, Nair TM, Yeakley JM, Kwon YS, et al. (2006) Twodimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res 66: 4079-4088.
19. Nakagawa T, Kollmeyer TM, Morlan BW, Anderson SK, Bergstralh EJ, et al. (2008) A tissue biomarker panel predicting systemic progression after PSA recurrence post-definitive prostate cancer therapy. PLoS ONE 3: e2318.
20. Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, et al. (2008) Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 359: 1995-2004.
21. Lee J, Hever A, Willhite D, Zlotnik A, Hevezi P (2005) Effects of RNA degradation on gene expression analysis of human postmortem tissues. Faseb J 19: 1356-1358.
22. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, et al. (2004) A novel, highperformance random array platform for quantitative gene expression profiling. Genome Res 14: 2347-2356.
23. 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.
24. Medeiros F, Rigl CT, Anderson GG, Becker SH, Halling KC (2007) Tissue handling for genome-wide expression analysis: a review of the issues, evidence, and opportunities. Arch Pathol Lab Med 131: 1805-1816.
25. Hewitt SM, Lewis FA, Cao Y, Conrad RC, Cronin M, et al. (2008) Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Arch Pathol Lab Med 132: 1929-1935.
26. Ribeiro-Silva A, Zhang H, Jeffrey SS (2007) RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 8: 118.
27. Linton K, Hey Y, Dibben S, Miller C, Freemont A, et al. (2009) Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays. Biotechniques 47: 587-596.
28. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH (2002) An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 30: E4.
29. Penland SK, Keku TO, Torrice C, He X, Krishnamurthy J, et al. (2007) RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest 87: 383-391.
30. Chung CH, Parker JS, Ely K, Carter J, Yi Y, et al. (2006) Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-kappaB signaling as characteristics of a high-risk head and neck squamous cell carcinoma. Cancer Res 66: 8210-8218.
31. Paik S, Kim CY, Song YK, Kim WS (2005) Technology insight: Application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Clin Pract Oncol 2: 246-254.
32. Hosey AM, Gorski JJ, Murray MM, Quinn JE, Chung WY, et al. (2007) Molecular basis for estrogen receptor alpha deficiency in BRCA1-linked breast cancer. J Natl Cancer Inst 99: 1683-1694.
33. Knight JF, Shepherd CJ, Rizzo S, Brewer D, Jhavar S, et al. (2008) TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer. Br J Cancer 99: 1849-1858.
34. Fedorowicz G, Guerrero S, Wu TD, Modrusan Z (2009) Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched freshfrozen ovarian adenocarcinomas. BMC Med Genomics 2: 23.
35. Casey T, Bond J, Tighe S, Hunter T, Lintault L, et al. (2009) Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat 114: 47-62.
36. Lassmann S, Kreutz C, Schoepflin A, Hopt U, Timmer J, et al. (2009) A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J Mol Med 87: 211-224.
37. Chien J, Fan JB, Bell DA, April C, Klotzle B, et al. (2009) Analysis of gene expression in stage I serous tumors identifies critical pathways altered in ovarian cancer. Gynecol Oncol 114: 3-11.