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. 10.1038/415530a.
Article
Google Scholar
Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004, 351: 2817-2826. 10.1056/NEJMoa041588.
Article
CAS
PubMed
Google Scholar
van't Veer LJ, Bernards R: Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature. 2008, 452: 564-570. 10.1038/nature06915.
Article
PubMed
Google Scholar
Lassmann S, Kreutz C, Schoepflin A, Hopt U, Timmer J, Werner M: A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J Mol Med. 2009, 87: 211-224. 10.1007/s00109-008-0419-y.
Article
CAS
PubMed
Google Scholar
Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Glickman JN, Ikeda K, Hashimoto M, Watanabe G, Daidone MG, Roayaie S, Schwartz M, Thung S, Salvesen HB, Gabriel S, Mazzaferro V, Bruix J, Friedman SL, Kumada H, Llovet JM, Golub TR: Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med. 2008, 359: 1995-2004. 10.1056/NEJMoa0804525.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glas AM, Floore A, Delahaye LJ, Witteveen AT, Pover RC, Bakx N, Lahti-Domenici JS, Bruinsma TJ, Warmoes MO, Bernards R, Wessels LF, Van't Veer LJ: Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics. 2006, 7: 278-10.1186/1471-2164-7-278.
Article
PubMed
PubMed Central
Google Scholar
van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, 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. 10.1056/NEJMoa021967.
Article
CAS
PubMed
Google Scholar
Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sørlie T, Dai H, He YD, van't Veer LJ, Bartelink H, van de Rijn M, Brown PO, van de Vijver MJ: Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci USA. 2005, 102: 3738-3743. 10.1073/pnas.0409462102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Troester MA, Hoadley KA, Sørlie T, Herbert BS, Børresen-Dale AL, Lønning PE, Shay JW, Kaufmann WK, Perou CM: Cell-type-specific responses to chemotherapeutics in breast cancer. Cancer Res. 2004, 64: 4218-4226. 10.1158/0008-5472.CAN-04-0107.
Article
CAS
PubMed
Google Scholar
Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K: Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res. 1999, 27: 4436-4443. 10.1093/nar/27.22.4436.
Article
CAS
PubMed
PubMed Central
Google Scholar
Balogh GA, Russo J, Mailo DA, Heulings R, Russo PA, Morrison P, Sheriff F, Russo IH: The breast of parous women without cancer has a different genomic profile compared to those with cancer. Int J Oncol. 2007, 31: 1165-1175.
CAS
PubMed
Google Scholar
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. 10.1016/S0002-9440(10)63985-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Madabusi LV, Latham GJ, Andruss BF: RNA extraction for arrays. Methods Enzymol. 2006, 411: 1-14.
Article
CAS
PubMed
Google Scholar
Cardoso F, Van't Veer L, Rutgers E, Loi S, Mook S, Piccart-Gebhart MJ: Clinical application of the 70-gene profile: The MINDACT trial. J Clin Oncol. 2008, 26: 729-735. 10.1200/JCO.2007.14.3222.
Article
PubMed
Google Scholar
Duenwald S, Zhou M, Wang Y, Lejnine S, Kulkarni A, Graves J, Smith R, Castle J, Tokiwa G, Fine B, Dai H, Fare T, Marton M: Development of a microarray platform for FFPET profiling: Application to the classification of human tumors. J Transl Med. 2009, 7: 65-10.1186/1479-5876-7-65.
Article
PubMed
PubMed Central
Google Scholar
Bibikova M, Talantov D, Chudin E, Yeakley JM, Chen J, Doucet D, Wickham E, Atkins D, Barker D, Chee M, Wang Y, Fan JB: Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol. 2004, 165: 1799-1807. 10.1016/S0002-9440(10)63435-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ravo M, Mutarelli M, Ferraro L, Grober OM, Paris O, Tarallo R, Vigilante A, Cimino D, De Bortoli M, Nola E, Cicatiello L, Weisz A: Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays. Lab Invest. 2008, 88: 430-440. 10.1038/labinvest.2008.11.
Article
CAS
PubMed
Google Scholar
Lee J, Hever A, Willhite D, Zlotnik A, Hevezi P: Effects of RNA degradation on gene expression analysis of human postmortem tissues. FASEB J. 2005, 19: 1356-1358.
Article
CAS
PubMed
Google Scholar
Waddell N, Cocciardi S, Johnson J, Healey S, Marsh A, Riley J, da Silva L, Vargas AC, Reid L, kConFab Investigators, Simpson PT, Lakhani SR, Chenevix-Trench G: Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay. J Pathol. 2010, 221: 452-461.
CAS
PubMed
Google Scholar
Da Silva L, Parry S, Reid L, Keith P, Waddell N, Kossai M, Clarke C, Lakhani SR, Simpson PT: Aberrant expression of E-cadherin in lobular carcinomas of the breast. Am J Surg Pathol. 2008, 32: 773-783. 10.1097/PAS.0b013e318158d6c5.
Article
PubMed
Google Scholar
Ton CC, Vartanian N, Chai X, Lin MG, Yuan X, Malone KE, Li CI, Dawson A, Sather C, Delrow J, Hsu L, Porter PL: Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL®sample preparation. Breast Cancer Res Treat.
Mulligan JM, McDyer F, Deharo S, Farztdinov V, Halfpenny I, Delaney T, Couch F, Quinn JE, Harkin P, Kennedy R: Identification of molecular subtypes within a formalin-fixed, paraffin-embedded breast cancer tumour cohort [abstract]. Breast Cancer Res. 2010, 12 (Suppl 1): 33-10.1186/bcr2530.
Article
Google Scholar
Wong V, Wang DY, Warren K, Kulkarni S, Boerner S, Done SJ, Leong WL: The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers. BMC Cancer. 2008, 8: 277-10.1186/1471-2407-8-277.
Article
PubMed
PubMed Central
Google Scholar
Abramovitz M, Ordanic-Kodani M, Wang Y, Li Z, Catzavelos C, Bouzyk M, Sledge GW, Moreno CS, Leyland-Jones B: Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. Biotechniques. 2008, 44: 417-423. 10.2144/000112703.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA. 2005, 102: 13550-13555. 10.1073/pnas.0506230102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rupp GM, Locker J: Purification and analysis of RNA from paraffin-embedded tissues. Biotechniques. 1988, 6: 56-60. 10.1038/nbt0188-56.
CAS
PubMed
Google Scholar
Medeiros F, Rigl CT, Anderson GG, Becker SH, Halling KC: Tissue handling for genome-wide expression analysis: A review of the issues, evidence, and opportunities. Arch Pathol Lab Med. 2007, 131: 1805-1816.
CAS
PubMed
Google Scholar
Hewitt SM, Lewis FA, Cao Y, Conrad RC, Cronin M, Danenberg KD, Goralski TJ, Langmore JP, Raja RG, Williams PM, Palma JF, Warrington JA: 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. 2008, 132: 1929-1935.
PubMed
Google Scholar
Ribeiro-Silva A, Zhang H, Jeffrey SS: 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. 2007, 8: 118-10.1186/1471-2199-8-118.
Article
PubMed
PubMed Central
Google Scholar
Linton K, Hey Y, Dibben S, Miller C, Freemont A, Radford J, Pepper S: Methods comparison for high-resolution transcriptional analysis of archival material on affymetrix plus 2.0 and exon 1.0 microarrays. Biotechniques. 2009, 47: 587-596. 10.2144/000113169.
Article
CAS
PubMed
Google Scholar
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: E4-10.1093/nar/30.2.e4.
Article
PubMed
PubMed Central
Google Scholar
Penland SK, Keku TO, Torrice C, He X, Krishnamurthy J, Hoadley KA, Woosley JT, Thomas NE, Perou CM, Sandler RS, Sharpless NE: RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest. 2007, 87: 383-391.
CAS
PubMed
Google Scholar
Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ: Acquisition of biologically relevant gene expression data by affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer. 2008, 98: 1403-1414. 10.1038/sj.bjc.6604316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paik S, Kim CY, Song YK, Kim WS: Technology insight: Application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Clin Pract Oncol. 2005, 2: 246-254.
Article
CAS
PubMed
Google Scholar
Frank M, Doring C, Metzler D, Eckerle S, Hansmann ML: Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: A comparison to snap-frozen material using oligonucleotide microarrays. Virchows Arch. 2007, 450: 699-711. 10.1007/s00428-007-0412-9.
Article
CAS
PubMed
Google Scholar
Farragher SM, Tanney A, Kennedy RD, Paul Harkin D: RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol. 2008, 130: 435-445. 10.1007/s00418-008-0479-7.
Article
CAS
PubMed
Google Scholar
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. 10.1016/S0002-9440(10)63093-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olakowski M, Tyszkiewicz T, Jarzab M, Król R, Oczko-Wojciechowska M, Kowalska M, Kowal M, Gala GM, Kajor M, Lange D, Chmielik E, Gubala E, Lampe P, Jarzab B: NBL1 and anillin (ANLN) genes over-expression in pancreatic carcinoma. Folia Histochem Cytobiol. 2009, 47: 249-255. 10.2478/v10042-009-0031-1.
Article
PubMed
Google Scholar
Skrzypski M, Jassem E, Taron M, Sanchez JJ, Mendez P, Rzyman W, Gulida G, Raz D, Jablons D, Provencio M, Massuti B, Chaib I, Perez-Roca L, Jassem J, Rosell R: Three-gene expression signature predicts survival in early-stage squamous cell carcinoma of the lung. Clin Cancer Res. 2008, 14: 4794-4799. 10.1158/1078-0432.CCR-08-0576.
Article
CAS
PubMed
Google Scholar
Shimo A, Tanikawa C, Nishidate T, Lin ML, Matsuda K, Park JH, Ueki T, Ohta T, Hirata K, Fukuda M, Nakamura Y, Katagiri T: Involvement of kinesin family member 2C/mitotic centromere-associated kinesin overexpression in mammary carcinogenesis. Cancer Sci. 2008, 99: 62-70.
CAS
PubMed
Google Scholar
Tanaka S, Nohara T, Iwamoto M, Sumiyoshi K, Kimura K, Takahashi Y: Tanigawa N. Tau expression and efficacy of paclitaxel treatment in metastatic breast cancer. Cancer Chemother Pharmacol. 2009, 64: 341-346. 10.1007/s00280-008-0877-5.
Article
CAS
PubMed
Google Scholar
Ikeda H, Taira N, Hara F, Fujita T, Yamamoto H, Soh J, Toyooka S, Nogami T, Shien T, Doihara H, Miyoshi S: The estrogen receptor influences microtubule-associated protein tau (MAPT) expression and the selective estrogen receptor inhibitor fulvestrant downregulates MAPT and increases the sensitivity to taxane in breast cancer cells. Breast Cancer Res. 2010, 12: R43-10.1186/bcr2598.
Article
PubMed
PubMed Central
Google Scholar