Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay

Laurent Praly1, Cheng Fan2, John Quackenbush3, Michael E. Mullins3, Nicholas Paul Gauthier3, Edward William Nelson4, Mary C. Mone4, Heidi Hansen4, Saundra S. Buys5, Karen Rasmussen6, Alejandra Ruiz Orrico7, Donna Dreher7, Robin G. Walters7, Joel S. Parker8, Zhiyuan Hu2, Xiaping He2, Juan Palazzo7, Olufunmilayo I. Olopade9, Anikó Szabó10, Charles M. Perou2, Philip S. Bernard3
1The ARUP Institute for Clinical and Experimental Pathology, SLC, Utah, USA
2Department of Genetics and Department of Pathology & Laboratory Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
3Department of Pathology, University of Utah School of Medicine, SLC, Utah, USA
4Department of Surgery, University of Utah School of Medicine, SLC, Utah, USA
5Department of Internal Medicine, University of Utah School of Medicine, SLC, Utah, USA
6Department of Clinical Genetics, Maine Center for Cancer Medicine, Scarborough, Maine, USA
7Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
8Constella Health Sciences, Durham, North Carolina, USA
9Department of Medicine, University of Chicago, Illinois, USA
10Department of Oncological Sciences, Huntsman Cancer Institute, SLC, Utah, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

American Joint Committee on Cancer. [ http://www.cancerstaging.org/cstage/index.html ]

Elston CW, Ellis IO: Pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long-term follow-up. Histopathology. 1991, 19: 403-410.

Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al: Molecular portraits of human breast tumours. Nature. 2000, 406: 747-752. 10.1038/35021093.

Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 2001, 98: 10869-10874. 10.1073/pnas.191367098.

Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA. 2003, 100: 8418-8423. 10.1073/pnas.0932692100.

Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET: Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci USA. 2003, 100: 10393-10398. 10.1073/pnas.1732912100.

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, et al: Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002, 415: 530-536. 10.1038/415530a.

van de Vijver MJ, He YD, van 't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002, 347: 1999-2009. 10.1056/NEJMoa021967.

Yu K, Lee CH, Tan PH, Tan P: Conservation of breast cancer molecular subtypes and transcriptional patterns of tumor progression across distinct ethnic populations. Clin Cancer Res. 2004, 10: 5508-5517. 10.1158/1078-0432.CCR-04-0085.

Taylor-Papadimitriou J, Stampfer M, Bartek J, Lewis A, Boshell M, Lane EB, Leigh IM: Keratin expression in human mammary epithelial cells cultured from normal and malignant tissue: relation to in vivo phenotypes and influence of medium. J Cell Sci. 1989, 94 (Part 3): 403-413.

Perou CM, Brown PO, Botstein D: Tumor classification using gene expression patterns from DNA microarrays. New Technologies for Life Sciences: A Trends Guide. 2000, Elsevier Inc. Science, Burlington MA, 67-76.

Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002, 13: 1977-2000. 10.1091/mbc.02-02-0030..

Ishida S, Huang E, Zuzan H, Spang R, Leone G, West M, Nevins JR: Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol. 2001, 21: 4684-4699. 10.1128/MCB.21.14.4684-4699.2001.

Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sorlie T, Dai H, He YD, van 't Veer LJ, Bartelink H, et al: 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.

Wittwer CT, Kusukawa N: Real-time PCR. Molecular Microbiology. Edited by: Persing DH, Tenover FC, Versalovic J, Tang YW, Unger ER, Relman DA, White TJ. 2004, Washington, DC: ASM Press

Rasmussen RP: Quantification on the LightCycler. Rapid Cycle Real-Time PCR: Methods and Applications. Edited by: Wittwer CT, Meuer S, Nakagawara K. 2001, Heidelberg: Springer Verlag, 21-34.

Szabo A, Perou CM, Karaca M, Perreard L, Quackenbush JF, Bernard PS: Statistical modeling for selecting housekeeper genes. Genome Biol. 2004, 5: R59-10.1186/gb-2004-5-8-r59.

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. 10.1073/pnas.95.25.14863.

Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30: e15-10.1093/nar/30.4.e15.

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics. 2001, 17: 520-525. 10.1093/bioinformatics/17.6.520.

Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, et al: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003, 31: 219-223. 10.1093/nar/gkg014.

Bair E, Tibshirani R: Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol. 2004, 2: E108-10.1371/journal.pbio.0020108.

Bullinger L, Dohner K, Bair E, Frohling S, Schlenk RF, Tibshirani R, Dohner H, Pollack JR: Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med. 2004, 350: 1605-1616. 10.1056/NEJMoa031046.

Dudoit S, Fridlyand J: A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol. 2002, 3: RESEARCH0036-10.1186/gb-2002-3-7-research0036.

Monti S, Tamayo P, Mesirov J, Golub T: Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learning. 2003, 52: 91-118. 10.1023/A:1023949509487.

Benito M, Parker J, Du Q, Wu J, Xiang D, Perou CM, Marron JS: Adjustment of systematic microarray data biases. Bioinformatics. 2004, 20: 105-114. 10.1093/bioinformatics/btg385.

Efron B, Tibshirani RJ: An Introduction to the Bootstrap. 1998, Boca Raton, FL: CRC Press LLC

Dai H, van 't Veer L, Lamb J, He YD, Mao M, Fine BM, Bernards R, van de Vijver M, Deutsch P, Sachs A, et al: A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res. 2005, 65: 4059-4066. 10.1158/0008-5472.CAN-04-3953.

Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, et al: Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA. 1999, 96: 9212-9217. 10.1073/pnas.96.16.9212.

Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, et al: Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000, 24: 227-235. 10.1038/73432.

Perreard L, Perou CM, Bernard PS: Biological classification of breast cancer by real-time quantitative RT-PCR: comparisons to microarray and histopathology. [abstract]. J Mol Diagnost. 2005, 7: 681-

Bilous M, Dowsett M, Hanna W, Isola J, Lebeau A, Moreno A, Penault-Llorca F, Ruschoff J, Tomasic G, Van De Vijver M: Current perspectives on HER2 testing: a review of national testing guidelines. Mod Pathol. 2003, 16: 173-182. 10.1097/01.MP.0000052102.90815.82.

Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, et al: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004, 351: 2817-2826. 10.1056/NEJMoa041588.

Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al: Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006, 98: 262-272.

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.

Tothill RW, Kowalczyk A, Rischin D, Bousioutas A, Haviv I, van Laar RK, Waring PM, Zalcberg J, Ward R, Biankin AV, et al: An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res. 2005, 65: 4031-4040. 10.1158/0008-5472.CAN-04-3617.