Keystone Symposia 2008 Conference Schedule Sign up for PNAS Online eTocs
Link: Info for AuthorsLink: Editorial BoardLink: AboutLink: SubscribeLink: AdvertiseLink: ContactLink: Sitemap Link: PNAS Home
Proceedings of the National Academy of Sciences
Link: Current Issue "" Link: Archives "" Link: Online Submission ""  Link: Advanced Search

Published online on September 18, 2001, 10.1073/pnas.201162998
PNAS | September 25, 2001 | vol. 98 | no. 20 | 11462-11467


This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supporting Information
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a colleague
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My File Cabinet
Right arrow Download to citation manager
Right arrow Request Copyright Permission
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (361)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by West, M.
Right arrow Articles by Nevins, J. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by West, M.
Right arrow Articles by Nevins, J. R.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg  
What's this?

 Previous Article  | Table of Contents |  Next Article 

Genetics
 Predicting the clinical status of human breast cancer by using gene expression profiles

Mike West*, Carrie Blanchettedagger , Holly DressmanDagger , Erich HuangDagger , Seiichi IshidaDagger , Rainer Spang*, Harry Zuzan*, John A. Olson Jr.dagger , Jeffrey R. Marksdagger , and Joseph R. NevinsDagger ,§,

* Institute of Statistics and Decision Sciences, Duke University, Durham, NC 27708; Departments of dagger  Surgery and Dagger  Genetics, Duke University Medical Center, Durham, NC 27710; and § Howard Hughes Medical Institute, Durham, NC 27710

Edited by Peter J. Bickel, University of California, Berkeley, CA, and approved August 3, 2001 (received for review April 3, 2001)

Prognostic and predictive factors are indispensable tools in the treatment of patients with neoplastic disease. For the most part, such factors rely on a few specific cell surface, histological, or gross pathologic features. Gene expression assays have the potential to supplement what were previously a few distinct features with many thousands of features. We have developed Bayesian regression models that provide predictive capability based on gene expression data derived from DNA microarray analysis of a series of primary breast cancer samples. These patterns have the capacity to discriminate breast tumors on the basis of estrogen receptor status and also on the categorized lymph node status. Importantly, we assess the utility and validity of such models in predicting the status of tumors in crossvalidation determinations. The practical value of such approaches relies on the ability not only to assess relative probabilities of clinical outcomes for future samples but also to provide an honest assessment of the uncertainties associated with such predictive classifications on the basis of the selection of gene subsets for each validation analysis. This latter point is of critical importance in the ability to apply these methodologies to clinical assessment of tumor phenotype.

To whom reprint requests should be addressed. E-mail: j.nevins{at}duke.edu.

www.pnas.org/cgi/doi/10.1073/pnas.201162998
Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg    What's this?


This article has been cited by other articles in HighWire Press-hosted journals:


Home page
 JAMAHome page
C. R. Acharya, D. S. Hsu, C. K. Anders, A. Anguiano, K. H. Salter, K. S. Walters, R. C. Redman, S. A. Tuchman, C. A. Moylan, S. Mukherjee, et al.
Gene Expression Signatures, Clinicopathological Features, and Individualized Therapy in Breast Cancer
JAMA, April 2, 2008; 299(13): 1574 - 1587.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
E. Garrett-Mayer, G. Parmigiani, X. Zhong, L. Cope, and E. Gabrielson
Cross-study validation and combined analysis of gene expression microarray data
Biostat., April 1, 2008; 9(2): 333 - 354.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
I. G. Yulug and B. Gur-Dedeoglu
Functional genomics in translational cancer research: focus on breast cancer
Brief Funct Genomic Proteomic, March 7, 2008; (2008) eln009v1.
[Abstract] [Full Text] [PDF]

Home page
 Stem CellsHome page
R. W. Cho, X. Wang, M. Diehn, K. Shedden, G. Y. Chen, G. Sherlock, A. Gurney, J. Lewicki, and M. F. Clarke
Isolation and Molecular Characterization of Cancer Stem Cells in MMTV-Wnt-1 Murine Breast Tumors
Stem Cells, February 1, 2008; 26(2): 364 - 371.
[Abstract] [Full Text] [PDF]

Home page
 Mol Cancer ResHome page
M. Wu, D. R. Soler, M. C. Abba, M. I. Nunez, R. Baer, C. Hatzis, A. Llombart-Cussac, A. Llombart-Bosch, and C. M. Aldaz
CtIP Silencing as a Novel Mechanism of Tamoxifen Resistance in Breast Cancer
Mol. Cancer Res., December 1, 2007; 5(12): 1285 - 1295.
[Abstract] [Full Text] [PDF]

Home page
 FASEB J.Home page
B. P. Gomez, R. B. Riggins, A. N. Shajahan, U. Klimach, A. Wang, A. C. Crawford, Y. Zhu, A. Zwart, M. Wang, and R. Clarke
Human X-Box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines
FASEB J, December 1, 2007; 21(14): 4013 - 4027.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
H. Lian
MOST: detecting cancer differential gene expression
Biostat., November 29, 2007; (2007) kxm042v1.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
L. Lusa, L. M. McShane, J. F. Reid, L. De Cecco, F. Ambrogi, E. Biganzoli, M. Gariboldi, and M. A. Pierotti
Challenges in Projecting Clustering Results Across Gene Expression Profiling Datasets
J Natl Cancer Inst, November 21, 2007; 99(22): 1715 - 1723.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
L. Harris, H. Fritsche, R. Mennel, L. Norton, P. Ravdin, S. Taube, M. R. Somerfield, D. F. Hayes, and R. C. Bast Jr
American Society of Clinical Oncology 2007 Update of Recommendations for the Use of Tumor Markers in Breast Cancer
J. Clin. Oncol., November 20, 2007; 25(33): 5287 - 5312.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
M. Garcia-Closas, M. A. Troester, Y. Qi, A. Langerod, M. Yeager, J. Lissowska, L. Brinton, R. Welch, B. Peplonska, D. S. Gerhard, et al.
Common Genetic Variation in GATA-Binding Protein 3 and Differential Susceptibility to Breast Cancer by Estrogen Receptor {alpha} Tumor Status
Cancer Epidemiol. Biomarkers Prev., November 1, 2007; 16(11): 2269 - 2275.
[Abstract] [Full Text] [PDF]

Home page
 Mol Cancer ResHome page
A. A.N. Rose, F. Pepin, C. Russo, J. E. Abou Khalil, M. Hallett, and P. M. Siegel
Osteoactivin Promotes Breast Cancer Metastasis to Bone
Mol. Cancer Res., October 1, 2007; 5(10): 1001 - 1014.
[Abstract] [Full Text] [PDF]

Home page
 Mol Cancer ResHome page
M. C. Abba, H. Sun, K. A. Hawkins, J. A. Drake, Y. Hu, M. I. Nunez, S. Gaddis, T. Shi, S. Horvath, A. Sahin, et al.
Breast Cancer Molecular Signatures as Determined by SAGE: Correlation with Lymph Node Status
Mol. Cancer Res., September 1, 2007; 5(9): 881 - 890.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Lottaz, J. Toedling, and R. Spang
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
Bioinformatics, September 1, 2007; 23(17): 2256 - 2264.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Buness, R. Kuner, M. Ruschhaupt, A. Poustka, H. Sultmann, and A. Tresch
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
Bioinformatics, September 1, 2007; 23(17): 2273 - 2280.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Pathol.Home page
S. M. Rodriguez-Pinilla, D. Sarrio, E. Honrado, G. Moreno-Bueno, D. Hardisson, F. Calero, J. Benitez, and J. Palacios
Vimentin and laminin expression is associated with basal-like phenotype in both sporadic and BRCA1-associated breast carcinomas
J. Clin. Pathol., September 1, 2007; 60(9): 1006 - 1012.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
J. Eeckhoute, E. K. Keeton, M. Lupien, S. A. Krum, J. S. Carroll, and M. Brown
Positive Cross-Regulatory Loop Ties GATA-3 to Estrogen Receptor {alpha} Expression in Breast Cancer
Cancer Res., July 1, 2007; 67(13): 6477 - 6483.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
B. Wu
Cancer outlier differential gene expression detection
Biostat., July 1, 2007; 8(3): 566 - 575.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Zhou and D. P. Tuck
MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data
Bioinformatics, May 1, 2007; 23(9): 1106 - 1114.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
D. J. Wilkinson
Bayesian methods in bioinformatics and computational systems biology
Brief Bioinform, April 12, 2007; (2007) bbm007v1.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
Y. Ma, Y. Qian, L. Wei, J. Abraham, X. Shi, V. Castranova, E. J. Harner, D. C. Flynn, and L. Guo
Population-Based Molecular Prognosis of Breast Cancer by Transcriptional Profiling
Clin. Cancer Res., April 1, 2007; 13(7): 2014 - 2022.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
F. Andre, C. Hatzis, K. Anderson, C. Sotiriou, C. Mazouni, J. Mejia, B. Wang, G. N. Hortobagyi, W. F. Symmans, and L. Pusztai
Microtubule-Associated Protein-tau is a Bifunctional Predictor of Endocrine Sensitivity and Chemotherapy Resistance in Estrogen Receptor-Positive Breast Cancer
Clin. Cancer Res., April 1, 2007; 13(7): 2061 - 2067.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
F. Huang, K. Reeves, X. Han, C. Fairchild, S. Platero, T. W. Wong, F. Lee, P. Shaw, and E. Clark
Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
Cancer Res., March 1, 2007; 67(5): 2226 - 2238.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
H. Li, P. Cherukuri, N. Li, V. Cowling, M. Spinella, M. Cole, A. K. Godwin, W. Wells, and J. DiRenzo
Nestin Is Expressed in the Basal/Myoepithelial Layer of the Mammary Gland and Is a Selective Marker of Basal Epithelial Breast Tumors
Cancer Res., January 15, 2007; 67(2): 501 - 510.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
A. V. Kapp and R. Tibshirani
Are clusters found in one dataset present in another dataset?
Biostat., January 1, 2007; 8(1): 9 - 31.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
C. A. Learn, P. E. Fecci, R. J. Schmittling, W. Xie, I. Karikari, D. A. Mitchell, G. E. Archer, Z. Wei, H. Dressman, and J. H. Sampson
Profiling of CD4+, CD8+, and CD4+CD25+CD45RO+FoxP3+ T Cells in Patients with Malignant Glioma Reveals Differential Expression of the Immunologic Transcriptome Compared with T Cells from Healthy Volunteers
Clin. Cancer Res., December 15, 2006; 12(24): 7306 - 7315.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
S. K Gruvberger-Saal, H. E Cunliffe, K. M Carr, and I. A Hedenfalk
Microarrays in breast cancer research and clinical practice - the future lies ahead
Endocr. Relat. Cancer, December 1, 2006; 13(4): 1017 - 1031.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
S Tozlu, I Girault, S Vacher, J Vendrell, C Andrieu, F Spyratos, P Cohen, R Lidereau, and I Bieche
Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach
Endocr. Relat. Cancer, December 1, 2006; 13(4): 1109 - 1120.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Hothorn and P. Buhlmann
Model-based boosting in high dimensions
Bioinformatics, November 15, 2006; 22(22): 2828 - 2829.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
M. Dolled-Filhart, L. Ryden, M. Cregger, K. Jirstrom, M. Harigopal, R. L. Camp, and D. L. Rimm
Classification of breast cancer using genetic algorithms and tissue microarrays.
Clin. Cancer Res., November 1, 2006; 12(21): 6459 - 6468.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Zhou and K. Z. Mao
The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms
Bioinformatics, October 15, 2006; 22(20): 2507 - 2515.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
M. Buyse, S. Loi, L. van't Veer, G. Viale, M. Delorenzi, A. M. Glas, M. Saghatchian d'Assignies, J. Bergh, R. Lidereau, P. Ellis, et al.
Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer.
J Natl Cancer Inst, September 6, 2006; 98(17): 1183 - 1192.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Malossini, E. Blanzieri, and R. T. Ng
Detecting potential labeling errors in microarrays by data perturbation
Bioinformatics, September 1, 2006; 22(17): 2114 - 2121.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Li, L. Wu, and Z. Zhang
Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
Bioinformatics, September 1, 2006; 22(17): 2143 - 2150.
[Abstract] [Full Text] [PDF]

Home page
 NEJMHome page
A. Potti, S. Mukherjee, R. Petersen, H. K. Dressman, A. Bild, J. Koontz, R. Kratzke, M. A. Watson, M. Kelley, G. S. Ginsburg, et al.
A Genomic Strategy to Refine Prognosis in Early-Stage Non-Small-Cell Lung Cancer
N. Engl. J. Med., August 10, 2006; 355(6): 570 - 580.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D.-S. Huang and C.-H. Zheng
Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
Bioinformatics, August 1, 2006; 22(15): 1855 - 1862.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Y. Qu and S. Xu
Quantitative Trait Associated Microarray Gene Expression Data Analysis
Mol. Biol. Evol., August 1, 2006; 23(8): 1558 - 1573.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
W. F. Anderson and R. Matsuno
Breast cancer heterogeneity: a mixture of at least two main types?
J Natl Cancer Inst, July 19, 2006; 98(14): 948 - 951.
[Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
T. Sakamaki, M. C. Casimiro, X. Ju, A. A. Quong, S. Katiyar, M. Liu, X. Jiao, A. Li, X. Zhang, Y. Lu, et al.
Cyclin d1 determines mitochondrial function in vivo.
Mol. Cell. Biol., July 1, 2006; 26(14): 5449 - 5469.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Prieto, M.J. Rivas, J.M. Sanchez, J. Lopez-Fidalgo, and J. De Las Rivas
Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes
Bioinformatics, May 1, 2006; 22(9): 1103 - 1110.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. Ein-Dor, O. Zuk, and E. Domany
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
PNAS, April 11, 2006; 103(15): 5923 - 5928.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
D. S. Oh, M. A. Troester, J. Usary, Z. Hu, X. He, C. Fan, J. Wu, L. A. Carey, and C. M. Perou
Estrogen-Regulated Genes Predict Survival in Hormone Receptor-Positive Breast Cancers
J. Clin. Oncol., April 10, 2006; 24(11): 1656 - 1664.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
M. R. Segal
Microarray gene expression data with linked survival phenotypes: diffuse large-B-cell lymphoma revisited
Biostat., April 1, 2006; 7(2): 268 - 285.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Choudhary, M. Brun, J. Hua, J. Lowey, E. Suh, and E. R. Dougherty
Genetic test bed for feature selection
Bioinformatics, April 1, 2006; 22(7): 837 - 842.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Z. Wang, Y. Wang, J. Xuan, Y. Dong, M. Bakay, Y. Feng, R. Clarke, and E. P. Hoffman
Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
Bioinformatics, March 15, 2006; 22(6): 755 - 761.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Pathol.Home page
J S Reis-Filho, C Westbury, and J-Y Pierga
The impact of expression profiling on prognostic and predictive testing in breast cancer.
J. Clin. Pathol., March 1, 2006; 59(3): 225 - 231.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Li
Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
Bioinformatics, February 15, 2006; 22(4): 466 - 471.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Wu
Differential gene expression detection and sample classification using penalized linear regression models
Bioinformatics, February 15, 2006; 22(4): 472 - 476.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
A. Potti, A. Bild, H. K. Dressman, D. A. Lewis, J. R. Nevins, and T. L. Ortel
Gene-expression patterns predict phenotypes of immune-mediated thrombosis
Blood, February 15, 2006; 107(4): 1391 - 1396.
[Abstract] [Full Text] [PDF]

Home page
 J. Am. Soc. Nephrol.Home page
R. Karra, S. Vemullapalli, C. Dong, E.E. Herderick, X. Song, K. Slosek, J.R. Nevins, M. West, P.J. Goldschmidt-Clermont, D. Seo, et al.
Stem Cells of Aging Donors--Insufficient Capacity to Repair Causes Progression of Atherosclerosis in the Recipient: Molecular Evidence for Arterial Repair in Atherosclerosis. Proc Natl Acad Sci U S A 102: 16789-16794, 2005
J. Am. Soc. Nephrol., February 1, 2006; 17(2): 317 - 322.
[Full Text] [PDF]

Home page
 EndocrinologyHome page
D. M. E. Harvell, J. K. Richer, D. C. Allred, C. A. Sartorius, and K. B. Horwitz
Estradiol Regulates Different Genes in Human Breast Tumor Xenografts Compared with the Identical Cells in Culture
Endocrinology, February 1, 2006; 147(2): 700 - 713.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. Zhang, R. Rekaya, and K. Bertrand
A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer
Bioinformatics, February 1, 2006; 22(3): 317 - 325.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Elfilali, S. Lair, C. Verbeke, P. La Rosa, F. Radvanyi, and E. Barillot
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D613 - D616.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Karra, S. Vemullapalli, C. Dong, E. E. Herderick, X. Song, K. Slosek, J. R. Nevins, M. West, P. J. Goldschmidt-Clermont, and D. Seo
Molecular evidence for arterial repair in atherosclerosis
PNAS, November 15, 2005; 102(46): 16789 - 16794.