The molecular portraits of breast tumors are conserved across microarray platforms
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Hu, Zhiyuan, et al. The Molecular Portraits of Breast Tumors Are Conserved Across Microarray Platforms. BioMed Central Ltd, 2006. https://doi.org/10.17615/hyr4-we03APA
Hu, Z., Fan, C., Oh, D., Marron, J., He, X., Qaqish, B., Livasy, C., Carey, L., Reynolds, E., Dressler, L., Nobel, A., Parker, J., Ewend, M., Sawyer, L., Wu, J., Liu, Y., Nanda, R., Tretiakova, M., Orrico, A., Dreher, D., Palazzo, J., Perreard, L., Nelson, E., Mone, M., Hansen, H., Mullins, M., Quackenbush, J., Ellis, M., Olopade, O., Bernard, P., & Perou, C. (2006). The molecular portraits of breast tumors are conserved across microarray platforms. BioMed Central Ltd. https://doi.org/10.17615/hyr4-we03Chicago
Hu, Zhiyuan, Cheng Fan, Daniel S Oh, Js Marron, Xiaping He, Bahjat Qaqish, Chad Livasy et al. 2006. The Molecular Portraits of Breast Tumors Are Conserved across Microarray Platforms. BioMed Central Ltd. https://doi.org/10.17615/hyr4-we03- Creator
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Hu, Zhiyuan
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center, School of Medicine, Department of Genetics
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Fan, Cheng
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
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Oh, Daniel S.
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center, School of Medicine, Department of Genetics
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Marron, JS
- Affiliation: College of Arts and Sciences, Department of Statistics and Operations Research
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He, Xiaping
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center, School of Medicine, Department of Genetics
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Qaqish, Bahjat
- Affiliation: Gillings School of Global Public Health, Department of Biostatistics
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Livasy, Chad
- Affiliation: School of Medicine, Department of Pathology and Laboratory Medicine
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Carey, Lisa
- Affiliation: School of Medicine, Department of Medicine
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Reynolds, Evangeline
- Affiliation: School of Medicine, Department of Medicine
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Dressler, Lynn
- Affiliation: School of Medicine, Department of Medicine
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Nobel, Andrew
- Affiliation: College of Arts and Sciences, Department of Statistics and Operations Research
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Parker, Joel
- Other Affiliation: Constella Health Sciences, 2605 Meridian Parkway, Durham, NC 27713, USA
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Ewend, Matthew G.
- Affiliation: School of Medicine, Department of Medicine
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Sawyer, Lynda R
- Affiliation: School of Medicine, Department of Medicine
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Wu, Junyuan
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
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Liu, Yudong
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
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Nanda, Rita
- Other Affiliation: Section of Hematology/Oncology, Department of Medicine, Committees on Genetics and Cancer Biology, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637- 1463, USA
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Tretiakova, Maria
- Other Affiliation: Section of Hematology/Oncology, Department of Medicine, Committees on Genetics and Cancer Biology, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637- 1463, USA
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Orrico, Alejandra
- Other Affiliation: Department of Pathology, Thomas Jefferson University, 132 South 10th Street Philadelphia, PA 19107, USA
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Dreher, Donna
- Other Affiliation: Department of Pathology, Thomas Jefferson University, 132 South 10th Street Philadelphia, PA 19107, USA
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Palazzo, Juan P
- Other Affiliation: Department of Pathology, Thomas Jefferson University, 132 South 10th Street Philadelphia, PA 19107, USA
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Perreard, Laurent
- Other Affiliation: The ARUP Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, Utah 84108, USA
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Nelson, Edward
- Other Affiliation: Department of Surgery, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Mone, Mary
- Other Affiliation: Department of Surgery, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Hansen, Heidi
- Other Affiliation: Department of Surgery, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Mullins, Michael
- Other Affiliation: Department of Pathology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Quackenbush, John F
- Other Affiliation: Department of Pathology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Ellis, Matthew J
- Other Affiliation: Department of Medicine, Division of Oncology, Washington University School of Medicine and Siteman Cancer Center, St Louis, Missouri, USA
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Olopade, Olufunmilayo I
- Other Affiliation: Section of Hematology/Oncology, Department of Medicine, Committees on Genetics and Cancer Biology, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637- 1463, USA
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Bernard, Philip S
- Other Affiliation: Department of Pathology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, Utah 84132, USA
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Perou, Charles
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center, School of Medicine, Department of Genetics
- Abstract
- Abstract Background Validation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification. However, validation is often unconvincing because the size of the test set is typically small. To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list. Results A 105-tumor training set containing 26 sample pairs was used to derive a new breast tumor intrinsic gene list. This intrinsic list contained 1300 genes and a proliferation signature that was not present in previous breast intrinsic gene sets. We tested this list as a survival predictor on a data set of 311 tumors compiled from three independent microarray studies that were fused into a single data set using Distance Weighted Discrimination. When the new intrinsic gene set was used to hierarchically cluster this combined test set, tumors were grouped into LumA, LumB, Basal-like, HER2+/ER-, and Normal Breast-like tumor subtypes that we demonstrated in previous datasets. These subtypes were associated with significant differences in Relapse-Free and Overall Survival. Multivariate Cox analysis of the combined test set showed that the intrinsic subtype classifications added significant prognostic information that was independent of standard clinical predictors. From the combined test set, we developed an objective and unchanging classifier based upon five intrinsic subtype mean expression profiles (i.e. centroids), which is designed for single sample predictions (SSP). The SSP approach was applied to two additional independent data sets and consistently predicted survival in both systemically treated and untreated patient groups. Conclusion This study validates the "breast tumor intrinsic" subtype classification as an objective means of tumor classification that should be translated into a clinical assay for further retrospective and prospective validation. In addition, our method of combining existing data sets can be used to robustly validate the potential clinical value of any new gene expression profile.
- Date of publication
- April 27, 2006
- DOI
- Identifier
- Resource type
- Article
- Rights statement
- In Copyright
- Rights holder
- Zhiyuan Hu et al.; licensee BioMed Central Ltd.
- License
- Journal title
- BMC Genomics
- Journal volume
- 7
- Journal issue
- 1
- Page start
- 96
- Language
- English
- Is the article or chapter peer-reviewed?
- Yes
- ISSN
- 1471-2164
- Bibliographic citation
- BMC Genomics. 2006 Apr 27;7(1):96
- Publisher
- BioMed Central Ltd
- Access right
- Open Access
- Date uploaded
- September 6, 2012
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1471-2164-7-96.pdf | 2019-05-07 | Public | Download | |
Supplemental Table 1. Clinical and microarray information associated with each patient in the 105-sample training dataset. | 2019-05-07 | Public | Download | |
Supplemental Figure 1. Complete hierarchical cluster diagram of the 315-sample combined test set analyzed using the Intrinsic_UNC gene set, which was reduced to 306 genes based upon the gene overlap between datasets. Sorlie et al. sample names begin | 2019-05-07 | Public | Download | |
1471-2164-7-96.xml | 2019-05-07 | Public | Download |