Research article
High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer
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* Corresponding author: Johan Staaf johan.staaf@med.lu.se
1 Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, SE 22185 Lund, Sweden
2 CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
3 Department of Pathology, Clinical Sciences, Lund University, University Hospital, SE 22185 Lund, Sweden
4 Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
5 Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
6 Department of Oncology, Landspitali-University Hospital, 101 Reykjavik, Iceland
7 Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, BMC B10, SE 22184, Lund, Sweden
Breast Cancer Research 2010, 12:R25 doi:10.1186/bcr2568
See related editorial by Theillet, http://breast-cancer-research.com/content/12/3/107
Published: 6 May 2010Additional files
Additional file 1:
Patient and tumor characteristics for HER2-amplified tumors. An Excel table containing clinical and experimental data on the 200 HER2-amplified tumors.
Format: XLS Size: 77KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
Supplementary methods. A Word document containing supplementary information about used methods and data processing.
Format: DOC Size: 33KB Download file
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Additional file 3:
Patient and tumor characteristics for HER2-negative tumors. A Word document containing a table of clinical data for HER2- tumors in the reference breast cancer data set.
Format: DOC Size: 50KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 4:
HER2 copy number evaluation and TOP2A mRNA expression levels. A pdf file containing figures of the result of the comparison of HER2 copy number estimates between aCGH and FISH for 13 FFPE samples (S1A) and mRNA expression levels and S-phase fractions for HER2+ and HER2- tumors in the Jönsson et al. data set (S1B).
Format: PDF Size: 248KB Download file
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Additional file 5:
Significant GISTIC regions in HER2-amplified breast cancer. An Excel table presenting the 117 GISTIC regions, including genes significantly correlated between mRNA expression levels and copy numbers, and frequency of high-level amplifications on chromosome 17q. Additionally, the frequency of GISTIC regions in HER2+ tumors overall and stratified by ER status is presented and compared to corresponding frequencies in HER2- tumors stratified by ER status.
Format: XLS Size: 137KB Download file
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Additional file 6:
Recurrent high-level amplifications in HER2-amplified breast cancer. A Word file describing recurrent high-level amplifications, excluding chromosome 17, in HER2+ breast tumors including genes in amplicons significantly correlated between mRNA expression levels and copy numbers.
Format: DOC Size: 54KB Download file
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Additional file 7:
Frequency of GISTIC regions in HER2-amplified and HER2-negative breast cancer. An Excel table containing the results from the comparison of frequencies of the identified GISTIC regions in HER2-amplified breast cancer compared to HER2- tumors classified according to gene expression subtypes.
Format: XLS Size: 40KB Download file
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Additional file 8:
Expression of ER gene expression modules in HER2-amplified and HER2-negative breast cancer. A pdf file containing two subpanels illustrating: (1) differences in expression of two ER gene expression modules in the Jönsson et al. data set for HER2+ tumors stratified according to ER status, and (2) HER2- tumors classified according to gene expression subtypes.
Format: PDF Size: 271KB Download file
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Additional file 9:
Frequency of GISTIC regions in HER2-amplified and HER2-negative breast cancer according to gene expression subtypes. A pdf file containing two panels illustrating: (1) GISTIC regions significantly different between HER2+ tumors classified to the ERBB2 gene expression subtype, compared to HER2- tumors classified as basal-like, luminal A, luminal B and normal-like subtype, and (2) CNA frequency in HER2- basal-like classified tumors.
Format: PDF Size: 205KB Download file
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Additional file 10:
Copy number alterations in HER2-amplified breast cancer stratified by ER status. A pdf file containing two subpanels illustrating CNA frequencies in HER2+/ER- tumors and HER2+/ER+ tumors, respectively.
Format: PDF Size: 328KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 11:
Global correlation of mRNA expression and gene dosage in HER2-amplified breast cancer. An Excel table listing genes that are found significantly correlated between gene expression data and aCGH in HER2+ tumors using a global matching.
Format: XLS Size: 361KB Download file
This file can be viewed with: Microsoft Excel Viewer