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Series GSE12665 Query DataSets for GSE12665
Status Public on Dec 08, 2011
Title Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial validates low estrogen receptor mRNA level as the main determinant of tamoxifen resistance in estrogen receptor positive breast cancer.

In NSABP Breast Cancer Prevention Trial (BCPT), tamoxifen reduced the incidence of estrogen receptor (ER) positive tumors but not estrogen receptor negative breast cancer. More importantly, only 69% of estrogen receptor positive tumors were prevented by tamoxifen. The ER positive tumors arising in tamoxifen arm provides an ideal clinical model for acquired tamoxifen resistance. Based on data from NSABP trial B14 which showed linear prediction of the degree of benefit from adjuvant tamoxifen by the levels of ESR1 mRNA coding for ER-alpha, we hypothesized a priori that level of ESR1 mRNA would be lower in ER positive tumors arising in tamoxifen arm compared to those in placebo arm of BCPT.

Keywords: Gene expression profiling analysis
 
Overall design Formalin fixed paraffin embedded tumor blocks with enough tumor tissue for RNA extraction were available from 108 cases (69 from placebo arm and 39 from tamoxifen arm) of the 264 that experienced invasive breast cancer (175 in placebo arm and 89 in tamoxifen arm) in BCPT before unblindings . Central ER immunohistochemistry identified 84 of them as ER positive (57 from placebo arm and 27 from tamoxifen arm). A novel protocol was developed and used to obtain microarray gene expression profiling from the degraded or fragmented RNA extracted from formalin fixed paraffin blocks.Hybridization intensity data were compiled using Partek Genomic Suite. After quantile normalization, genes with mean intensity below 500 were filtred out, which left 7743 probes with informative data. Data were log2 transformed for statistical analysis.
 
Contributor(s) Pogue-Geile K, Costantino JP, Bohn O, Fumagalli D, Kim C, Taniyama Y, Lee A, Reilly M, Vogel VG, McCaskil-Stevens W, Ford LG, Wolmark N, Wickerham DL, Paik S
Citation(s) 21947828
Submission date Sep 04, 2008
Last update date Jan 23, 2019
Contact name Soonmuyung Paik
Organization name NSABP Foundation
Department Pathology
Street address 1307 Federal Street, Suite 303
City Pittsburgh
State/province PA
ZIP/Postal code 15212
Country USA
 
Platforms (1)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (108)
GSM317936 ER-positive placebo-treated patient 1
GSM317937 ER-positive placebo-treated patient 2
GSM317938 ER-positive tamoxifen-treated patient 3
Relations
BioProject PRJNA112733

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12665_RAW.tar 962.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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