Agilent gene expression microarray raw data for STO-3
SND-ID: 2021-340-1. Version: 1. DOI: https://doi.org/10.5878/3vxa-3c28
Associated documentation
Citation
Creator/Principal investigator(s)
Annelie Johansson
- Karolinska Institutet, Department of Oncology-Pathology
Linda Lindström
- Karolinska Institutet, Department of Oncology-Pathology
Research principal
Karolinska Institutet
- Department of oncology-pathology
Description
Agilent microarray profiling of primary breast tumors in the Stockholm tamoxifen trial (STO-3) was performed in 2014. The STO-3 trial enrolled 1780 postmenopausal lymph node-negative patients with tumors smaller than or equal to 30 mm and were randomized to tamoxifen vs no endocrine therapy. Molecular analysis was possible for 808 patients with available formalin-fixed paraffin-embedded (FFPE) tissue blocks from the primary breast cancer tumor. Eighty-one patients were excluded from analysis due to insufficient invasive tumor cells, leaving 727 samples available for further analysis. Gene expression data were independently generated using custom-designed arrays, Agilent Technologies (CA, USA), containing approximately 32.1K probes, representing approximately 21.5K unique genes from FFPE breast cancer tumor tissue. 652 of 727 breast cancer tumors passed the RNA quality check according to the diagnostic quality model and were used in the analysis, of which 538 were ER-positive.
The datasetet consists of a table in one (1) txt file containing: Gene expression data (Agilent custom 32K microarray)
The datasetet consists of a table in one (1) txt file containing: Gene expression data (Agilent custom 32K microarray) generated in 2014 for 652 primary tumors from the STO-3 trial. The variables are the 31195 probes included in the Agilent microarray used to generate the data.
File name: STO3_Agilent_microarray_gMeanSignals_652.txt
The 31195 probes included in the Agilent microarray used to generate the data are listed and mapped to gene names in an annotation file.
Annotation file name: List_of_probes_STO3_Agilent_microarray_gMeanSignals_652.txt Show less..
Data contains personal data
Yes
Sensitive personal data
Yes
Type of personal data
Pseudonymised data
Code key exists
Yes
Language
Population
Breast cancer patients diagnosed in Stockholm 1976-1990
Study design
Randomised controlled trial (RCT)
Biobank is connected to the study
This study has used existing samples from a scientific collection or biobank
Scientific collection or biobank name: Biobank Sverige, Stockholm tamoxifenstudierna (STO)
Type(s) of sample: formalin-fixed paraffin-embedded (FFPE) primary breast tumors
Variables
31195
Number of individuals/objects
652
Data format / data structure
Geographic spread
Geographic location: Stockholm County
Responsible department/unit
Department of oncology-pathology
Ethics Review
Stockholm - Ref. 2017/2066-32, 97-451, 76-51.
The STO-3 trial was approved by the ethics committee at Karolinska Institutet and participants provided oral consent. The trial was conducted at the Regional Cancer Center Stockholm-Gotland, Sweden, and began in 1976
Research area
Genetics (Standard för svensk indelning av forskningsämnen 2011)
Cancer and oncology (Standard för svensk indelning av forskningsämnen 2011)
Keywords
Breast neoplasms, Tamoxifen, Gene expression, Clinical trial
Johansson & Lindström et al., Clinical and Molecular Characteristics of ER-Positive Ultralow Risk Breast Cancer Tumors Identified by the 70-Gene Signature, International Journal of Cancer, 2022
DOI:
https://doi.org/10.1002/ijc.33969
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