Agilent gene expression microarray raw data for STO-3

SND-ID: 2021-340-1. Version: 1. DOI: https://doi.org/10.5878/3vxa-3c28

Citation

Creator/Principal investigator(s)

Annelie Johansson - Karolinska Institutet, Department of Oncology-Pathology orcid

Linda Lindström - Karolinska Institutet, Department of Oncology-Pathology orcid

Research principal

Karolinska Institutet - Department of oncology-pathology rorId

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)

... Show more..
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) 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

Method and outcome

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

Data collection
  • Mode of collection: Registry extract and/or access to biobank sample
  • Time period(s) for data collection: 2013 – 2014
  • Source of the data: Biological samples
Geographic coverage

Geographic spread

Geographic location: Stockholm County

Administrative information

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

Topic and keywords

Research area

Genetics (Standard för svensk indelning av forskningsämnen 2011)

Cancer and oncology (Standard för svensk indelning av forskningsämnen 2011)

Publications

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

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Versions

Version 1. 2022-03-02

Version 1: 2022-03-02

DOI: https://doi.org/10.5878/3vxa-3c28

Contacts for questions about the data

Annelie Johansson

annelie.johansson@ki.se

Linda Lindström

linda.lindstrom@ki.se

Published: 2022-03-02