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Series GSE234114 Query DataSets for GSE234114
Status Public on Jun 09, 2023
Title The Validation set of the genomic nodal index (GNI) in 2014
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The aim of this study was to construct a prediction model for axillary lymph node metastasis (ALNM) using a DNA microarray assay for gene expression in breast tumor tissues. Luminal A breast cancers, diagnosed by PAM50 testing, were analyzed, and a prediction model (genomic nodal index (GNI)) consisting of 292 probe sets for ALNM was constructed in a training set of patients (n=388), and was validated in the first (n=59) and the second (n=103) validation sets. AUCs of ROC were 0.820, 0.717, and 0.749 in the training, first, and second validation sets, respectively. GNI was most significantly associated with ALNM, independently of the other conventional clinicopathological parameters in all cohorts. It is suggested that GNI can be used to identify the patients with a low risk for ALNM so that sentinel lymph node biopsy can be spared safely. This DATA set: J03 contains 120 (n+ 60, n- 60) samples of the above first and second validation sets from Japan (OUH_1,2). A long time passed, and now it is unclear how these 120 cases were distributed among the first and second validation sets. *Note: This old data has been updated multiple times by others. Then, there are some differences from the original 2014 paper and unclear points still remain. Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. PMID: 25016059 DOI: 10.1016/j.canlet.2014.07.003
 
Overall design RNA was extracted from 120 fresh frozen tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.
 
Contributor(s) Sota Y, Tsunashima R, Naoi Y
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Submission date Jun 05, 2023
Last update date Jun 11, 2023
Contact name Yoshiaki Sota
E-mail(s) y_sota123@onsurg.med.osaka-u.ac.jp
Phone 0668793772
Organization name Osaka University
Department Breast and Endocrine Surgery
Lab Shinzaburo Noguchi
Street address Yamadaoka 2-15
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (120)
GSM7445967 breast tumor tissue, J03_001
GSM7445968 breast tumor tissue, J03_002
GSM7445969 breast tumor tissue, J03_003
Relations
BioProject PRJNA980140

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
GSE234114_RAW.tar 539.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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