GEO series

Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

GSE25055 Homo sapiens (human) Expression microarray 310 samples Submitted 2011/05/11 Platform GPL96

At a glance

Expression microarray · human · 310 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 310 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy.

Read the full summary ↓

Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared.

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE25055_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA142759. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21558518) ↗

Samples in this study

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+ 310 more — browse all 310 samples with per-sample file links →

Datasets on a similar topic

GSE25065 Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 198 samples shares taxane-anthracycline, chemotherapy, neoadjuvant, predictor, following, survival, cohort
GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares taxane-anthracycline, chemotherapy, neoadjuvant, predictor, following, survival
GSE247185 Impact of immune repertoire in Muscle – Invasive Bladder Cancer (MIBC) on predicting response and survival after neoadjuvant cisplatin-based chemotherapy (NAC) 13 samples shares chemotherapy, neoadjuvant, survival
GSE4779 A stroma-related gene signature predicts sensitivity to epirubicin-containing neoadjuvant chemotherapy in breast cancer. 102 samples shares chemotherapy, neoadjuvant
GSE279390 Basal/squamous and mixed subtype bladder cancers present poor outcomes after neoadjuvant chemotherapy in the VESPER trial 540 samples shares chemotherapy, neoadjuvant
GSE222557 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors 148 samples shares chemotherapy, neoadjuvant
GSE241934 Neoadjuvant sintilimab plus chemotherapy in early-stage EGFR-mutant NSCLC: phase 2 trial interim results (NEOTIDE/CTONG2104) 88 samples shares chemotherapy, neoadjuvant
GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares chemotherapy, neoadjuvant

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