GEO series

Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma

GSE66166 Homo sapiens (human) Expression microarray 138 samples Submitted 2015/07/16 Platform GPL13938

At a glance

Expression microarray · human · 138 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Follicular lymphomaThis series is part of our curated briefing on it.
Samples: 138 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Background: Follicular lymphoma (FL) is a clinically and genetically heterogeneous disease. The prognostic value of somatic mutations has not been systematically evaluated and no genetic factors have been identified that distinguish patients at highest risk of treatment failure. Methods: We performed deep sequencing of 74 genes in 151 patients treated with R-CHOP from a phase III trial.

Read the full summary ↓

Mutations and clinical factors were incorporated into a risk model using multivariable L1-penalized Cox regression. We validated the risk model in an independent cohort of 107 patients treated with R-CVP. Results: The final clinicogenetic index, the “m7-FLIPI”, contained the FL International Prognostic Index (FLIPI), ECOG performance status, and mutation status of 7 genes (EZH2, ARID1A, MEF2B, EP300, FOXO1, CREBBP and CARD11). In the training cohort, the m7-FLIPI defined a high-risk group (28% of patients) with 5-year failure-free survival (FFS) of 38% vs 77% for the low-risk group (Hazard ratio (HR) 4.1, confidence Interval (CI)=[2.5;6.9], p<0.0001). In the validation cohort, the m7-FLIPI defined a high-risk group (22% of patients) with 5-year FFS of 25% versus 68% (HR 3.6, CI=[2.0;6.4], p<0.0001) in the low-risk group. In both cohorts, the m7-FLIPI outperformed the FLIPI alone. Strikingly, all 66 patients with EZH2 mutations in both cohorts were categorized as low-risk m7-FLIPI, and EZH2 mutations defined a distinct transcriptional profile. Conclusions: The combination of clinical factors and mutations in 7 genes can identify the subset of patients with FL at highest risk of treatment failure. The m7-FLIPI can be widely utilized for risk prognostication and patient stratification.

This dataset

Open GSE66166 in finder → Find more human microarray datasets → Follicular lymphoma landscape →

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 (GSE66166_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 PRJNA276026. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26256760) ↗

Samples in this study

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+ 138 more — browse all 138 samples with per-sample file links →

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GSE93261 Transcriptome analysis of Follicular Lymphomas from the PRIMABIO cohort 149 samples same disease briefing · shares follicular, lymphoma
GSE103944 Gene Expression Profiling reveals a close relationship between Follicular lymphoma Grade 3A and 3B, but distinct profiles of Follicular Lymphoma Grade 1 and 2 84 samples same disease briefing · shares follicular, lymphoma
GSE148070 Microarray expression data from follicular lymphoma patients' lymph node biopsies (frozen) 40 samples same disease briefing · shares follicular, lymphoma
GSE52562 Gene expression profiling of tumor biopsies before and after pidilizumab therapy in patients with relapsed follicular lymphoma grade 1 or grade 2. 26 samples same disease briefing · shares follicular, lymphoma
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