GEO series

Gene expression profiling of atypical T-ALL

GSE8879 Homo sapiens (human) Expression microarray 55 samples Submitted 2009/05/15 Platform GPL96

At a glance

Expression microarray · human · 55 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
Samples: 55 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Despite improved therapy, approximately one-fifth of children with acute T-lymphoblastic leukemia (T-ALL) succumb to the disease, suggesting unrecognized biologic heterogeneity that may contribute to drug resistance. We studied leukemic cells, collected at diagnosis, to identify features that could define this high-risk subgroup. A total of 139 patients with T-ALL were treated consecutively from 1992 to 2006 at this institution.

Read the full summary ↓

Their leukemic cells were examined with multiparameter flow cytometry, single nucleotide polymorphism arrays and other methods of genomic analysis. Survival rates and probabilities of treatment failure were calculated for subgroups considered to have biologically distinct forms of T-ALL. The lymphoblasts of 17 patients (12.2%) had immunophenotypes that clearly differed from those of the remaining patients. Most striking features were the low or absent expression of common T-lineage markers (CD5, CD1a and CD8), and expression of myeloid and stem cell markers, suggesting stem-cell like properties. These atypical blasts also showed a distinct gene expression profile and increased genomic instability overall. Patients with this form of T-ALL had a very low probability of surviving for 10 years after diagnosis: 19% ± 12% (mean ± SE) versus 84% ± 6% for all other patients ( P<0.001). The cumulative incidence of remission failure / hematologic relapse was 72% ± 16% versus 10% ± 3% (P < 0.001). A subset of children with T-ALL have atypical blast cell immunophenotypes that predict a dire outcome with use of standard intensive chemotherapy. Alternative treatment strategies are need for patients with this sybtype of leukemia. Keywords: Analysis of gene expression profiles of typical versus atypical T-ALL

This dataset

Open GSE8879 in finder → Find more human microarray datasets → Acute lymphoblastic leukemia 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 (GSE8879_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 PRJNA102253. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19147408) ↗

Samples in this study

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+ 55 more — browse all 55 samples with per-sample file links →

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