E-GEOD-14615 - Transcription profiling of human T-ALL (COG study 9404)

Status
Submitted on 28 January 2009, released on 9 February 2009, last updated on 15 May 2013
Organism
Homo sapiens
Samples (50)
Array (1)
Protocols (5)
Description
The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. We identified a 116-member genomic classifier that could accurately distinguish all 6 induction failure (IF) cases from 44 patients who achieved remission; network analyses suggest a prominent role for genes mediating cellular quiescence. Seven genes were similarly upregulated in both the genomic classifier for IF patients and T-ALL cell lines having acquired resistance to neoplastic agents, identifying potential target genes for further study in drug resistance. We tested whether our classifier could predict IF within 42 patient samples obtained from COG 8704 and, using PAM to define a smaller classifier for the U133A chip, correctly identified the single IF case and patients with persistently circulating blasts. Genetic profiling may identify T-ALL patients who are likely to fail induction and for whom alternate treatment strategies might be beneficial. Experiment Overall Design: This was a case-controlled, retrospectively designed study. We performed expression profiles on 92 patients with T-ALL treated on Children's Oncology Group studies 8704 (42 patients) and 9404 (50 patients). Experiment Overall Design: Expression profiles were obtained from patients with newly diagnosed T-ALL. NR = no response (induction failure); F= failure (relapse); C= Complete Continous Remission. Experiment Overall Design: NOTE: non-sequential numbers were removed for reasons other than relapse, or poor hybridization during chip preparation.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Identification of genomic classifiers that distinguish induction failure in T-lineage acute lymphoblastic leukemia: a report from the Children's Oncology Group. Stuart S Winter, Zeyu Jiang, Hadya M Khawaja, Timothy Griffin, Meenakshi Devidas, Barbara L Asselin, Richard S Larson.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-14615.idf.txt
Sample and data relationshipE-GEOD-14615.sdrf.txt
Raw data (2)E-GEOD-14615.raw.1.zip, E-GEOD-14615.raw.2.zip
Processed data (1)E-GEOD-14615.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-14615.eSet.r
Links