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Series GSE6891 Query DataSets for GSE6891
Status Public on Mar 12, 2008
Title Acute myeloid leukemia samples of samples =< 60yrs on HG-U133 plus 2
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The pretreatment karyotype of leukemic blasts is currently the key determinant in therapy decision-making in acute myeloid leukemia (AML). However, approximately fifty percent of AML patients, often carrying a normal karyotype, are currently unclassifiable based these established methods. Gene expression profiling has proven to be valuable for risk stratification of AML.

The gene expression profiles of AML samples of two independent cohorts (n=247 and n=214) were determined using Affymetrix U133Plus2.0 GeneChips: all Samples below 4000 are in the training cohort; all Samples higher than 4000 are in the validation cohort.

Data analyses were carried out to discover and predict prognostically relevant subtypes in AML (<60 years) based on their gene expression signatures. Statistical analyses were performed to determine the prognostic significance of cases of AML with specific molecular signatures. Unsupervised cluster analyses of the gene expression signatures of both independent cohorts of AML patients confirmed that chromosomal lesions and mutations, often resulting in aberrant transcription factors, induce discriminatory patterns of gene expression. In contrast, however, mutations in signalling molecules do not establish strong molecular signatures. Consequently, prognostically important subtypes, which express mutated trancription factors were predicted with high accuracy using minimal sets of genes. We identified several novel clusters, some consisting of patients with normal karyotypes. Gene expression profiling allows classification of AML subtypes characterized by the expression of abnormal transcription factors, however, prediction of clinically relevant mutations affecting signalling molecules is impossible and thus still requires addition molecular methods.

Keywords: acute myeloid leukemia, patient blood or bone marrow samples
 
Overall design 461 blood or bone marrow samples of acute myeloid leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips. 76 additonal samples added on 7/28/2011.
 
Contributor(s) Verhaak RG, Wouters BJ, Erpelinck CA, Abbas S, Beverlo B, Lugthart S, Löwenberg B, Delwel R, Valk PJ
Citation(s) 18838472, 20522712
Submission date Jan 29, 2007
Last update date Mar 25, 2019
Contact name Roel Verhaak
E-mail(s) rverhaak@mdanderson.org
URL http://odin.mdacc.tmc.edu/~rverhaak/
Organization name MD Anderson Cancer Center
Department Bioinformatics and Comp Bio
Lab Verhaak
Street address 1400 Pressler St
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (537)
GSM158711 AML 2199
GSM158712 AML 2200
GSM158713 AML 2201
Relations
BioProject PRJNA98571

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
GSE6891_RAW.tar 2.9 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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