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Series GSE35656 Query DataSets for GSE35656
Status Public on Jul 01, 2013
Title Affymetrix SNP array data for myelodysplastic syndrome with 5q deletion treated with lenalidomide
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Lenalidome is a drug especially effective in low risk myelodysplastic syndromes (MDS) with isolated 5q deletion. However, 25% of the patients did not respond. TP53 mutations have been described to play a role in the disease progression, and karyotypic complexity also has an important impact in the outcome. We selected 53 MDS patients with 5q deletion and treated with lenalidomide and we studied by the following techniques: conventional G-banding cytogenetics (CC), single nucleotide polymorphism arrays (SNP-A) and sequencing, in order to assess their impact on treatment response and disease progression. Low karyotypic complexity (by CC), a high baseline platelet count (>280x103/L) and TP53 unmutated gene status are associated with the achievement of hematological response (P=0.005, P=0.008 and P=0.057, respectively). In a multivariate model, the most important predictors for lenalidomide failure are karyotypic complexity (P=0.014) and a platelet count below 280x103/L (P=0.042). Additionally, none of the TP53 mutated cases achieved complete cytogenetics response. Nevertheless, inclusion of defects by SNP-A did not allow for a better separation of responders and non responders. These findings constitute a useful reference data to be considered before lenalidomide treatment enrollment.
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from bone marrow or peripheral blood and, in some cases, also lymphocytes CD3 isolated from peripheral blood samples.
Copy number analyses of Affymetrix 250K and 6.0 SNP arrays were performed for 53 MDS with 5q deletion samples. There are also 30 samples from lymphocytes CD3 isolated from peripheral blood, which were used as germ-line DNA (control).
Contributor(s) Mallo M, del Rey M, Hernández JM, Solé F, Maciejewski JP
Citation(s) 23614682
Submission date Feb 09, 2012
Last update date Nov 27, 2018
Contact name Mar Mallo
Organization name Josep Carreras Leukaemia Research Institute
Street address Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC
City Badalona
ZIP/Postal code 08916
Country Spain
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (81)
GSM872928 Bone marrow Mostra 1 (NM14177) 5q 8
GSM872929 CD3 lymphocytes from Mostra 1 (NM14177) 5q 8
GSM872930 Bone marrow Mostra 5 C.4.1 MO
BioProject PRJNA152425

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
GSE35656_RAW.tar 4.8 Gb (http)(custom) TAR (of CEL, CNCHP, LOHCHP)
Processed data included within Sample table
Processed data provided as supplementary file

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