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Series GSE23452 Query DataSets for GSE23452
Status Public on Nov 30, 2010
Title Acquired Genomic Copy Number Aberrations and Survival in Adult Acute Myelogenous Leukemia
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary Purpose: Genomic aberrations are of dominant importance to the biology and clinical outcome of patients with acute myelogenous leukemia (AML), and conventional karyotyping-based risk classifications are routinely used in clinical decision making in AML. One of the known limitations of karyotyping is the low sensitivity of this method to detect genomic abnormalities in the sub-megabase (Mb) to ~5 Mb range, and it is currently unclear whether overcoming this limitation with array-based high-resolution karyotyping could be clinically relevant. Furthermore, given the heterogeneity of molecular mechanisms/aberrations that underlie the risks inherent in conventional karyotyping-based risk classifications, it is likely that further refinements in genomic risk prognostication can be achieved. Here, we have analyzed FACS-sorted AML blast-derived and paired buccal DNA from 114 previously untreated prospectively enrolled AML patients for acquired genomic copy number changes and LOH using Affymetrix SNP 6.0 arrays, and we have correlated genomic lesion load and specific chromosomal abnormalities with patient survival.

Conclusions: Using multivariate analyses, we found that having ≥2 genomic lesions detected through SNP 6.0 array profiling approximately doubles the risk of death when controlling for age and karyotype-based risk. Finally, we identified an independent negative prognostic impact of p53 mutations, 17p-LOH or both on survival in AML.
Overall design Experimental design: We analyzed DNA from highly purified AML blasts and paired buccal cells from 114 patients using ultra-high density Affymetrix SNP 6.0 array-based genomic profiling. Patients 1 and 211 lack a correlate normal sample.
Contributor(s) Parkin B, Erba H, Ouillette P, Roulston D, Purkayastha A, Karp J, Talpaz M, Kujawski L, Shakhan S, Li C, Shedden K, Malek SN
Citation(s) 20729466
Submission date Aug 06, 2010
Last update date Nov 27, 2018
Contact name Sami N Malek
Phone 734-763-1222
Organization name University of Michigan
Department Internal Medicine, Hematology-Oncology
Street address 4410 Cancer Center; 1500 E Medical Center Dr
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (226)
GSM630959 MIAML001T
GSM630960 MIAML006N
GSM630961 MIAML006T
BioProject PRJNA130995

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
GSE23452_RAW.tar 6.8 Gb (http)(custom) TAR (of CEL)
GSE23452_copy_number_data.txt.gz 263.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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