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Series GSE32462 Query DataSets for GSE32462
Status Public on Feb 07, 2012
Title High-Resolution Genomic Profiling of Adult and Pediatric Core-Binding-Factor Acute Myeloid Leukemia Reveals New Recurrent Genomic Alterations
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary To identify cooperating lesions in core-binding-factor acute myeloid leukemia (CBF-AML), we performed single-nucleotide polymorphism (SNP)-array analysis on 300 diagnostic and 41 relapse adult and pediatric leukemia samples. We identified a mean of 1.28 copy number alterations (CNAs) per case at diagnosis in both patient populations. Recurrent minimally deleted regions (MDRs) were identified at 7q36.1 (7.7%), 9q21.13 (5%), 11p13 (2.3%), and 17q11.2 (2%). Recurrent focal gains were identified at 8q24.21 (4.7%) and 11q25 (1.7%), both containing a single non-coding RNA. Recurrent regions of copy-neutral loss-of-heterozygosity were identified at 1p (1%), 4q (0.7%), and 19p (0.7%), with known mutated cancer genes present in the minimally altered region. Analysis of relapse samples identified recurrent MDRs at 3q13 (12.2%), 5q (4.9%), and 17p (4.9%).
Overall design SNP genotyping was performed on 300 adult and pediatric CBF-AMLs; t(8;21), n=157 (adult, n=114; pediatric, n=43); and inv(16), n=143 (adult, n=104; pediatric, n=39). Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 175 patients. In addition, for 41 patients, matched relapse samples were analyzed. Data were processed using reference alignment, dChipSNP and circular binary segmentation.
Contributor(s) Kühn MW, Radtke I, Bullinger L, Goorha S, Cheng J, Edelmann J, Gohlke J, Su X, Paschka P, Pounds S, Krauter J, Ganser A, Quessar A, Ribeiro R, Gaidzik VI, Shurtleff S, Krönke J, Holzmann K, Ma J, Schlenk RF, Rubnitz JE, Döhner K, Döhner H, Downing JR
Citation(s) 22234698
Submission date Sep 28, 2011
Last update date Nov 27, 2018
Contact name Guangchun Song
Phone 901-595-5722
Organization name St Jude Children's Research Hospital
Department Pathology
Lab Klco
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (516)
GSM802976 AE001
GSM802977 AE003
GSM802978 AE004
BioProject PRJNA147873

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
GSE32462_RAW.tar 14.6 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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