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Series GSE21780 Query DataSets for GSE21780
Status Public on Dec 31, 2010
Title SNP arrays in matched diagnosis/remission samples of normal karyotype-acute myeloid leukemia
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary We analysed, by last-generation high-resolution SNP arrays, Normal Karyotype (NK)-AML patients at diagnosis (Dx) and remission (R) phases, in order to determine the number of tumor-associated copy number abnormalities (CNAs) and copy neutral-loss of heterozygosity (CN-LOH) regions per patient and to identify possible recurring genomic abnormalities. The number of tumor-associated CNAs was detemined after comparison of 11 matched Dx/R samples using stringent conditions able to reduce the number of false positive CNAs. 8 additional unmatched Dx samples were included in the analysis of recurring CNAs and for detection of broad CN-LOH segments. With the exception of a single outlier case, a low number of CNAs per patient was detected (median value of 1 somatic loss or gain per patient). However, a high prevalence of CNAs (60-70% of the patients showed at least 1 tumor-associated gain or loss) and few recurring CNAs were observed, thus providing new hints towards identification of cooperating mutations. An extensive search of all CN-LOH regions > 1 Mb revealed only 3 broad regions (terminal 12Mb of 22q, terminal 27Mb of 1p and the whole chromosome 21) in three patients out of 19 (16%). CN-LOH of the whole chromosome 21 was responsible for homozygosity of a missense mutation (R80C) of RUNX1/AML1. Our study suggests that a relative submicroscopic copy number stability NK-AML genomes is associated with low recurrence of specific CNAs and CN-LOH in NK-AML patient population.
Overall design Nineteen AML bone marrow samples were collected at the time of diagnosis (>90% blasts), defined as karyotypically-normal on the basis of standard metaphase cytogenetics (MC) and analysed by the Affymetrix SNP 6.0 arrays. In 11 of such cases (matched Dx) we obtained a bone marrow sample at the remission phase (matched R) of comparable high quality as evaluated by Contrast QC and MAPD values. In 8 cases (unmatched Dx) the corresponding R sample was not available or was not of comparable quality. As a reference set the publicly available data from 270 HapMap individuals were used.
Contributor(s) Barresi V, Condorelli DF
Citation(s) 20725993
Submission date May 11, 2010
Last update date Nov 27, 2018
Contact name Vincenza Barresi
Organization name University of Catania
Street address V.le A Doria, 6
City Catania
ZIP/Postal code 95125
Country Italy
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (30)
GSM542614 Patient_9 at diagnosis
GSM542615 Patient_9 at remission
GSM542616 Patient_11 at diagnosis
BioProject PRJNA127305

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
GSE21780_RAW.tar 2.5 Gb (http)(custom) TAR (of CEL, CNCHP, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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