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| 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
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| 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.
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| 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.
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| Contributor(s) |
Barresi V, Condorelli DF |
| Citation(s) |
20725993 |
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| Submission date |
May 11, 2010 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Vincenza Barresi |
| E-mail(s) |
barregi@unict.it
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| Organization name |
University of Catania
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| Street address |
V.le A Doria, 6
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| City |
Catania |
| ZIP/Postal code |
95125 |
| Country |
Italy |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA127305 |
| 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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