 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 13, 2009 |
| Title |
SNP chip data of MCL |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
|
| Summary |
Mantle cell lymphoma (MCL) is a lymphoma characterized by aberrant activation of CCND1/cyclin D1 followed by sequential genetic abnormalities. Genomic abnormalities in MCL have been extensively examined by classical cytogenetics and microarray-based comparative genomic hybridization techniques, pointing out a number of alterations in genomic regions that correlate with the neoplastic phenotype and survival. Recently, single nucleotide polymorphism genomic microarrays (SNP-chip) have been developed and used for analysis of cancer genomics. This technique allows detection of genomic changes with higher resolution, including loss of heterozygosity without changes of gene dosage, so-called acquired uniparental disomy (aUPD). As a result of the analysis, known alterations were confirmed by SNP arrays, including deletion of INK4A/ARF, duplication/amplification of MYC, deletion of ATM, and deletion of TP53. We also identified a duplication/amplification that occurred at 13q involving oncogenic microRNA, miR17-92. We found other genomic abnormalities, including duplication/amplification of cyclin D1, del(1p), del(6q), dup(3q) and dup(18q). Our SNP-chip analysis detected these abnormalities at high resolution, allowing us to narrow the size of the commonly deleted regions, including 1p and 6q. Our SNP-chip analysis detected a number of aUPD sites, including whole chromosome 9 aUPD and 9p aUPD. We also found an MCL case with 19p, leading to homozygous deletion of TNFSF genes.
keyword: SNP-chip; Kawmata_MCL
|
| |
|
| Overall design |
To identify oncogenic lesions in mantle cell lymphoma (MCL), we performed a genome-wide analysis of primary MCL samples using high-density SNP arrays (Affymetrix GeneChip).
|
| |
|
| Contributor(s) |
Kawamata N, Ogawa S, Gueller S, Ross SH, Huynh T, Kato M, Chen J, Chang A, Nabavi-Nouis S, Megrabian N, Siebert R, Martinez-Climentd JA, Koeffler HP |
| Citation(s) |
19477219 |
| |
| Submission date |
Oct 30, 2009 |
| Last update date |
May 17, 2017 |
| Contact name |
Motohiro Kato |
| Organization name |
University of Tokyo
|
| Street address |
7-3-1, Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
|
| Samples (34)
|
|
| Relations |
| BioProject |
PRJNA121685 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE18820_RAW.tar |
941.4 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...