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Series GSE18820 Query DataSets for GSE18820
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)
GSM466647 Jeko1_N_Mapping250K_Nsp
GSM466648 MCL-1132_N_Mapping250K_Nsp
GSM466649 MCL-1143_N_Mapping250K_Nsp
BioProject PRJNA121685

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
GSE18820_RAW.tar 941.4 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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