GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE12906 Query DataSets for GSE12906
Status Public on May 01, 2009
Title SNP data from lymphoma samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary B cell non-Hodgkin's lymphoma (B-NHL) consists of different pathological entities that are frequently characterized by distinct genetic alterations. However, the knowledge on these genetic lesions in B-NHL is still limited. In order to obtain a more comprehensive view of genetic lesions in B-NHL, we performed genome-wide analysis of copy number (CN) alterations as well as allelic imbalances using Affymetrix SNP arrays with B-NHL cases, including SNP array data were analyzed with CNAG/AsCNAR software, which enabled sensitive detection of CN alterations in allele-specific manner, and thus allelic imbalances, without depending on availability of paired normal controls. Most frequent numerical abnormalities in B-NHL were gains of chromosomes 3 and 18, although gains of chromosome 3 were less prominent in FL. Chromosomal deletions that lead to loss of heterozygosity (LOH) were commonly found in 1p, 6q and 10q. High-grade amplifications and homozygous deletions frequently provide a clue to identify relevant gene targets. In our series, 12 loci of high-grade amplifications and 14 loci of homozygous deletions were identified, and helped to specify the candidate genes. These regions included, FCGR2B amplified in 5 cases of DLBCL, RERE amplified in 2 cases of FL and CDKN2A/CDKN2B deleted in 9 cases of DLBCL.
Overall design To identify oncogenic lesions in neuroblastoma, we performed a genome-wide analysis of primary tumor samples from 241 lymphoma samples (238 fresh tumors and 3 cell lines) using high-density 50K and/or 250K SNP arrays (Affymetrix GeneChip).
Contributor(s) Kato M, Sanada M, Takita J, Sato Y, Takeuchi K, Chen Y, Nakazaki K, Nomoto J, Asakura Y, Muto S, Tamura A, Akatsuka Y, Hayashi Y, Igarashi T, Kurokawa M, Chiba S, Mori S, Ishikawa Y, Tobinai K, Yoshino T, Kobayashi Y, Ogawa' S
Citation(s) 19412163
Submission date Sep 23, 2008
Last update date Dec 22, 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 (4)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (332)
GSM322973 MALT082_Mapping50K_Xba240
GSM322974 MALT033_Mapping250K_Nsp
GSM322975 MALT066_Mapping50K_Xba240
BioProject PRJNA110811

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
GSE12906_RAW.tar 7.6 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap