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Series GSE42525 Query DataSets for GSE42525
Status Public on Oct 01, 2013
Title Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions.
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from follicular lymphoma (FL), transformed follicular lymphoma (tFL) and matching germline (GL) sample (if available).
Copy number analysis of Affymetrix SNP 6.0 Array were performed on 91 DNA samples, consisting of 31 patients. Among the 31 patients, 19 had matching germline samples, while 12 had no germline samples. The Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated to search for copy number aberrations and copy neutral (CN)-LOH in the FL and tFL samples. Paired and unpaired analyses were performed accordingly.
Contributor(s) Okosun J, Bodor C, Wang J, Fitzgibbon J
Citation(s) 24362818
Submission date Nov 26, 2012
Last update date Nov 27, 2018
Contact name Jun Wang
Organization name Barts Cancer Institute, Queen Mary, London
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (91)
GSM1041499 Sample AD1557
GSM1041500 Sample 790
GSM1041501 Sample AD1508
BioProject PRJNA182209

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
GSE42525_RAW.tar 2.5 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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