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Series GSE23120 Query DataSets for GSE23120
Status Public on Jul 24, 2010
Title Basal gene expression data from Human Variation Panel
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We used microarrays to identify the variation of basal gene expression level among 287 lymphoblastoid cell lines.
Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels and 1.3 million genome-wide SNP markers from both Affymetrix and Illumina platforms were assayed for all 277 human LCLs. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. 27 loci, each containing at least 2 SNPs within 50kb with p-values <10-4, were associated with radiation AUC. 270 expression probe sets were associated with radiation AUC with p<10-3. The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes that were also associated with radiation AUC (p<10-3). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52 and DEPDC1B each significantly altered radiation sensitivity in at least 2 cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation.
 
Overall design EBV-transformed LCLs from 95 African-American (AA), 96 Caucasian-American (CA), and 96 Han Chinese-American (HCA) unrelated healthy subjects (sample sets HD100AA, HD100CAU, HD100CHI) were purchased from the Coriell Cell Repository (Camden, NJ).
 
Contributor(s) Wang L, Weinshilboum R
Citation(s) 20923822, 20525348, 19898621, 19572260, 18757419, 20876420, 21775533, 28173075, 29593529, 27749787, 26503816, 36128656
Submission date Jul 23, 2010
Last update date Nov 16, 2022
Contact name Liewei Wang
E-mail(s) wang.liewei@mayo.edu
Phone 507-284-5264
Fax 507-284-4455
URL http://mayoresearch.mayo.edu/staff/wang_l2.cfm
Organization name Mayo Clinic
Department Molecular Pharmacology and Experimental Therapeutics
Street address 200 First street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (287)
GSM569492 GM17201
GSM569493 GM17203
GSM569494 GM17102
This SubSeries is part of SuperSeries:
GSE24277 Human Variation Panel: Gene Expression and Genotype
Relations
BioProject PRJNA133245

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
GSE23120_RAW.tar 1.3 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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