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Series GSE7761 Query DataSets for GSE7761
Status Public on Jun 06, 2007
Title Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Cisplatin, a platinating agent commonly used in treating several cancers is associated with nephrotoxicity, neurotoxicity and ototoxicity that have hindered its utility. To gain a better understanding of the genetic variants associated with cisplatin induced toxicity, we present a step-wise approach integrating genotypes, gene expression and sensitivity of HapMap cell lines to cisplatin. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were utilized to develop a preclinical model to identify genetic variants and gene expression that contribute to cisplatin induced cytotoxicity in two different populations. Cytotoxicity was determined as cell growth inhibition at increasing concentrations of cisplatin for 48 h. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip® Human Exon 1.0 ST Array. We identified 6, 2 and 9 representative SNPs that contribute to cisplatin-induced cytotoxicity through their effects on 8, 2 and 16 gene expressions in the combined, CEPH and Yoruban populations, respectively. These genetic variants contribute to 27, 29 and 45% of the overall variation in cell sensitivity to cisplatin in the combined, CEPH and Yoruban populations, respectively. Our whole genome approach can be used to elucidate expression quantitative trait loci contributing to a wide range of cellular phenotypes.
Keywords: exon array
 
Overall design Gene expression on 176 HapMap cell lines.
 
Contributor(s) Huang RS, Duan S, Shukla SJ, Kistner EO, Clark TA, Chen TX, Schweitzer AC, Blume JE, Dolan ME
Citation(s) 17701890, 20442332, 21691150, 24609542, 18765826
Submission date May 08, 2007
Last update date Nov 08, 2019
Contact name Eileen Dolan
E-mail(s) edolan@medicine.bsd.uchicago.edu
Phone 773-702-4441
Fax 773-702-0963
Organization name University of Chicago
Department Medicine
Lab Dolan Lab
Street address 5841 S. Maryland
City Chicago
State/province IL
ZIP/Postal code 60657
Country USA
 
Platforms (1)
GPL5175 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
Samples (176)
GSM188687 GM06985
GSM188688 GM07048
GSM188689 GM18521
Relations
BioProject PRJNA99891

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
GSE7761_LCL-cell-line-and-characteristics.txt 6.8 Kb (ftp)(http) TXT
GSE7761_RAW.tar 6.5 Gb (http)(custom) TAR (of CEL)
GSE7761_mask-probeset-ge2.txt 922.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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