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| Status |
Public on Sep 25, 2010 |
| Title |
Genome-wide SNP array data from Human Variation Panel by Illumina 550K |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
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 (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) 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.
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| Overall design |
EBV-transformed LCLs from 96 Caucasian-American (CA), and 96 Han Chinese-American (HCA) unrelated healthy subjects (sample sets HD100CAU, HD100CHI) were purchased from the Coriell Cell Repository (Camden, NJ).
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| Contributor(s) |
Wang L, Weinshilboum R |
| Citation(s) |
20923822, 20525348, 19898621, 28173075, 27749787, 26503816 |
| Submission date |
Sep 21, 2010 |
| Last update date |
Oct 04, 2019 |
| 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 |
| |
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| Platforms (1) |
| GPL6434 |
Illumina HumanHap550 Genotyping BeadChip v3 |
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| Samples (192)
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| This SubSeries is part of SuperSeries: |
| GSE24277 |
Human Variation Panel: Gene Expression and Genotype |
|
| Relations |
| BioProject |
PRJNA133733 |
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