RT Journal
A1 Niu, Nifang
A1 Qin, Yuxin
A1 Fridley, Brooke L.
A1 Hou, Junmei
A1 Kalari, Krishna R.
A1 Zhu, Minjia
A1 Wu, Tse-Yu
A1 Jenkins, Gregory D.
A1 Batzler, Anthony
A1 Wang, Liewei
T1 Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines
JF Genome Research 
JO Genome Research 
YR 2010 
FD November 01 
VO 20 
IS 11 
SP 1482 
OP 1492 
DO 10.1101/gr.107672.110 
UL http://genome.cshlp.org/content/20/11/1482.abstract 
AB 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 single nucleotide polymorphism (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. A total of 27 loci, each containing at least two SNPs within 50 kb with P-values less than 10−4 were associated with radiation AUC. A total of 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, which 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 two 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.