1. www.polyomx.org A Comprehensive Genomic Approach to the Identification of Predictive Markers using DNA and Tissue Repair Gene Polymorphisms in Radiation Induced Late Toxicity in Prostate Cancer Patients Treated with Conformal Radiotherapy Damaraju S 1,2, Murray D 2, Dufour J 1, Carandang D 1, Myrehaug S 2,3, Fallone G 2,3, Field C 2,3, Greiner R 1,3, Hanson J 2, Cass CE 1,2 and Parliament M 1,2 1 Alberta Cancer Board PolyomX Program at Cross Cancer Institute, 2 Department of Oncology, 3 Division of Medical Physics, 4 Department of Computing Science, University of Alberta, Edmonton. A radio-genomic approach to explore the possible relationship between single nucleotide polymorphisms (SNPs) in clinical radiation toxicity in a retrospective cohort of prostate cancer patients previously treated with conformal radiotherapy (3DCRT) is attempted. We selected 279 SNPs in candidate genes encoding DNA damage recognition/ repair/ response, steroid metabolism, cytokine and tissue repair proteins for this study We report initial analysis of association for late tissue toxicity in 83 patients in a retroactive cohort using 128 SNPs. Methods This study was approved by the institutional ethics board. Informed consent was obtained from eighty three patients who received radiation therapy for prostate cancer. These patients experienced late tissue (GI) toxicity. We grouped patients with RTOG scores of 0-2 (n=55) and 2+ and above (n=28) for analysis, and genotype calls for individual SNPs were also grouped dichotomously to maximize the differences in time to toxicity. Analysis also included radiation dosimetric variables and age covariates. Cumulative risk of late toxicity curves were derived according to genotype class for each SNP using Kaplan- Meier method and log-rank tests were performed to obtain univariate significance. Exploratory multivariate analysis was performed using the SAS score method to determine the best overall model fit. Results and Conclusions Significant univariate associations with late rectal or bladder toxicity (gr. 2+) were found for XRCC3 (A>G 5' UTR NT 4541), LIGIV (T>C Asp568Asp), MSH6 (T>C, D180D), MLH1 (C>T V2191), CYP2D6*4 (G>A splicing defect), mean rectal and bladder dose, dose to 30% of rectum or bladder, and age C Asp568Asp), ERCC2 (G>A, D711D), CYP2D6*4 (G>A, splicing defect), mean bladder dose >60 Gray, and dose to 30% of rectal volume >75 Gray on Cox multivariate analysis. A study with larger sample size to validate these findings is warranted to justify radio-genomic approaches in the clinic. Study Design and Scope -- DNA Repair Pathways Base Excision Repair- Oxidized bases, spontaneous damage (ADPRT, APE1, Lig, Pol B, XRCC1 etc) Nucleotide Excision Repair- UV and Chemicals (ERCC, Lig, Pol D1, XPA, XPC, RAD23A, and RAD23B) Double Strand Break/Recombination Repair- Ionizing Radiation and radiometric drugs (Lig, NBS1, XRCC, RAD50, RAD51) Damage Recognition and Cell Cycle Check Points- Indirect Role in Repair (CDK4, CDKN2A, RAD52, RAD54, XRCC9, MLH, MSH) Mismatch Repair- Replication errors (MSH) Supported by ACF and ACB Fig 1: Kaplan-Meier graphs of radiation induced toxicity in prostate cancer patients and significance levels for the variables in univariate analysis Table 4:Multivariate analysis of factors associated with RTOG grade 2+ chronic toxicity Best Subset of 4 predictors Score Chi-Square = 36.6, p < 0.0001 Second Best Subset of 4 predictors Score Chi-Square = 34.9, p < 0.0001 Variablep-valueHazard95% CIp-valueHazard95% CI LIG IV T>C, Asp568Asp0.00044.862.04 - 11.560.00343.561.52 - 8.31 CYP2D6*4 G>A, Splicing defect---0.01102.851.27 - 6.38 Age at diagnosis0.01080.240.08 - 0.720.00020.130.04 - 0.38 Mean bladder dose0.01113.021.29 - 7.08--- Dose to 30% of rectal volume0.00373.271.47 - 7.290.00054.141.87 - 9.17 Best Subset of 5 predictors Score Chi-Square = 42.0, p < 0.0001 Second Best Subset of 5 predictors Score Chi-Square = 41.7, p < 0.0001 Variablep-valueHazard95% CIp-valueHazard95% CI LIG IV T>C, Asp568Asp0.00025.372.22 - 12.970.00035.222.14 - 12.73 ERCC2 G>A, D711D0.02073.541.21 - 10.35--- MSH6 T>C, D180D---0.00743.081.35 - 7.01 Age at diagnosis0.00360.190.06 - 0.580.00570.220.07 - 0.64 Mean bladder dose0.00863.191.34 - 7.590.00293.901.60 - 9.55 Dose to 30% of rectal volume0.01052.891.28 - 6.530.00123.811.70 - 8.55