Genome-Wide Study to Identify SNPs and CNPs Associated with Radiation Injury

描述（由申请人提供）：一个亚组接受近距离放疗的前列腺癌患者经历放射性损伤，表现为泌尿系统疾病、直肠炎或勃起功能障碍（ED）。一系列研究结果表明临床放射敏感性具有遗传基础，并推测许多表现出正常组织辐射毒性的患者具有特异性单核苷酸多态性（snp）和拷贝数多态性（CNPs），这些多态性与前列腺癌放射治疗后不良反应的易感性相关。然而，迄今为止的研究仅限于对一小部分候选基因中有限数量的snp进行基因分型。由于认识到我们对辐射引起的泌尿系统疾病、直肠炎和ED的发展途径的理解不足，以及对这些形式的辐射毒性发展所涉及的基因/蛋白质谱的认识不完整，我们很可能未能识别出与这些辐射损伤表现的发展相关的许多snp和CNPs。因此，我们提出了一种新的创新策略来实现这一目标，其中将进行全基因组关联研究，以发现与临床放射敏感性相关的SNPs和CNPs（和基因）的更完整谱。这将是一项病例对照研究，每个出现泌尿系统疾病、直肠炎或ED的前列腺癌患者将在年龄、种族、分期、诊断日期和剂量学参数上进行匹配，并与没有出现这种形式的辐射损伤的适当对照患者进行匹配。在这项研究中，每种形式的辐射损伤将有200个病例和200个对照。首先使用Affymetrix 6.0 SNP阵列筛选一半受试者的SNP和CNPs。拒绝零假设的I型误差(a)设为0.0001。因此，根据次要等位基因的频率，我们将能够确定snp和CNPs，其基因组相对风险（GRRs）的发展为每种形式的辐射诱导损伤大于约2.5。尽管对于全基因组关联研究来说，这是一个相对较少的受试者数量，因此只能识别grr相对较高的snp或CNPs，但重要的是要注意，考虑到与标准放射治疗相关的剂量学不确定性，只有grr大于大约2.5的snp和CNPs才可能在实际临床环境中具有有用的预测价值。第二阶段的验证研究将使用一个单独的复制集进行，其中包括为该项目选择的另一半受试者，使用0.01的A，这将消除在初始阶段发现的几乎所有假阳性。最后，我们将对所有受试者的DNA区域周围的每个SNP进行全面的SNP筛选，证明与受试者复制集中每种形式的辐射损伤呈正相关，以便在单倍型块中对所有SNP进行基因分型。

DESCRIPTION (provided by applicant): A subgroup of prostate cancer patients treated with brachytherapy experience radiation-induced injury manifested as either urinary morbidity, proctitis or erectile dysfunction (ED). Results have been obtained from a series of studies suggestive of a genetic basis for clinical radiosensitivity and it has been hypothesized that many patients who exhibit normal tissue radiation toxicity harbor specific single nucleotide polymorphisms (SNPs) and copy number polymorphisms (CNPs) associated with a susceptibility for the development of adverse effects resulting from a radiation treatment for prostate cancer. However, the research performed to date has been restricted to genotyping only a limited number of SNPs in a small group of candidate genes. In recognition of our inadequate understanding of the pathways involved in the development of radiation-induced urinary morbidity, proctitis and ED, as well as the incomplete knowledge of the spectrum of genes/proteins involved in the development of these forms of radiation toxicity, it is likely that we have failed to identify many of the SNPs and CNPs that are associated with the development of these manifestations of radiation injury. Therefore, we are proposing a new and innovative strategy to achieve this goal in which a genome wide association study will be performed to discover a more complete spectrum of the SNPs and CNPs (and genes) that are associated with clinical radiosensitivity. This will be a case-control study in which each prostate cancer patient that develops either urinary morbidity, proctitis or ED will be matched on age, race, stage, date of diagnosis and dosimetric parameters, with an appropriate control patient who did not develop that form of radiation injury. There will be 200 cases and 200 controls for each form of radiation injury in this study. Half of the subjects will first be screened for SNPs and CNPs using the Affymetrix 6.0 SNP array. The type I error (a) for rejection of the null hypothesis will be set at 0.0001. Therefore, depending on the minor allele frequency, we will be able to identify SNPs and CNPs whose genome relative risks (GRRs) for the development of each form of radiation induced injury is greater than approximately 2.5. Although this is a relatively modest number of subjects for a genome wide association study, therefore enabling identification of SNPs or CNPs only with relatively high GRRs, it is important to note that only SNPs and CNPs with GRRs greater than roughly 2.5 will likely be of useful predictive value in the actual clinical setting considering the dosimetric uncertainties associated with a standard radiotherapy treatment. A second phase validation study will be performed with a separate replication set comprising the other half of the subjects selected for this project using an a of 0.01, which should eliminate virtually all false positives identified in the initial phase. Finally, we will perform comprehensive SNP screening for all subjects of the DNA region surrounding every SNP that proves positively associated with each form of radiation injury in the replication set of subjects in order to genotype all SNPs in a haplotype block. PUBLIC HEALTH RELEVANCE: This project represents the first study to use the powerful results obtained through the HapMap project and the low cost SNP/CNP genotyping that has become possible with the creation of high density SNP/CNP arrays to perform a genome wide association study to identify SNPs or CNPs associated with the development of radiation injury resulting from treatment for prostate cancer. The results of this project should provide a basis for a predictive screening assay to identify prostate cancer patients who are most likely to develop urinary morbidity, proctitis or ED following radiotherapy.