High Throughput Method to Assess SNP Functionality in Prostate Cancer

描述（由申请人提供）：实现个性化医疗的关键未满足需求是能够对人类基因组中存在的数百万个单核苷酸多态性（snp）进行分类，并确定哪些DNA变异是导致疾病的原因。一个关键的被研究的SNPs的功能是它们产生或破坏与癌症有关的转录因子的基因组结合位点的能力。为了实现这一目标，我们正在发明SNP- snap（蛋白质特异性和亲和力）微阵列作为原型高通量设备来评估SNP功能。SNP- snap阵列将用于显示25万个与前列腺癌相关的SNP作为双链DNA分子，并检测转录因子（即药物靶点）与这些SNP DNA序列的结合。所得数据将与前列腺癌发病率相关。来自SNP- snap阵列的百万多个数据点将使用SNP序列特异性景观进行分析，创建与转录因子结合，SNP偏好和最近基因的染色体位置相关的前列腺癌“分子特征”。我们的发现也将前列腺癌相关SNP功能与癌症分期和侵袭性联系起来。通过提供个体化疾病风险评估、确定新的个体化治疗靶点、预测常用治疗方法的疗效和潜在的脱靶副作用，了解SNP功能将对个体化医疗产生重大影响。这个第一阶段项目的目标是：1。设计并合成一个定制的SNP-SNAP DNA微阵列，以覆盖与前列腺癌相关的25万个snp。2. 在SNP-SNAP阵列上检测5种前列腺癌相关转录因子（纯化蛋白和细胞裂解物）的DNA结合特异性和亲和力，并用snp引起的转录因子结合差异来注释人类基因组。验证前列腺癌细胞染色质免疫沉淀的结果。3. 获取前列腺癌患者的SNP数据，确定功能性SNP与前列腺癌发病率之间是否存在统计学意义上的显著相关性，功能性SNP在SNP- snap阵列上产生前列腺癌特异性转录因子的差异结合。该技术可以同时检测数百万个SNP和多个转录因子，从而代表了以高通量方式评估SNP功能的第一种方法之一。我们的SNP- SNAP技术，凭借阵列定制设计和检测数百万种DNA排列的能力，也广泛适用于任何癌症类型和疾病模型。

DESCRIPTION (provided by applicant): A critical unmet need in implementing personalized medicine is the ability to sort through the millions of single nucleotide polymorphisms (SNPs) present in the human genome and to pinpoint which of these DNA variations are causative in disease. A key under-studied function of SNPs is their ability to generate or disrupt genomic binding sites for transcription factors involved in cancer. Toward this goal, we are inventing the SNP-SNAP (Specificity and Affinity for Proteins) microarray as a prototype high throughput device to evaluate SNP function. The SNP-SNAP arrays will be used to display a quarter-million prostate cancer- related SNPs as double-stranded DNA molecules and to assay transcription factors (i.e., drug targets) for their binding to these SNP DNA sequences. The resulting data will be correlated with prostate cancer incidence. The million-plus data points from the SNP-SNAP arrays will be analyzed using SNP-Sequence Specificity Landscapes, creating a prostate cancer "molecular signature" that relates transcription factor binding, SNP preferences, and chromosomal position of the nearest genes. Our findings will also relate prostate cancer-associated SNP function with cancer stage and aggressiveness. Understanding SNP function will have a major impact on personalized medicine, by providing individualized disease risk assessment, identifying new personalized therapeutic targets, and predicting efficacy and potential off- target side effects of common therapeutics. The goals of this Phase I project are to: 1. Design and synthesize a customized SNP-SNAP DNA microarray to tile across a quarter-million SNPs that are associated with prostate cancer. 2. Examine the DNA binding specificity and affinity of 5 prostate cancer-related transcription factors, as purified proteins and from cell lysates, on the SNP-SNAP array and annotate the human genome with the transcription factor binding differences due to SNPs. Verify results with chromatin immunoprecipitation in prostate cancer cells. 3. Obtain SNP data from patients with prostate cancer and determine if there is a statistically significant association of functional SNPs, which yielded differential binding of prostate cancer specific transcription factors on the SNP-SNAP array, with prostate cancer incidence. This technology can assay millions of SNPs and multiple transcription factors simultaneously, thus representing one of the first methods to evaluate SNP functionality in a high throughput manner. Our SNP- SNAP technology, by virtue of the array custom design and ability to examine millions of DNA permutations, is also broadly applicable to any cancer type and disease model. PUBLIC HEALTH RELEVANCE: A critical unmet need in implementing personalized medicine is the ability to sort through the millions of single nucleotide polymorphisms (SNPs) present in the human genome and to pinpoint which of these DNA variations are causative in disease. A key under-studied function of SNPs is their ability to generate or disrupt genomic binding sites for transcription factors which regulate genes involved in cancer. Toward this goal, we are inventing the SNP-SNAP (Specificity and Affinity for Proteins) microarray as a prototype high throughput device to evaluate SNP function by displaying a quarter-million prostate cancer-related SNPs as double-stranded DNA molecules, assaying transcription factors (i.e. drug targets) for their binding to these SNP DNA sequences, and correlating these findings with prostate cancer incidence.