Exploiting Urine Derived DNA for the Assessment of Bladder Cancer using High Accuracy Sequencing

项目摘要 已经进行了许多尝试来开发用于膀胱癌监测的基于尿的生物标志物， 监测.然而，最广泛使用的方法，尿细胞学，是最有效的高级别病变。到 迄今为止，由于灵敏度低（55%-70%），目前FDA批准的检测方法都没有被广泛采用， 特异性（71%-83%）。由于非整倍体细胞丰度低，低级别肿瘤的性能较差 和观察者间的高度变异性。先前的研究发现了几个反复突变的基因 发生在70-80%的肌肉浸润性和非肌肉浸润性膀胱癌（MIBC和NMIBC， 分别）。检测这些突变有助于早期癌症检测， 选择，检测微小残留病，或识别新出现的化疗耐药。如同 大多数其他实体癌，通过活组织检查或手术切除进入肿瘤组织通常是有限的， 无法获得。此外，这些特征性的小样本不一定代表整个 肿瘤出于这个原因，肿瘤细胞和/或DNA脱落到尿液中，有望产生详细的遗传学信息。 使用简单的非侵入性尿液测试来获得关于肿瘤的信息。下一代测序技术的出现 (NGS)已经开辟了临床上利用DNA作为癌症监测分析物的可能性。但高 NGS的错误率已被证明是将该技术用于低频变体的主要障碍 侦测为了克服这一限制，我们先前开发了双链测序（Duplex-Seq）。使用 该技术可以检测存在于约5 × 107个野生型碱基中的单个变体。我们假设 通过双链测序评估尿来源的DNA（uDNA）将比尿细胞学或常规方法更好地进行。 用于检测治疗后残留癌症的基于NGS的方法。这些信息最终将被用于 在确定治疗反应和临床决策方面。我们建议发展和验证使用 Duplex-Seq用于常见的临床情况，以及正常的无癌个体。在 具体目标1，我们将确定膀胱癌相关突变的生物学发生在正常 个体，并在几个不同的频繁突变的基因之间建立年龄定义的阈值。在特定 目的2，我们将确定uDNA中NMIBC肿瘤突变的存在或不存在是否可预测肿瘤的发生。 膀胱内BCG治疗结束时复发，可能减少重复和 不愉快的膀胱镜检查

PROJECT SUMMARY Many attempts have been made to develop urine-based biomarkers for bladder cancer surveillance and monitoring. However, the most widely used approach, urine cytology, is most effective for high-grade lesions. To date, none of the current FDA-approved tests have been widely adopted due to low sensitivities (55%–70%) and specificities (71%–83%). Performance is poor for low-grade tumors due to the low abundance of aneuploid cells and high levels of interobserver variability. Previous studies identified several recurrently mutated genes occurring in 70-80% of both muscle invasive and non-muscle invasive bladder cancers (MIBC and NMIBC, respectively). Detection of these mutations could help in early cancer detection, initial stratification for treatment options, detection of minimal residual disease, or identification of emerging chemotherapy resistance. As with most other solid cancers, accessing tumor tissue either by biopsy or surgical resection is often limited or unobtainable. Furthermore, these characteristically small samples are not necessarily representative of the entire tumor. For this reason, tumor cells and/or DNA shed into the urine holds the promise of yielding detailed genetic information about a tumor using a simple, non-invasive, urine test. The advent of next-generation sequencing (NGS) has opened up the possibility of clinically exploiting DNA as a cancer monitoring analyte. However, high error rates of NGS has proven to be a major impediment for using this technology for low frequency variant detection. To overcome this limitation, we have previously developed Duplex Sequencing (Duplex-Seq). Using this technique we can detect a single variants present in ~5x107 wild-type bases. We hypothesize that assessment of urine derived DNA (uDNA) by Duplex-Seq will perform better than urine cytology or conventional NGS-based approaches for detecting post-treatment residual cancer. Such information would eventually be used in determining treatment response and clinical decision making. We propose to develop and validate the use of Duplex-Seq for use in frequently encountered clinical scenarios, as well as in normal, cancer free, individuals. In Specific Aim 1, we will determine the biological occurrence of bladder cancer-associated mutations in normal individuals and establish age-defined thresholds across several different frequently mutated genes. In Specific Aim 2, we will determine if the presence or absence of NMIBC tumor mutations in uDNA is predictive of recurrence at the conclusion of intravesical BCG therapy, potentially reducing the need for repeated and unpleasant cystoscopies.