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

项目总结 已经进行了许多尝试来开发基于尿液的生物标记物，用于膀胱癌的监测和 监控。然而，最广泛使用的方法，尿细胞学，对高度恶性病变最有效。至 迄今为止，由于敏感性低(55%-70%)，目前FDA批准的测试都没有得到广泛采用 特异性(71%-83%)。对于低级别肿瘤，由于非整倍体细胞丰度低，表现较差。 以及观察者间高度的可变性。以前的研究发现了几个反复突变的基因 70%-80%的肌肉浸润性和非肌肉浸润性膀胱癌(MIBC和NMIBC， )。检测这些突变有助于癌症的早期检测，有助于治疗的初步分层 选择、检测微小残留病或识别新出现的化疗耐药。和以前一样 大多数其他实体癌，通过活组织检查或手术切除获取肿瘤组织通常是有限的或 得不到。此外，这些典型的小样本不一定代表整个 肿瘤。因此，排入尿液的肿瘤细胞和/或dna有望产生详细的基因。 使用一种简单的、非侵入性的尿液测试来了解肿瘤的信息。下一代测序的到来 美国国家癌症研究所(NGS)已经开启了将DNA作为癌症监测分析物用于临床的可能性。然而，高 NGS的误码率已被证明是将该技术用于低频变化的主要障碍 侦测。为了克服这一限制，我们以前已经开发了双链测序(Duplex-Seq)。vbl.使用 这项技术我们可以检测到存在于~5x107个野生型碱基中的单个变异体。我们假设 用Duplex-Seq方法检测尿液衍生DNA(UDNA)优于尿细胞学或常规方法 基于NGS的检测治疗后残留癌症的方法。这样的信息最终将被使用 在决定治疗反应和临床决策方面。我们建议开发并验证 DUPLEX-SEQ用于经常遇到的临床场景，以及正常的、无癌症的个人。在……里面 具体目标1，我们将确定膀胱癌相关突变在正常人群中的生物学发生情况 并在几个不同的频繁突变基因上建立年龄定义的阈值。具体而言 目的2，我们将确定uDNA中nMIBC肿瘤突变的存在或不存在是否预测 膀胱内卡介苗治疗结束后复发，潜在地减少了重复和 令人不快的膀胱镜检查。

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.