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

利用尿液衍生 DNA 通过高精度测序评估膀胱癌

基本信息

批准号：
10197377
负责人：
Scott Robert Kennedy
金额：
$ 18.17万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-04-01 至 2023-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10197377
关键词：
Address Adopted Aftercare Age Aneuploid Cells BCG Live Bacillus Calmette-Guerin Therapy Biological Biological Markers Biopsy Cancer Detection Cancer Diagnostics Cancer Patient Case-Control Studies Characteristics Chemoresistance Clinical Cystoscopy Cytology DNA Detection Detection of Minimal Residual Disease Diagnosis Diagnostic Disease Disease Progression Early Diagnosis Effectiveness Evaluation Excision Exhibits FDA approved Frequencies Genes In complete remission Individual Interobserver Variability Lesion Malignant Neoplasms Malignant neoplasm of urinary bladder Methods Monitor Muscle Mutate Mutation Mutation Detection Oncogenes Operative Surgical Procedures Patients Performance Population Recurrence Reference Values Relapse Research Residual Cancers Residual Neoplasm Residual Tumors Sampling Screening for cancer Sensitivity and Specificity Solid Somatic Mutation Specificity Techniques Technology Testing Time Treatment Effectiveness Tumor Expansion Tumor Tissue Urine Variant age related base clinical decision-making clinical encounter clinical sequencing clinically relevant design genetic information high risk improved intravesical neoplastic cell next generation sequencing non-invasive monitor non-muscle invasive bladder cancer potential biomarker prognostic relapse prediction screening treatment response treatment stratification tumor variant detection

项目摘要

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.

项目概要人们已经进行了许多尝试来开发基于尿液的生物标志物，用于膀胱癌监测和然而，最广泛使用的方法是尿细胞学检查，对于高级别病变最有效。迄今为止，由于敏感性低（55%–70%），目前 FDA 批准的测试均未被广泛采用由于非整倍体细胞丰度低，低级别肿瘤的特异性较差（71%–83%）。先前的研究发现了几个经常突变的基因。 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早期癌症检测和治疗的初步分层选项，检测微小残留病，或识别新出现的化疗耐药性。对于大多数其他实体癌，通过活检或手术切除来获取肿瘤组织通常是有限的或此外，这些特征性的小样本并不一定能代表整体。因此，脱落到尿液中的肿瘤细胞和/或 DNA 有望产生详细的遗传信息。使用简单、非侵入性的尿液检测来获取有关肿瘤的信息下一代测序的出现。 (NGS) 开辟了在临床上利用 DNA 作为癌症监测分析物的可能性。 NGS 的错误率已被证明是使用该技术进行低频变异的主要障碍为了克服这一限制，我们之前开发了双工测序（Duplex-Seq）。通过这种技术，我们可以检测到约 5x107 个野生型碱基中存在的单个变体。通过 Duplex-Seq 评估尿源 DNA (uDNA) 的效果优于尿细胞学或传统方法最终将使用基于 NGS 的方法来检测治疗后残留的癌症。我们建议开发和验证使用。 Duplex-Seq 适用于常见的临床情况以及正常、无癌症的个体。具体目标 1，我们将确定正常人中膀胱癌相关突变的生物学发生情况个体并针对几个不同的经常突变的基因建立年龄定义的阈值。目标 2，我们将确定 uDNA 中 NMIBC 肿瘤突变的存在或不存在是否可以预测膀胱内 BCG 治疗结束时复发，可能减少重复和治疗的需要不愉快的膀胱镜检查。