Microsatellite Instability Sequencing via Single-Molecule DNA Re-Reading

项目摘要 肿瘤学家非常需要改进的DNA测序技术， 细胞可以提供有关驱动疾病的特定突变的有价值的信息， 治疗决定。此外，对健康组织进行测序可以提供关于个体遗传基因的信息。 癌症的危险因素。特别感兴趣的一个领域是称为微卫星的重复DNA序列，它 发生高水平的多态性，定义为微卫星不稳定性（MSI）。MSI是一种遗传性 在许多癌细胞中经常发现的改变，特别是在某些类型的肿瘤中，如结直肠癌。 MSI的检测对于肿瘤患者的诊断和治疗具有重要意义。例如，MSI高 肿瘤对免疫疗法更敏感，免疫疗法是一种增强人体免疫系统的癌症治疗方法。 来攻击癌细胞因此，精确的微卫星测序对于肿瘤学家来说至关重要， 为患者做出治疗决定。目前可用的DNA测序技术，如桑格 测序、下一代测序（NGS）和单分子测序（SMS）都有局限性 当涉及到准确性、成本和可扩展性时。在第一阶段SBIR计划期间，Electronic BioSciences，Inc. (EBS)将开发一种“第四代”DNA测序技术， 精确测序，专门针对肿瘤学应用的微卫星。该项目直接 利用基于纳米孔的测序和单分子链控制/操作的最新进展， 能够直接，连续地对单个DNA分子进行重新测序，这将使前所未有的水平 单分子序列覆盖和随后在取样期间高准确度序列测定 分析/筛选。该项目期间开发的技术将能够可靠地检测MSI， 比任何现有的方法都精确。该系统还将实现自动化和可扩展， 最终的高通量测序。此外，为了验证在此期间实现的测序改进， 在项目中，开发的技术将以目前可用的方法为基准。最终这 该项目有可能通过使肿瘤学和癌症基因组学领域的 准确和有效的DNA测序，包括具有挑战性的微卫星区域，这可以作为关键的 癌症诊断和预后的生物标志物，并指导有效的治疗干预措施的发展。

Project Summary Oncologists have a great need for improved DNA sequencing technology because sequencing the DNA of cancer cells can provide valuable information about the specific mutations driving the disease and inform/guide treatment decisions. Additionally, sequencing healthy tissue can provide information about an individual's genetic risk factors for cancer. One area of particular interest is repetitive DNA sequences called microsatellites, which undergo a high level of polymorphism, defined as microsatellite instability (MSI). MSI is a type of genetic alteration that is often found in many cancer cells, especially in certain types of tumors, such as colorectal cancer. The detection of MSI is important for the diagnosis and management of cancer patients. For example, MSI-high tumors are more responsive to immunotherapy, a type of cancer treatment that boosts the body's immune system to attack cancer cells. Therefore, accurate microsatellite sequencing is crucial for oncologists to make informed treatment decisions for their patients. Currently available DNA sequencing technologies, such as Sanger sequencing, next-generation sequencing (NGS), and single-molecule sequencing (SMS), all have limitations when it comes to accuracy, cost, and scalability. During this Phase I SBIR program, Electronic BioSciences, Inc. (EBS) will be developing a “Fourth Generation” DNA sequencing technology that enables de-novo, ultra-high accuracy sequencing, specifically targeting microsatellites for oncology applications. This project directly leverages recent advances in nanopore-based sequencing and single-molecule strand control/manipulation to enable the direct, continuous re-sequencing of individual DNA molecules, which will enable unprecedented levels single-molecule sequence coverage and subsequent high-accuracy sequence determinations during sample profiling/screening. The technology developed during this project will enable the confident detection of MSIs with greater precision than any currently available methods. The system will also be automated and scalable for eventual high-throughput sequencing. Further, to validate the sequencing improvements achieved during this project, the developed technology will be benchmarked against currently available approaches. Ultimately, this project has the potential to significantly advance the fields of oncology and cancer genomics by enabling the accurate and efficient sequencing of DNA, including challenging microsatellite regions, which can serve as critical biomarkers for cancer diagnosis and prognosis, and guide the development of effective therapeutic interventions.