The Development and Optimization of Long-Read Sequencing Applications to Cancer Genomics in a Core Setting

癌症是一种高度复杂和异质性的疾病，由多种基因组机制控制。 测序技术对于推动癌症诊断新方法的研究至关重要， 治疗随着测序通量的增加和成本的降低，研究揭示了基因组 以前没有意识到的复杂性。随着这些复杂性的揭示，必须开发新的方法 去调查他们下一代共享资源（NGSSR）核心的工作重点是使 新兴的测序技术，并开发其在生物科学中的应用。在 近年来，长读段测序已被应用于癌症基因组学。NGSSR已经， 仍然是长读序测序的前沿。2011年，CSHL收购了第一代长- 读取测序仪器。这项技术被证明是非常宝贵的研究SK-BR-3乳腺癌 癌细胞系，揭示了许多结构变异，一些融合转录，没有检测到的 短读法。鉴于这些结果，NGSSR继续探索长读序测序 技术.目前正在开发这些方法，以支持CSHL的一系列项目，包括， 对乳腺癌类器官进行高深度牛津纳米孔和PacBio测序，以更好地了解 驱动肿瘤发生的机制，并验证类器官作为癌症的分子模型。通过利用 独特的Oxford Nanopore检测甲基化的能力，沿着测序数据，可能是癌症特异性的 已经鉴定了与乳腺癌中重排热点相关的甲基化谱。的 NGSSR还开发了一种利用牛津纳米孔技术检测大插入的管道， 急性髓性白血病（AML）中的缺失。已知这些变化是结果的标记，因此 驾驶治疗选择。这种方法可以促进AML亚型的即时检测，提供新的 诊断工具。全长RNA测序和分析也正在开发中， NGSSR以定量可变前mRNA剪接事件。这些剪接事件可用于表征 探讨肿瘤发生发展的机制。的作用 NGSSR在这些项目中一直致力于开发与技术和材料一起工作的方法， 考察这包括从DNA/RNA提取、文库制备和数据分析的所有步骤。的 NGSSR提供的关于这些技术的服务和教育/建议，为CSHL的研究人员提供了一个 极大地推动了他们的研究工作。除了进行独立研究外，NGSSR 核心经理将继续运行NGSSR的日常操作，确保所有测序相关 CSHL的研究采用了新的和旧的方法，具有最高的质量，以促进开创性的研究 癌症研究。

Cancer is a highly complex and heterogeneous disease governed by a multitude of genomic mechanisms. Sequencing technologies have been essential to driving research into new methods of cancer diagnosis and treatment. As sequencing has increased in throughput and decreased in cost, research has revealed genomic complexities not previously appreciated. As these complexities are revealed, new methods must be developed to investigate them. The work of the Next-Generation Shared Resource (NGSSR) Core focuses on making emerging technologies in sequencing available and developing their applications to biological science. In recent years, long-read sequencing has been applied to cancer genomics. The NGSSR has been, and continues to be, on the forefront of long-read sequencing. In 2011, CSHL acquired the first generation of long- read sequencing instruments. This technology was shown to be invaluable to studies of the SK-BR-3 breast cancer cell line, revealing that many structural variations, some with fusion transcripts, are not detected by short-read methods. Given these results, the NGSSR has continued to explore long-read sequencing technologies. These methods are currently being developed to support an array of projects at CSHL, including, high depth Oxford Nanopore and PacBio sequencing of breast cancer organoids to better understand the mechanisms driving tumorigenesis and to validate organoids as molecular models of cancer. By leveraging the unique Oxford Nanopore ability to detect methylation along with sequencing data, possible cancer specific methylation profiles correlated with rearrangement hot spots in breast cancers have been identified. The NGSSR has also developed a pipeline exploiting Oxford Nanopore technology to detect large insertions and deletions in Acute Myeloid Leukemia (AML). These variations are known to be markers for outcome, thus driving treatment choice. This method can facilitate point-of-care testing for AML subtype, providing a new diagnostic tool to oncologists. Full length RNA sequencing and analysis is also being developed by the NGSSR to quantify alternative pre-mRNA splicing events. These splicing events can be used to characterize cancer subtype and to explore the mechanisms of cancer development and progression. The role of the NGSSR in these projects has been to develop methods to work with the technologies and the materials to be examined. This includes all steps from DNA/RNA extraction, library preparation, and data analysis. The services and education/advice the NGSSR provides about these technologies gives CSHL researchers a tremendous boost in their research endeavors. In addition to conducting independent research, the NGSSR core manager will continue to run the day-to-day operation of the NGSSR ensuring that all sequencing related studies at CSHL, using both new and old methods, are of the highest quality to facilitate ground breaking cancer research.