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

核心环境下癌症基因组学长读长测序应用的开发和优化

• 批准号: 10020349
• 负责人: SARA GOODWIN
• 金额: $ 12.27万
• 依托单位: COLD SPRING HARBOR LABORATORY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-11 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10020349
• 关键词: Acute Myelocytic Leukemia; Automobile Driving; Bedside Testings; Biological; Biological Sciences; Breast Cancer cell line; Cancer Model; Cause of Death; Cessation of life; Characteristics; Complex; DNA; Data; Data Analyses; Development; Diagnosis; Disease; Education; Emerging Technologies; Ensure; Epigenetic Process; Event; Generations; Genome; Genomics; Hot Spot; Length; Libraries; Malignant Neoplasms; Methods; Methylation; Oncologist; Organoids; Outcome; Preparation; RNA; RNA Splicing; RNA analysis; Research; Research Personnel; Resource Sharing; Role; Running; SKBR3; Services; Stretching; Structure; Techniques; Technology; Transcript; Variant; Work; anticancer research; cancer diagnosis; cancer genomics; cancer subtypes; cancer therapy; cost; genetic profiling; innovation; insertion/deletion mutation; instrument; mRNA Precursor; malignant breast neoplasm; molecular modeling; nanopore; next generation; novel diagnostics; operation; tool; transcriptome sequencing; treatment choice; tumorigenesis

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.

癌症是一种高度复杂和异质的疾病，受多种基因组机制控制。 测序技术对于推动癌症诊断和治疗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，研究表明基因组 以前没有意识到的复杂性。随着这些复杂性的暴露，必须开发新的方法 调查他们。下一代共享资源（NGSSR）核心的工作重点是使 可用的测序新兴技术及其在生物科学中的应用。在 近年来，长读长测序已应用于癌症基因组学。 NGSSR 已经并且 仍然处于长读测序的最前沿。 2011年，CSHL收购了第一代长 读取测序仪器。事实证明，这项技术对于 SK-BR-3 乳房的研究具有无价的价值 癌细胞系，揭示了许多结构变异，其中一些具有融合转录本，未被检测到 短读方法。鉴于这些结果，NGSSR 继续探索长读长测序 技术。目前正在开发这些方法来支持 CSHL 的一系列项目，包括： 对乳腺癌类器官进行高深度 Oxford Nanopore 和 PacBio 测序，以更好地了解乳腺癌类器官 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 能够检测甲基化以及测序数据，可能具有癌症特异性 与乳腺癌重排热点相关的甲基化谱已被确定。这 NGSSR 还开发了一种利用 Oxford Nanopore 技术来检测大插入和 急性髓系白血病（AML）中的缺失。已知这些变化是结果的标志，因此 驾驶治疗选择。该方法可以促进 AML 亚型的即时检测，提供一种新的方法 肿瘤学家的诊断工具。全长RNA测序和分析也正在由 NGSSR 用于量化替代前 mRNA 剪接事件。这些剪接事件可以用来表征 癌症亚型并探讨癌症发生和进展的机制。的作用 NGSSR 在这些项目中一直致力于开发使用技术和材料的方法 检查了。这包括 DNA/RNA 提取、文库制备和数据分析的所有步骤。这 NGSSR 提供​​的有关这些技术的服务和教育/建议为 CSHL 研究人员提供了 极大地促进了他们的研究工作。除了进行独立研究外，NGSSR 核心经理将继续运行 NGSSR 的日常运营，确保所有测序相关的 CSHL 使用新旧方法进行的研究具有最高质量，可促进突破性进展 癌症研究。