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: 10689098
• 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/10689098
• 关键词: Acute Myelocytic Leukemia; Automobile Driving; 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; Genetic; 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; Techniques; Technology; Transcript; Variant; Work; anticancer research; cancer diagnosis; cancer genomics; cancer subtypes; cancer therapy; cost; diagnostic tool; innovation; insertion/deletion mutation; instrument; mRNA Precursor; malignant breast neoplasm; molecular modeling; nanopore; next generation; novel diagnostics; operation; point of care testing; 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和新方法的研究至关重要 治疗。随着测序能力的提高和成本的降低，研究揭示了基因组 以前没有意识到的复杂性。随着这些复杂性的显现，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 现有测序方面的新兴技术及其在生物科学中的应用。在……里面 近年来，长阅读测序已被应用于癌症基因组学。NGSSR一直是，并且 继续走在长篇测序的前列。2011年，CSHL收购了第一代Long- 阅读测序仪器。这项技术被证明对SK-BR-3乳房的研究是无价的 癌细胞株，揭示了许多结构变异，其中一些带有融合转录本，不能被 短读法。鉴于这些结果，NGSSR继续探索长阅读测序 技术。目前正在开发这些方法，以支持CSHL的一系列项目，包括， 牛津纳米孔和PacBio高深度测序乳腺癌有机物以更好地理解 推动肿瘤发生的机制，并验证有机化合物作为癌症的分子模型。通过利用 独特的牛津纳米孔检测甲基化和测序数据的能力，可能是癌症特异性的 与乳腺癌中重排热点相关的甲基化特征已经被确定。这个 NGSSR还开发了一种管道，利用牛津纳米孔技术来检测大型插入和 急性髓系白血病(AML)的缺失。众所周知，这些变化是结果的标志，因此 驾车治疗选择。这种方法可以促进AML亚型的护理点检测，提供了一种新的 肿瘤学家的诊断工具。全长RNA测序和分析也正在由 NGSSR来量化可供选择的前mRNA剪接事件。这些剪接事件可以用来表征 肿瘤亚型，探讨肿瘤发生发展的机制。美国政府的角色 NGSSR在这些项目中一直在开发与技术和材料一起工作的方法 检查过了。这包括从DNA/RNA提取、文库准备和数据分析的所有步骤。这个 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努力。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，以确保所有相关的排序 CSHL的研究，使用新的和旧的方法，是最高质量的，以促进破土动工 癌症研究。

项目成果

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.

云上 MaizeCODE 数据的管理、分析和分发。

• DOI: 10.3389/fpls.2020.00289
• 发表时间: 2020
• 期刊: Frontiers in plant science
• 影响因子: 5.6
• 作者: Wang,Liya;Lu,Zhenyuan;delaBastide,Melissa;VanBuren,Peter;Wang,Xiaofei;Ghiban,Cornel;Regulski,Michael;Drenkow,Jorg;Xu,Xiaosa;Ortiz-Ramirez,Carlos;Marco,CristinaF;Goodwin,Sara;Dobin,Alexander;Birnbaum,KennethD;Jackson,DavidP
• 通讯作者: Jackson,DavidP