Sequencing and Bioinformatics

测序和生物信息学

• 批准号: 10508449
• 负责人: Andrew Laurence Routh
• 金额: $ 21.62万
• 依托单位: SEATTLE CHILDREN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-22 至 2027-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10508449
• 关键词: Area; Behavior; Bioinformatics; Biological; Biology; Capsid; Cell Culture Techniques; Cells; Chromatin Structure; Chromosome Structures; Clinical; Collaborations; Communities; Complementary DNA; Computer Analysis; Computer software; Core Facility; DNA Sequencing Facility; Data; Databases; Development; Drug resistance; Environment; Event; Evolution; Experimental Designs; Exposure to; Gene Expression; Genetic Recombination; Genome; Genomic approach; HIV; HIV Genome; Human Resources; In Situ; In Vitro; Individual; Integrase; Length; Location; Measures; Messenger RNA; Minority; Molecular; Molecular Biology; Molecular Virology; Mutation; Nucleic Acids; Nucleotides; Nuts; Output; Pattern; Pharmacotherapy; Polymerase; Process; Protein Isoforms; Proteins; RNA; RNA Splicing; RNA Viruses; RNA-Protein Interaction; Research; Research Personnel; Research Project Grants; Resolution; Resources; Role; Sampling; Services; Single Nucleotide Polymorphism; Site; Specimen; Structure; System; Techniques; Technology; Training; Universities; Variant; Viral; Viral Genome; Virus; Virus Replication; Work; antiretroviral therapy; base; chromosomal location; crosslink; experience; experimental study; genome sequencing; innovation; insight; integration site; molecular sequence database; nanopore; new technology; next generation; next generation sequencing; novel; novel strategies; particle; pressure; resistance mutation; response; sequencing platform; single cell sequencing; single cell technology; single molecule; skills; small molecule inhibitor; tool; transcriptome sequencing; transcriptomics; viral genomics; virology

ABSTRACT, CORE 4 Next-Generation Sequencing is an essential and fundamental approach in molecular virology. In vitro, it can capture and characterize protein-nucleic interactions and RNA structure. In cell culture and in clinical settings, it can measure rates of viral polymerase error, viral response to small molecule inhibitors or changes in host gene expression. NGS can chart viral evolution, patterns of genome conservation, characterize origins of drug resistance and discover new viruses. As such, NGS has been transformative in our ability to study virus diversity and evolution and is still a burgeoning field. The Sequencing Core comprises a group of experts with experience with the implementation of the wide range of approaches in terms of molecular biology, experimental design, and downstream computational analyses. We will provide expert support and resources to provide Next- Generation Sequencing and downstream computational analyses to the B-HIVE Research Projects. Importantly, a key focus of the core will be to develop and apply approaches that go beyond what is accessible via commercial and university core facilities. We will provide and develop state-of-the-art technologies in close collaboration with the Research Projects that will help provide unique insights into HIV biology and evolution, whilst also providing novel platforms for deployments in other viral systems. A central focus of the B-HIVE is to understand the molecular mechanisms governing HIV entry, integration, particle assembly, and egress. Each of these processes involve profiling the viral and host nucleic acids during the viral lifecycle. The sequencing core will support the entire B-HIVE reflecting stages throughout the viral replication cycle. We will develop single-cell sequencing approaches, leveraging our extensive expertise in this area, to characterize the effects of integration site location, chromatin structure, HIV mutations, and exposure to latency reversing agents (LRAs) on proviral expression. We will apply and advance long-read sequencing technologies using the Oxford Nanopore Technologies MinION platform for both host transcriptomics and full- length HIV genome sequencing to characterize host and virus splicing. We will develop and implement novel approaches in virus genomics to characterize virus sequence diversity in both clinical and experimental settings in support of the main Research Projects. The Sequencing Core has extensive experience developing, deploying and maintaining new computational software and sequencing databases. These will provide an important resource to the B-HIVE centers, as well as allow the rapid dissemination and sharing of capabilities with the broader HIV and virus research community. Finally, we will provide training in each of our respective platforms and technologies in view of disseminating these skills throughout the B-HIVE and to support the development and progression of trainees working with the B-HIVE and its collaborators. 1

摘要，核心4 下一代测序是分子病毒学中必不可少的基本方法。在体外，它可以 捕获并表征蛋白质核相互作用和RNA结构。在细胞培养和临床环境中 可以测量病毒聚合酶误差的速率，对小分子抑制剂的病毒反应或宿主基因的变化 表达。 NGS可以绘制病毒进化，基因组保存模式，表征药物的起源 抵抗并发现新病毒。因此，NGS在我们研究病毒多样性的能力方面具有变革性 和进化，仍然是一个新兴的领域。测序核心包括一群具有经验的专家 通过在分子生物学，实验设计方面实施广泛的方法， 和下游计算分析。我们将提供专家支持和资源来提供下一步 生成测序和下游计算分析对B-HY研究项目进行了测序。 重要的是，核心的重点将是开发和应用超越可访问的方法 通过商业和大学核心设施。我们将在附近提供和开发最先进的技术 与研究项目的合作，将有助于提供对HIV生物学和进化的独特见解， 同时还为其他病毒系统部署提供了新颖的平台。 B hive的一个主要重点是了解有关HIV进入，整合，， 粒子组件和出口。这些过程中的每一个都涉及分析病毒和宿主核酸。 病毒生命周期。测序核心将支持整个病毒中的整个B-hive反射阶段 复制周期。我们将开发单细胞测序方法，利用我们广泛的专业知识 区域，以表征整合位点位置的影响，染色质结构，HIV突变以及暴露于 潜伏期逆转剂（LRA）对病毒表达。我们将申请并推进长阅读测序 使用牛津纳米孔技术的技术，用于宿主转录组学和完整的技术 长度HIV基因组测序以表征宿主和病毒剪接。我们将开发和实施小说 病毒基因组学的方法来表征临床和实验环境中病毒序列多样性 支持主要研究项目。测序核心具有广泛的经验，部署 并维护新的计算软件和测序数据库。这些将提供重要的 向B-hive中心的资源，并允许快速传播和共享能力与 更广泛的艾滋病毒和病毒研究界。最后，我们将在每个平台中提供培训 以及鉴于整个B-hive传播这些技能并支持开发的技术 以及与B-HY及其合作者合作的受训者的进步。 1