Integrated Genomics and Bioinformatics

综合基因组学和生物信息学

• 批准号: 10617288
• 负责人: Kristin A Knouse
• 金额: $ 42.18万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-06-17 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10617288
• 关键词: Binding Sites; Bioinformatics; Biological Markers; Biometry; Cancer Center Support Grant; Cells; Chromosome abnormality; Client; Cloud Computing; Communities; Computer software; Consultations; DNA Sequence Determination; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Development; Education; Educational workshop; Epigenetic Process; Event; Experimental Designs; Funding; Gene Expression; Gene Expression Profiling; Generations; Genes; Genome; Genomics; High Performance Computing; Informatics; Institution; Investigation; Libraries; Messenger RNA; Methodology; Methods; MicroRNAs; Mission; Modernization; Modification; Mutation; Pathway interactions; Point Mutation; Preparation; Protocols documentation; Publications; Quality Control; RNA Splicing; Research; Research Institute; Research Personnel; Resource Sharing; Resources; SNP genotyping; Sampling; Services; Side; Technology; Training; anticancer research; cluster computing; complex data; computer infrastructure; computing resources; cost; epigenomics; experimental study; functional genomics; genome-wide; genomic data; informatics training; instrument; member; open source; programs; success; therapeutic target; transcription factor; transcriptome sequencing; web interface

Integrated Genomics & Bioinformatics Core: Project Summary/Abstract Modern cancer research relies on a broad array of genome-wide approaches. The mission of the Koch Institute Integrated Genomics & Bioinformatics Core (IGB Core) is to support the acquisition of genomic and gene expression data and the organization and analyses of the resulting large and complex data sets through advanced technology service platforms, state-of-the-art computational infrastructure and expert bioinformatics capabilities. It provides Center Members with integrated and comprehensive services including consultative services and training in experimental design and data analyses and technical pipelines from sample generation and quality control to sequencing and informatic analysis to allow investigation of: mRNA, microRNA and lncRNA expression; splicing events; transcription factor binding sites; epigenetic modifications; point mutations and chromosomal abnormalities; and single cell genomics. In the prior renewal, the Genomics and Bioinformatics Cores were presented as separate entities. We have now combined these into the IGB Core, reflecting the critical importance of integrating genomics data generation with downstream informatic analysis. The IGB Core is an Institutional Shared Resource between the Koch Institute and three other MIT units. During the current period, usage of the IGB Core increased from 80% to 87% of Center Members. To support this demand, the IGB Core expanded sample preparation, quality control and processing, data analysis, and hardware and software capabilities. This includes expanded offerings for ii) sequencing library preparation, including development of multiple high-throughput (HT) protocols; ii) single cell acquisition/sequencing and analysis approaches; iii) long read sequencing services and analysis; and iv) RNAseq and Epigenomics analysis capabilities. The IGB Core also deployed new compute and data storage resources. Core staff provided additional direct support to this CCSG through development of financial and publication database and client-side interfaces. Thus, this Shared Resource is essential to the success of the Koch Institute mission. In the upcoming period, The IGB Core is committed to continued enhancement of genomics technologies and informatics expertise as well as maintaining IT hardware to support these efforts and the KI research community. Planned initiatives include: developing additional HT methods for sequencing library preparation; further strengthening expertise in single cell genomics applications; expanding data storage and compute cluster and/or cloud computing in line with investigator needs; and expanding informatics training offerings to include more hands-on workshop opportunities. This shared Core is of exceptional value to the CCSG because Koch Institute Members account for 47% of the Genomic services usage and 87% of Informatics services usage, but the CCSG contribution to the Core (8%) is comparable to that of the other sponsoring entities (7%) and far less than the costs covered by user chargebacks (78%).

综合基因组学与生物信息学核心：项目摘要/摘要 现代癌症研究依赖于广泛的全基因组方法。科赫研究所的使命 集成基因组学和生物信息学核心(IGB Core)是支持基因组和基因获取的核心 表达数据以及通过以下方式组织和分析所产生的大型复杂数据集 先进的技术服务平台、最先进的计算基础设施和专业的生物信息学 能力。它为中心成员提供集成和全面的服务，包括咨询 从样品生成到实验设计、数据分析和技术管道的服务和培训 以及对测序和信息分析的质量控制，以便于研究：mRNA、microRNA和lncRNA 表达；剪接事件；转录因子结合位点；表观遗传修饰；点突变和 染色体异常和单细胞基因组学。在之前的更新中，基因组学和生物信息学 核心是作为单独的实体提出的。我们现在已经将这些组合到了IGB核心中，反映了关键的 将基因组数据生成与下游信息分析相结合的重要性。IGB核心是一种 科赫研究所和其他三个麻省理工学院之间的机构共享资源。 在本期间，中心成员的IGB核心使用率从80%增加到87%。支持 在这种需求下，IGB核心扩展了样品准备、质量控制和处理、数据分析和 硬件和软件功能。这包括用于ii)测序文库制备的扩展产品， 包括开发多种高通量(HT)协议；ii)单细胞采集/测序和 分析方法；三)长读测序服务和分析；四)RNAseq和表观基因组学分析 能力。IGB核心还部署了新的计算和数据存储资源。提供核心员工 通过开发财务和出版物数据库和客户端，为该CCSG提供额外的直接支持 接口。因此，这种共享资源对于科赫研究所任务的成功至关重要。 在即将到来的时期，IGB核心致力于继续加强基因组学技术和 信息学专业知识以及维护IT硬件，以支持这些努力和KI研究社区。 计划的举措包括：开发更多的用于测序文库准备的HT方法； 加强单细胞基因组应用方面的专业知识；扩展数据存储和计算集群和/或 符合调查人员需求的云计算；以及扩展信息学培训课程，以包括更多 亲身实践的研讨会机会。此共享核心对CCSG具有特殊价值，因为科赫研究所 成员占基因组服务使用量的47%，占信息学服务使用量的87%，但CCSG 对核心基金的捐款(8%)与其他赞助实体的捐款(7%)相当，远远低于 用户按存储容量使用计费支付的成本(78%)。