Genomics

基因组学

• 批准号: 9391970
• 负责人: Corbin D Jones
• 金额: $ 35.17万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9391970
• 关键词: Animal Model; Archives; Area; Automation; Bioinformatics; Bioinformatics Shared Resource; Budgets; Cancer Center; Cancer Center Support Grant; Cell physiology; Cells; ChIP-seq; Chromatin; Clinical Data; Communities; Complement; Complex; Computer Analysis; Consultations; Contract Services; Copy Number Polymorphism; Custom; DNA; DNA Methylation; Data; Education; Ensure; Environment; Equipment; Funding; Future; Gene Chips; Gene Dosage; Gene Expression; Generations; Genes; Genetic Polymorphism; Genetic Transcription; Genomic Library; Genomic approach; Genomics; Genomics Shared Resource; Genotype; Goals; Grant; High-Throughput Nucleotide Sequencing; Hour; Human; Human Genome; Human Resources; Hybrids; Individual; Investments; Ions; Link; Malignant Neoplasms; Measures; Mediating; Methods; Methylation; Nature; Phenotype; Preparation; Price; Protein Isoforms; Protocols documentation; Publications; RNA; RNA Interference; RNA interference screen; RNA library; Records; Research; Research Infrastructure; Research Personnel; Robot; Robotics; Running; SNP genotyping; Sampling; Services; Source; Surveys; System; Technology; The Cancer Genome Atlas; Translating; Validation; Whole-Genome Shotgun Sequencing; Work; base; bead chip; cancer genomics; clinical sequencing; clinically actionable; comparative genomic hybridization; computer infrastructure; cost; cost effective; cost efficient; data acquisition; defined contribution; density; design; exome; exome sequencing; experience; experimental study; human model; innovation; member; next generation sequencing; transcriptome sequencing; tumor; whole genome

ABSTRACT – Sequencing and Genomics (GEN) Shared Resource The Sequencing and Genomics Shared Resource (GEN SR) is a ‘super SR’ that provides an integrated platform of technology, expertise, education, and infrastructure creating an accessible environment for LCCC researchers to design and undertake cutting edge genomics projects. This SR is led by a team of highly experienced genomic biologists with proven track records in cancer-related research. The SR specializes in five major technologies: Agilent Microarrays, Affymetrix Microarrays, Illumina bead array genotyping, NextGen sequencing (Illumina, PacBio, and Ion Platforms) and RNAi screening for functional validation. These areas are complemented by major LCCC investments in computational infrastructure and analysis. The SR provides state-of-the-art equipment and specialized expertise to guide users through any and all stages of a project: consultation, sample QC, data generation, and analysis. These services are being used by LCCC researchers to understand fundamental cellular processes that contribute to cancer. For example, these facilities have contributed extensively to the data generated at UNC as part of The Cancer Genome Atlas project. Additionally, several groups are using these SRs to translate cancer genomic information into actionable clinical data as part of the NCGENES and UNCseq projects. In addition to an increase in these translational projects, we expect that the next five years there will be increased demand for integrative genomics projects that generate data from a variety of sources and SRs and then, working with the Bioinformatics Shared Resource teams, produce comprehensive analyses of tumor samples. From the end of June 2013 to July 2014, the GEN SR was used by 96 LCCC members (85% of total use). Since 2009 use of this combined facility has nearly tripled (measured in terms of grant and recharge dolla rs). Highlights for the GEN SR during the last funding period include extensive expansion of our NextGen sequencing services and automation of all array platforms, as well as relocation to a new shared facility space custom renovated to support the specific infrastructure required to run these systems 24/7. As a result, in fiscal year 2013-2014 alone this SR made 13,303 genomic libraries, sequenced over 100 Trillion bp, genotyped 1,945,409,504 SNPs, and ran 13,517 microarray experiments. This work has contributed to over a hundred publications, including seven in Nature as part of The Cancer Genome Atlas project. For 2015, the LCCC requests $254,659 to maintain personnel to support genomics efforts and offset service contract costs. CCSG funds are projected to be 4% of operating costs.

摘要-测序和基因组学（GEN）共享资源 测序和基因组学共享资源（GEN SR）是一个“超级SR”，提供了一个集成的 技术、专业知识、教育和基础设施平台，为LCCC创造一个无障碍环境 研究人员设计和承担尖端的基因组学项目。该SR由一个高度专业的团队领导， 经验丰富的基因组生物学家，在癌症相关研究方面有着良好的记录。SR专门从事 五大技术：Agilent微阵列、Affyssin微阵列、Illumina微珠阵列基因分型、NextGen 测序（Illumina、PacBio和Ion Platforms）和RNAi筛选用于功能验证。这些领域 LCCC在计算基础设施和分析方面的重大投资是其补充。SR提供 最先进的设备和专业知识，指导用户完成项目的任何和所有阶段： 咨询、样品质量控制、数据生成和分析。LCCC研究人员正在使用这些服务 了解导致癌症的基本细胞过程。例如，这些设施有 作为癌症基因组图谱项目的一部分，他对在癌症研究所产生的数据做出了广泛的贡献。 此外，有几个小组正在使用这些SR将癌症基因组信息转化为可操作的信息。 作为NCGENES和UNCseq项目的一部分。除了这些翻译的增加， 项目，我们预计未来五年对整合基因组学项目的需求将增加 从各种来源和SR中生成数据，然后与生物信息学共享 资源团队对肿瘤样本进行全面分析。 从2013年6月底到2014年7月，96个LCCC成员使用了GEN SR（占总使用量的85%）。 自2009年以来，这一综合设施的使用几乎增加了两倍（以赠款和充值美元计算）。 GEN SR在上一个融资期间的亮点包括我们的NextGen的广泛扩展 所有阵列平台的测序服务和自动化，以及迁移到新的共享设施空间 定制翻新，以支持这些系统全天候运行所需的特定基础设施。结果在 仅在2013-2014财年，该SR就构建了13，303个基因组文库，测序超过100个Trilingbp， 基因分型1，945，409，504个SNPs，并运行13，517个微阵列实验。这项工作有助于超过一个 发表了数百篇论文，其中7篇发表在《自然》杂志上，是癌症基因组图谱项目的一部分。2015年， LCCC要求254，659美元用于维持人员，以支持基因组学工作并抵消服务合同费用。 CCSG资金预计将占运营成本的4%。