Genomics

摘要测序与基因组学(GEN)共享资源 测序与基因组学共享资源(Gen SR)是一种提供集成 技术、专业知识、教育和基础设施平台，为LCCC创造无障碍环境 研究人员设计和承担尖端基因组学项目。这个SR是由一个高度 经验丰富的基因组生物学家，在癌症相关研究方面有良好的记录。SR专门从事 五大技术：安捷伦微阵列、Affymetrix微阵列、Illumina珠阵列基因分型、NextGen 测序(Illumina、PacBio和Ion平台)和RNAi筛选以进行功能验证。这些地区 LCCC在计算基础设施和分析方面的重大投资是相辅相成的。服务请求提供了 最先进的设备和专业知识，可指导用户完成项目的任何阶段： 咨询、样品质量控制、数据生成和分析。LCCC的研究人员正在使用这些服务 以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，为北卡罗来纳大学产生的数据做出了广泛贡献。 此外，有几个小组正在使用这些SRS将癌症基因组信息转化为可操作的信息 临床数据是NCGENES和UNSEQ项目的一部分。除了增加这些翻译版本之外 项目，我们预计未来五年对综合基因组学项目的需求将会增加 从各种来源和SR生成数据，然后与共享的生物信息学合作 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，共有96名LCCC成员使用了Gen SR(占总使用量的85%)。 自2009年以来，这一合并贷款的使用几乎增加了两倍(以赠款和充值美元衡量)。 在上一个资助期内，Gen SR的亮点包括广泛扩展我们的下一代 所有阵列平台的排序服务和自动化，以及搬迁到新的共享设施空间 定制翻新，以支持全天候运行这些系统所需的特定基础架构。因此，在 仅2013-2014财年，该SR就建立了13,303个基因组文库，测序超过100万亿个核苷酸， 对1945,409,504个SNPs进行了基因分型，并进行了13,517个微阵列实验。这项工作已经为 100份出版物，包括作为癌症基因组图谱项目一部分的7份《自然》杂志。2015年， LCCC要求提供254,659美元以维持人员，以支持基因组学工作并抵消服务合同成本。 CCSG资金预计将占运营成本的4%。

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.