Genomics Shared Resource

摘要 概述：遗传学和基因组学技术是癌症研究的重要工具，有助于改善 关爱癌症患者。基因组学共享资源(GSR)为科罗拉多大学癌症中心提供 (UCCC)成员为高通量基因组提供高质量和高性价比的服务和技术支持 研究癌症的发病机制、治疗方法、遗传易感性和生物标记物的开发 制定有针对性和个性化的医疗策略。服务和专业知识：GSR提供方法论 用于DNA/RNA的定量评估，包括评估含有shRNA和 UCCC成员从功能基因组共享资源(FGSR)获得的CRISPR文库。GSR 使用NEXT提供DNA序列、转录本、表观遗传学和细胞基因组学的全基因组分析 世代测序(NGS)和基因微阵列；以及单细胞基因组和转录分析 包括单细胞免疫图谱和空间基因表达。设备：GSR容纳设备以 支持DNA下一代测序(NGS)(Illumina NovaSeq 6000和Illumina MiSeq)；单细胞 基因组学(10倍基因组铬；使命生物Tapestri；Fluidigm C1和BioMark HD系统)；DNA 微阵列分析(Affymetrix基因芯片系统、Illumina iScan系统和Agilent SureScan微阵列 系统)和Affymetrix、Agilent和Illumina微阵列和测序软件。管理：GSR是一种 机构核心由UCCC管理，并由基础研究副主任H·福特监督。 服务使用：自2016年7月以来，GSR已为432名调查人员提供服务。29%的人 用户(125)是UCCC成员，代表所有四个项目，并导致118个同行审查 出版物，18%，IF≥10.运营预算：CCSG资金占年度运营的2% 预算为440万美元。剩余的支持来自用户费用(98%，430万美元)。创新与发展： GSR团队用商业基因组学工具支持UCCC成员，包括用于癌症的单细胞基因组学 研究。GSR为特定的癌症研究应用开发和优化定制方法。 咨询和教育：GSR为设计和分析可靠的基因组学提供咨询 与生物统计和生物信息学SR(BBSR)相结合的实验，并帮助成员保持最新 随着技术的进步，通过研讨会和实践培训。未来方向：GSR有四个 UCCC研究人员未来需求较高的主要方向：1)优化10X基因组学维西姆空间 基因表达溶液和单细胞基因组学方法；2)采用Olink蛋白质组学和NGS读出； 3)采用纳米孔单分子测序；4)通过不断升级我们的 技术。

ABSTRACT Overview: Genetics and genomics technologies are essential tools for cancer research and help to improve care for cancer patients. The Genomics Shared Resource (GSR) provides University of Colorado Cancer Center (UCCC) members high-quality and cost-effective services and technical support for high-throughput genomic investigation to study cancer pathogenesis, therapeutics, genetic susceptibility, and biomarker development, and develop strategies for targeted and personalized medicine. Services and Expertise: GSR offers methodologies for quantitative assessment of DNA/RNA including evaluation of human and murine cells harboring shRNA and CRISPR libraries that UCCC members obtain from the Functional Genomics Shared Resource (FGSR). GSR provides genome-wide analyses of DNA sequence, transcriptomes, epigenetics and cytogenomics using next generation sequencing (NGS) and gene microarrays; and single cell genomic and transcriptomic analyses including single cell immune profiling and spatial gene expression. Equipment: GSR houses equipment to support DNA next-generation sequencing (NGS) (Illumina NovaSeq 6000 and Illumina MiSeq); single-cell genomics (10X Genomics Chromium; Mission Bio Tapestri; Fluidigm C1 and Biomark HD Systems); DNA microarray analysis (Affymetrix GeneChip systems; Illumina iScan system; and Agilent SureScan Microarray system) and Affymetrix, Agilent and Illumina microarray and sequencing software. Management: GSR is an institutional core managed by the UCCC, and is overseen by H Ford, Associate Director for Basic Research. Use of Services: Since July 2016, GSR has provided services to 432 investigators. Twenty-nine percent of users (125) were UCCC members, representing all four programs and resulting in 118 peer reviewed publications, 18% with an IF ≥ 10. Operating Budget: CCSG funding represents 2% of the annual operating budget of $4.4M. The remaining support is from user fees (98% $4.3M). Innovation and Developments: The GSR team supports UCCC members with commercial genomic tools including single cell genomics for cancer research. GSR develops and optimizes customized methods for specific cancer research applications. Consultation and Education: GSR provides consultation for designing and analyzing reliable genomics experiments in conjunction with the Biostatistics and Bioinformatics SR (BBSR) and helps members stay updated with the advancement of technology through seminars and hands-on training. Future Directions: GSR has four main future directions that are in high demand by UCCC investigators: 1) optimize 10X Genomics Visium spatial gene expression solution and methods for single cell genomics; 2) adopt Olink proteomics with NGS readouts; 3) adopt Nanopore single molecule sequencing; and 4) enhance NGS capability by continuously upgrading our technologies.