Sequencing and Genomics

测序和基因组学

• 批准号: 10089833
• 负责人: Corbin D Jones
• 金额: $ 29.11万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-06-01 至 2025-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10089833
• 关键词: Basic Science; Bioinformatics; Biological Assay; Biological Sciences; Budgets; Cancer Center Support Grant; Cancer Research Project; Cell physiology; Center for Translational Science Activities; Clinical; Clinical Pathways; Clinical Trials; Complement; Computer Analysis; Consultations; Contracts; DNA Resequencing; Data; Databases; Detection; Education; Environment; Equipment; Faculty; Future; Generations; Genome; Genomics; Genomics Shared Resource; Genotype; Glean; Heritability; Infrastructure; Intake; Investments; Knowledge; Laboratories; Malignant Neoplasms; Molecular; Molecular Epidemiology; Molecular Genetics; National Clinical Trials Network; North Carolina; Pathologist; Patient Care; Patients; Population Study; Precision Medicine Initiative; Preparation; Primary Neoplasm; Process; Production; Protocols documentation; Publications; RNA; RNA interference screen; Records; Repetitive Sequence; Reproducibility; Research; Research Personnel; Sampling; Services; Source; Specimen; Structure; System; Technical Expertise; Technology; Tennessee; Testing; The Cancer Genome Atlas; Universities; Validation; Variant; cancer genetics; cancer genomics; cancer predisposition; cancer type; computer infrastructure; data sharing; design; digital; epidemiology study; experience; genome sequencing; instrumentation; malignant breast neoplasm; member; nano-string; nanopore; next generation; peer; transcriptome; transcriptome sequencing; transcriptomics; translational cancer research; translational genomics; translational study; treatment arm; tumor; whole genome

ABSTRACT: SEQUENCING AND GENOMICS SHARED RESOURCE Sequencing and Genomics (SEQ) provides an integrated platform of technology, expertise, education, and infrastructure to create an accessible environment for LCCC researchers to undertake cutting-edge genomics projects. The Core specializes in six major technologies: Next Generation short-read sequencing (Illumina), long-read sequencing and genomic mapping (Oxford Nanopore Technologies, BioNano Inc.), NanoString digital RNA quantification, Affymetrix microarrays, Illumina bead array genotyping, and RNAi screening for functional validation. Through reciprocity with North Carolina State University, the SR also has access to the Pacific Biosciences Sequel system. These are complemented by LCCC investments in computational infrastructure and analysis. Over the past five years, LCCC has integrated two new units in partnership with TPF and CPDM to compliment SEQ, specifically to facilitate translational cancer genomics to seamlessly support the coordination, project management, and tracking necessary to perform genomics studies on patient samples from protocol-driven trials. In addition the Translational Genomics Laboratory (TGL) focuses solely on cancer sample preparation for downstream sequencing, NanoString analysis, or other molecular testing. This laboratory uses automated instrumentation and stable protocols optimized for limited input and degraded cancer specimens collected from clinical trials and translational studies. TGL initiates a pathway for clinical genomics projects through SEQ and subsequent analysis by the bioinformatics SR (BIOIN). SEQ SR requests $195,591, 3% of the total fiscal year 2019 budget. LCCC faculty were 43% of fiscal year 2020 users. During the past five years SEQ supported the LCCC investigators involved in TCGA. This project oversaw the molecular characterization of over 20,000 primary tumor and matched normal samples across 33 cancer types. Within the next year, SEQ will acquire an ONT PromethION 24 system, which uses a high- capacity, long-read sequencing technology capable of high production whole genome sequencing and transcriptomics. This technology allows for efficient resequencing of whole genomes including repetitive elements, structural variation, and other problematic regions of the genome. ONT sequencing provides reproducible detection of small, medium, and large size structural variations, and in the near future the detection of 5mC.

摘要：测序和基因组共享资源 测序和基因组学（SEQ）提供了技术，专业知识，教育和 基础设施为LCCC研究人员创造一个可访问的环境，以进行尖端的基因组学 项目。核心专门研究六种主要技术：下一代短阅读测序（Illumina）， 长阅读测序和基因组映射（牛津纳米孔技术，Bionano Inc.），纳米弦 数字RNA定量，Affymetrix微阵列，Illumina珠阵列基因分型和RNAi筛选 功能验证。通过与北卡罗来纳州立大学的互惠，SR也可以进入 太平洋生物科学续集系统。 LCCC对计算的投资补充了这些 基础架构和分析。在过去的五年中，LCCC与 tpf和cpdm以赞美SEQ，特别是为了促进转化的癌症基因组学无缝 支持对患者进行基因组学研究所必需的协调，项目管理和跟踪 来自协议驱动试验的样本。此外，转化基因组学实验室（TGL）仅关注 用于下游测序，纳米串分析或其他分子测试的癌症样品制备。这 实验室使用针对有限输入优化的自动仪器和稳定协议 从临床试验和翻译研究中收集的癌症标本。 TGL启动了临床的途径 基因组学通过SEQ和随后的生物信息学SR（Bioin）进行了分析。 SEQ SR要求$ 195,591，占2019财年预算总预算的3％。 LCCC教师是财政年度的43％ 2020用户。在过去的五年中，SEQ支持参与TCGA的LCCC调查人员。这个项目 监督超过20,000个原发性肿瘤的分子表征，并匹配33个正常样品 癌症类型。在明年，SEQ将获得一个ONT Promethion 24系统，该系统使用高 容量，长阅读的测序技术能够高产生整个基因组测序和 转录组学。该技术允许有效地重新纠正整个基因组，包括重复性 基因组的元素，结构变异和其他有问题的区域。 ONT测序提供 可重复检测小，中和大尺寸结构性变化，在不久的将来 检测5MC。