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：测序和基因组学共享资源 测序和基因组学（SEQ）提供了一个技术，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研究 项目核心专注于六大技术：下一代短读测序（Illumina）， 长读序测序和基因组作图（Oxford Nanopore Technologies，BioNano Inc.），NanoString 数字RNA定量、Affyssin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州立大学的互惠，SR还可以访问 太平洋生物科学续集系统。这些都是补充LCCC投资计算 基础设施和分析。在过去的五年里，LCCC已经整合了两个新的单位， TPF和CPDM与SEQ互补，特别是促进翻译癌症基因组学无缝地 支持对患者进行基因组学研究所需的协调、项目管理和跟踪 来自方案驱动试验的样本。此外，翻译基因组学实验室（TGL）只专注于 用于下游测序、NanoString分析或其他分子检测的癌症样本制备。这 实验室使用自动化仪器和针对有限输入和降级优化的稳定协议 从临床试验和转化研究中收集的癌症标本。TGL启动了一条临床 通过SEQ和随后的生物信息学SR（BIOIN）分析的基因组学项目。 SEQ SR要求195，591美元，占2019财年预算总额的3%。LCCC教师占财政年度的43% 2020用户。在过去的五年里，SEQ支持了参与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和33个国家的匹配正常样本 癌症类型。在明年，SEQ将收购ONT PromethION 24系统，该系统使用高- 大容量、长读段测序技术，能够进行高产量全基因组测序， 转录组学该技术允许对整个基因组进行有效的重新测序，包括重复的 元件、结构变异和基因组的其他问题区域。ONT测序提供了 可重复检测小，中，大尺寸的结构变化，并在不久的将来， 检测5 mC。