Sequencing and Genomics

摘要：测序与基因组学资源共享 测序和基因组学(SEQ)提供了一个集技术、专业知识、教育和 基础设施为LCCC研究人员从事尖端基因组学创造便利的环境 项目。核心专注于六项主要技术：下一代短读测序(Illumina)， 长读测序和基因组图谱(牛津纳米孔技术公司，BioNano Inc.)，纳米串 数字RNA定量、Affymetrix微阵列、Illumina微珠阵列基因分型和RNAi筛查 功能验证。通过与北卡罗来纳州立大学的互惠，SR还可以访问 太平洋生物科学续集系统。这些都得到了LCCC在计算领域的投资的补充 基础设施和分析。在过去的五年中，LCCC与以下公司合作整合了两个新部门 TPF和CPDM将补充SEQ，特别是促进翻译癌症基因组学无缝 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，翻译基因组实验室(TGL)仅专注于 用于下游测序、纳米串分析或其他分子测试的癌症样品准备。这 实验室使用自动化仪器和稳定的协议，针对有限的输入和降级进行优化 从临床试验和翻译研究中收集的癌症标本。TGL为临床开辟了一条道路 基因组学项目通过SEQ和生物信息学SR(BIOIN)随后的分析进行。 SEQ SR申请195,591美元，占2019财年总预算的3%。LCCC教职员工占本财年的43% 2020个用户。在过去的五年中，SEQ支持了参与TCGA的LCCC调查人员。这个项目 监督了20,000多个原发肿瘤的分子特征，并与33个正常样本进行了匹配 癌症类型。在接下来的一年内，SEQ将收购ONT Prometation 24系统，该系统使用高性能的 容量大、读数长的测序技术，能够高产的全基因组测序和 转录学。这项技术允许对整个基因组进行有效的重新测序，包括重复的 基因组的元素、结构变异和其他有问题的区域。ONT测序提供了 可重复检测到小、中、大尺寸的结构变化，并在不久的将来 检测到5mC。

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.