Genomics Core

基因组学核心

• 批准号: 8306402
• 负责人: Ronald Wayne Davis
• 金额: $ 40.63万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-18 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8306402
• 关键词: Alleles; Base Sequence; Binding; Clonality; Collaborations; Communicable Diseases; Communities; Consensus Sequence; Data; Data Analyses; Databases; Deposition; Dideoxy Chain Termination DNA Sequencing; Discrimination; Emulsions; Ensure; Exons; Fire - disasters; Genes; Genetic Polymorphism; Genome; Genomics; Genotype; Goals; Grant; HLA Antigens; HLA-A gene; Haplotypes; Health; Housing; Human; Immune response; Immunoglobulins; Immunologic Receptors; Individual; Infection; Laboratories; Leukocytes; Management Information Systems; Organism; Participant; Patients; Pattern; Peptide Fragments; Peptides; Performance; Persons; Preparation; Protocols documentation; Reading; Research; Research Personnel; Running; Sampling; Sequence Analysis; Sequence Determination; Severity of illness; Solutions; Structure; System; T-Cell Receptor; T-Lymphocyte; Technology; Titania; Titanium; V(D)J Recombination; Vaccination; Vaccines; adaptive immunity; cohort; cost; design; human leukocyte antigen gene; human subject; improved; insight; instrument; next generation; novel; pathogen; programs; rapid technique; response; tool; user-friendly; web page; web site

The primary responsibility of the Genomic Core will be to provide high-throughput sequencing support to the program using the Roche/454 Genome Sequencer FLX Titanium platform to determine the sequence variability in Human Leukocyte Antigen related genes (HLA/MIC) and to interrogate the repertoire of rearranged immunoglobulin (Ig) and T cell receptor (TcR) loci in samples isolated from the vaccine studies. More specifically the core will design and provide solutions for sample preparation for sequencing, run the 454/sequencer, offer comprehensive Laboratory Information Management System (LIMS) that will ensure sample tracking and data dissemination, and perform the primary analysis ofthe data. The specific aims of this Genomics Core are: 1) Amplify and Sequence HLA Class I and II exons from patients. Sample preparation and novel exon amplification protocols that have been developed at the Stanford Genome Technology Center will be used to amplify selected HLA/MIC target sequences to determine sequence polymorphisms. Singleplex amplified exons from each patient will be pooled together and re-amplified with barcoded primer sequences design to be compatible with the 454/Sequencer. Up to 200 barcoded samples from individual participants in the vaccine studies will be pooled and sequenced in a single instrument run. 2) Analyze Exon sequences to determine the haplotype of exons. After the completion of each sequence run, the Genomics Core will compare each sequence to available reference sequences of HLA genes in the public database using our in-house tools that run on high-performance computational platforms, build the consensus sequence, and determine the haplotype for each HLA allele using the Assign SBT program. Both sequencing data and analysis results will be deposited into a central database and rendered through user-friendly web pages that will be available to the consortium. This web site can be made public when the steering committee decides to disseminate this information to the research community. 3) Analyze the sequences of VDJ recombination. An additional responsibility of the Genomics Core will be provide high-throughput sequencing support for rearranged immunoglobulin (Ig) and T cell receptor (TcR) loci, analyze those sequences for VDJ usage, and search for biologically significant patterns of VDJ sequences. A similar web site and database like these developed for HLA genotyping will be developed for both reviewing and sharing both sequence and sequence analysis results.

基因组核心的主要职责是为基因组测序提供高通量测序支持。 使用 Roche/454 Genome Sequencer FLX Titanium 平台的程序来确定序列 人类白细胞抗原相关基因 (HLA/MIC) 的变异性并询问 重新排列了从疫苗研究中分离出的样本中的免疫球蛋白 (Ig) 和 T 细胞受体 (TcR) 位点。 更具体地说，核心将设计并提供用于测序的样品制备解决方案，运行 454/测序仪，提供全面的实验室信息管理系统（LIMS），确保 样本跟踪和数据发布，并对数据进行初步分析。 该基因组学核心的具体目标是： 1) 对患者的 HLA I 类和 II 类外显子进行扩增和测序。样品制备和新型外显子 斯坦福基因组技术中心开发的扩增方案将用于 扩增选定的 HLA/MIC 靶序列以确定序列多态性。单重扩增 来自每位患者的外显子将被汇集在一起​​，并使用带有条形码的引物序列设计重新扩增，以 与 454/Sequencer 兼容。多达 200 个来自个人参与者的条形码样本 疫苗研究将在单一仪器运行中进行汇总和排序。 2) 分析外显子序列以确定外显子的单倍型。每完成一个项目后 序列运行时，Genomics Core 会将每个序列与 HLA 的可用参考序列进行比较 使用我们在高性能计算平台上运行的内部工具在公共数据库中获取基因， 构建共有序列，并使用分配 SBT 确定每个 HLA 等位基因的单倍型 程序。测序数据和分析结果都将存入中央数据库并呈现 通过联盟可用的用户友好网页。该网站可以公开 当指导委员会决定向研究界传播此信息时。 3) 分析VDJ重组序列。基因组学核心的额外职责将 为重排免疫球蛋白（Ig）和T细胞受体（TcR）提供高通量测序支持 位点，分析这些序列的 VDJ 使用情况，并搜索 VDJ 的生物学显着模式 序列。将为 HLA 基因分型开发类似的网站和数据库， 审查和共享序列和序列分析结果。