Genomics Core

基因组学核心

• 批准号: 8509598
• 负责人: Ronald Wayne Davis
• 金额: $ 22.31万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8509598
• 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 sequencing; 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.

基因组核心的主要责任是向 使用Roche/454基因组测序仪FLX钛平台的程序来确定序列 人白细胞抗原相关基因（HLA/MIC）的变异性，并审问 从疫苗研究中分离出的样品中，重新排列的免疫球蛋白（IG）和T细胞受体（TCR）基因座。 更具体地说，核心将设计并提供用于测序样本准备的解决方案，运行 454/Suequencer，提供全面的实验室信息管理系统（LIMS），以确保 样本跟踪和数据传播，并对数据进行主要分析。 该基因组学核心的具体目的是： 1）来自患者的I和II级外显子的放大和序列。样品制备和新颖的外显子 斯坦福基因组技术中心开发的放大协议将用于 放大选定的HLA/MIC目标序列以确定序列多态性。单个复合物放大 每个患者的外显子将被汇总在一起，并用条形码底漆序列设计到 与454/序列兼容。最多200个来自个人参与者的条形码样本 疫苗研究将在单个仪器运行中汇总和测序。 2）分析外显子序列以确定外显子的单倍型。每个人完成后 序列运行，基因组核心将将每个序列与HLA的可用参考序列进行比较 公共数据库中的基因使用我们的内部工具，该工具在高性能计算平台上运行， 构建共识序列，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放到中央数据库中并渲染 通过用户友好的网页，该页面将用于财团。该网站可以公开 指导委员会决定将此信息传播给研究界。 3）分析VDJ重组的序列。基因组核心的另一个责任将 为重排的免疫球蛋白（IG）和T细胞受体（TCR）提供高通量测序支持 基因座，分析这些序列的VDJ使用情况，并搜索VDJ的生物学意义模式 序列。将为HLA基因分型开发的类似网站和数据库用于 审查和共享序列和序列分析结果。