Genomics Core

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 重排免疫球蛋白（IG）和T细胞受体（TcR）基因座。 更具体地说，核心将设计和提供测序样品制备的解决方案，运行 454/测序仪，提供全面的实验室信息管理系统（LIMS）， 样品跟踪和数据发布，并对数据进行初步分析。 该基因组学核心的具体目标是： 1)扩增和测序患者的HLA I类和II类外显子。样品制备和新外显子 斯坦福大学基因组技术中心开发的扩增方案将用于 扩增选择的HLA/MIC靶序列以确定序列多态性。单重放大 将来自每名患者的外显子合并在一起，并用条形码引物序列重新扩增， 与454/Sequencer兼容。多达200个条形码样本，来自 疫苗研究将在单一仪器运行中合并和测序。 2)分析外显子序列以确定外显子的单倍型。在每一个完成之后， 序列运行后，Genomics Core将每个序列与HLA的可用参考序列进行比较， 基因在公共数据库使用我们的内部工具，运行在高性能计算平台， 构建共有序列，并使用Assign 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， 通过将提供给联合体的方便用户的网页。这个网站可以公开 当指导委员会决定向研究界传播这一信息时。 3)分析VDJ重组的序列。基因组学核心的额外责任将 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 基因座，分析VDJ使用的那些序列，并寻找VDJ的生物学显著模式 序列的一个类似的网站和数据库，如这些开发的HLA基因分型将开发， 两者都审查和共享序列和序列分析结果。

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.