Cancer Genomics

项目总结(见说明)： 基梅尔癌症中心(KCC)-癌症基因组共享资源(CGSR)的目标是为KCC成员提供基因组学和生物信息学方面的领导，以促进基础、翻译和临床研究的项目，从而帮助研究人员实现他们的总体目标。通过作为各种平台的集中资源、数据分析和存储的重要计算基础设施以及基于基因组学方法的经验丰富的专业人员，CGSR以具有成本效益的价格为研究人员提供广泛的服务和高质量的控制，用于DNA和RNA分析。服务包括：1)核酸分离和纯化，以及相关的分子生物学服务，包括聚合酶链式反应、克隆、亚克隆和定点突变；2)成本效益高、可靠、长阅读、自动化的Sanger测序和快速周转；3)基于微卫星的基因分型和片段分析；4)高质量的全基因组SNP基因分型、拷贝数变异、aCGH和DNA甲基化分析；5)在Affymetrix微阵列以及定制的疾病和/或途径靶向阵列上进行全基因组的信使核糖核酸和微核糖核酸表达谱分析；6)通过定量聚合酶链式反应分析独立验证候选基因座/基因；7)提供基于网络的途径分析软件，协助研究人员进行实验设计和结果分析；8)Sanger测序和Affymetrix阵列数据的存档。最近增加的基于应用生物系统公司Solid 4和5500x1以及Lon Torrent PGM的服务包括：1)全基因组测序以及人类和模式生物的定向重测序；2)染色质IP样本测序；3)用数字基因表达和RNA测序(包括长短非编码RNA)测量RNA表达；以及4)全基因组DNA甲基化测序。此外，最近还获得了CLIA认证，以促进临床研究导向的研究的分子图谱。上述服务范围，加上资源总监的专业知识，使CGSR能够为KCC调查人员提供全面支持，以促进基因发现、功能表征和其他基础研究工作，以阐明人类癌症的分子发病机制。63个KCC成员在过去一年中使用了此共享资源。KCC成员的使用量占共享资源总使用量的90%，KCC支持占拟议运营预算的91%，其余资金来自按存储容量使用计费和机构支持。

PROJECT SUMMARY (See instructions): The goal of the Kimmel Cancer Center (KCC) - Cancer Genomics Shared Resource (CGSR) is to provide genomics and bioinformatics leadership to KCC members to facilitate projects in basic, translational and clinical research thus assisting investigators to achieve their overall goals. By serving as a centralized resource with a variety of platforms, a significant computational infrastructure for data analysis and storage, and experienced professionals in genomics-based methods, the CGSR offers a wide spectrum of services and high quality control at cost-effective prices to investigators for DNA and RNA analysis. Services include: 1) nucleic acid isolation and purification, and related molecular biological services including PCR, cloning, sub-cloning and site-directed mutagenesis; 2) cost-effective, reliable, long-read, automated Sanger sequencing with fast turnaround; 3) microsatellite-based genotyping and fragment analysis; 4) high-quality genome-wide SNP genotyping, copy number variation, aCGH and DNA methylation profiling analysis; 5) genome-wide mRNA and microRNA expression profiling on Affymetrix microarrays as well as custom made disease- and/or pathway-targeted arrays; 6) independent validation of candidate loci/genes by quantitative PCR analysis; 7) assisting investigators with experimental design and analyzing results providing web-based pathway analysis software; and, 8) archiving of both Sanger sequencing and Affymetrix array data. Recently added services based on Applied Biosystems SOLID 4 and 5500x1 and lon Torrent PGM include: 1) whole genome sequencing as well as targeted resequencing of human and model organisms; 2) chromatin-IP sample sequencing; 3) measuring RNA expression with both digital gene expression and RNA-sequencing (whole transcriptome) including short and long non-coding RNA; and, 4) genome-wide DNA methylation sequencing. In addition, CLIA certification was received recently to facilitate molecular profiling for clinical research-oriented studies. The range of services mentioned above coupled with the expertise of the resource director, enables the CGSR to provide full support to KCC investigators to facilitate gene discovery, functional characterization and other basic research efforts to elucidate the molecular pathogenesis of human cancers. 63 KCC members have used this Shared Resource in the last year. KCC members' usage represents 90% of the total Shared Resource usage and KCC support represents 91% of the proposed operating budget with the remaining funding coming from charge-backs and institutional support.