Cancer Genomics Facility

癌症基因组学设施

基本信息

批准号：
9753958
负责人：
YURI E NIKIFOROV
金额：
$ 9.36万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
财政年份：
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/9753958
关键词：
10 year old Academic Medical Centers Address Algorithms Archives Basic Science Bioinformatics Biological Biological Assay Biological Sciences Biometry Blood Cancer Center Cancer Center Support Grant Cells Clinical Clinical Research Computer software Computers Consultations Custom DNA Data Databases Development Disease Doctor of Philosophy Ensure Faculty Formalin Freezing Funding Gene Dosage Genomic DNA Genomics Genotype Goals Individual Ions Leadership Liquid substance Malignant Neoplasms Manuals Measures Methods Modeling Molecular Biology Normal tissue morphology Nucleotides Paraffin Embedding Pathology Pathway interactions Patients Population Sciences Preparation Process Protocols documentation RNA Research Research Design Research Personnel Resource Sharing Saliva Sampling Scientist Secure Services Single Nucleotide Polymorphism Site Specimen Specimen Handling Statistical Data Interpretation Technology Testing Time TimeLine Tissues Translational Research Tumor Stem Cells Tumor Tissue Universities University of Pittsburgh Cancer Institute Untranslated RNA Urine Variant Work anticancer research base cancer biomarkers cancer genomics clinically relevant cost effective drug discovery epigenomics exome exome sequencing genome sequencing genome-wide high reward high risk improved instrumentation laser capture microdissection member new technology novel operation programs research study sample collection targeted sequencing tool transcriptome transcriptome sequencing transcriptomics tumor heterogeneity whole genome

项目摘要

Abstract: Cancer Genomics Facility (CGF) The Cancer Genomics Facility (formerly a component of the Cancer Biomarkers Facility) performs quantitative sample assessment, comprehensive genotyping, and transcriptome profiling of tumor tissues, cells and related biological fluids (blood, urine, saliva) of clinical relevance. Analysis incorporates optimized hybridization or primer driven assays for genomic capture and interrogation utilizing state of the art PCR, microarray (bead, plate, cartridge) and, since 2012, sequencing (whole genome, exome, custom targeted) technologies. The Specific Aims of the CGF are to 1) provide “state of the art” genomic and transcriptomic services, 2) assist with study design and provide consultation services, 3) provide integrated bioinformatics and statistical analysis support, 4) strategically develop and implement advanced technologies, and 5) provide genomics leadership, administrative, and operational excellence. The facility is located adjacent to the UPCI Tissue and Research Pathology Services shared resource to expedite processing of specimens from diverse preparations ranging from whole mounted tissues (fresh, flash frozen, formalin fixed) to individual tumor stem cells. Protocols routinely incorporate manual and laser capture microdissection to mitigate effects of tumor heterogeneity. Novel methods have been developed to capture and amplify limiting amounts of DNA and RNA (<1ng) from archival (>10 years old) formalin fixed, paraffin embedded specimens. The CGF has generated an extensive reference database of single nucleotide polymorphisms and genomic sequence (70 samples) from “normal” tissues for patient samples lacking matched germline specimens e.g. to serve as a gene copy number control. CGF collaborates closely with TARPS and CBS to ensure that UPCI investigators have benefit from optimized workflows. The facility routinely provides services to researchers from UPCI Programs, spanning basic, population science, and translational drug discovery and disease-site programs as well as each of the 3.5 SPOREs housed at UPCI. The CGF is also an integral component of the UPCI high- risk, high-reward initiative supporting development of early stage investigators and promoting new research pathways for established investigators. During the current project period investigators in nine UPCI Research Programs used the CGF.

摘要：癌症基因组学设施（CGF）癌症基因组学设施（以前是癌症生物标志物设施的组成部分）执行肿瘤组织的定量样本评估、综合基因分型和转录组分析，临床相关的细胞和相关生物液体（血液、尿液、唾液）分析纳入了优化。利用最先进的 PCR 进行基因组捕获和询问的杂交或引物驱动测定，微阵列（珠、板、盒），以及自 2012 年以来的测序（全基因组、外显子组、定制靶向） CGF 的具体目标是 1) 提供“最先进的”基因组和转录组学。服务，2）协助研究设计并提供咨询服务，3）提供综合生物信息学和统计分析支持，4）战略性地开发和实施先进技术，以及 5）提供该设施毗邻 UPCI，具有基因组学领导力、管理和运营优势。组织和研究病理学服务共享资源，以加快来自不同样本的处理制备范围从整个组织（新鲜、速冻、福尔马林固定）到单个肿瘤干协议通常结合手动和激光捕获显微切割来减轻肿瘤的影响。已经开发出新的方法来捕获和扩增有限数量的 DNA 和来自档案（>10 年）福尔马林固定、石蜡包埋标本的 RNA（<1ng） CGF 具有。生成了一个广泛的单核苷酸多态性和基因组序列参考数据库（70 来自“正常”组织的样本），用于缺乏匹配种系样本的患者样本，例如作为 CGF 与 TARPS 和 CBS 密切合作，以确保 UPCI 研究人员能够控制基因拷贝数。该设施定期为 UPCI 的研究人员提供服务。项目涵盖基础、人口科学、转化药物发现和疾病现场项目，例如以及 UPCI 中的每个 3.5 SPORE 也是 UPCI 高通量的组成部分。风险高回报的举措，支持早期研究人员的发展并促进新的研究在当前项目期间，九个 UPCI 研究中心的研究人员的途径。程序使用了 CGF。