Core 2: Data Analysis and Translational Application Core

核心2：数据分析和转化应用核心

基本信息

批准号：
10091981
负责人：
Aris Floratos
金额：
$ 34.27万
依托单位：
COLUMBIA UNIVERSITY HEALTH SCIENCES
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-16 至 2023-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10091981
关键词：
16S ribosomal RNA sequencing Academic Medical Centers Algorithms Alopecia Areata Antigens Binding Biochemistry Bioinformatics Biological Biological Markers Biomedical Research Biophysics Biopsy Blood Cancer Center Cells Classification Clinical Complement Computational Biology Computer Analysis Core Facility Custom Data Data Analyses Data Set Databases Development Discipline Doctor of Philosophy Drug Targeting Ensure Environment Experimental Designs Expression Profiling Faculty Gene Expression Gene Expression Profiling Generations Genomics Genotype High Performance Computing High-Throughput Nucleotide Sequencing Human Human Resources Immune Immunologics Immunology Infrastructure Literature Mediating Medical Methods Mission Modeling Molecular Profiling Network-based Pathogenicity Patients Pharmaceutical Preparations Process Proteomics Publishing Research Research Personnel Research Project Grants Research Support Resources Sampling Scientist Services Skin Standardization Systems Biology T cell receptor repertoire sequencing Tissues Training Translational Research United States National Institutes of Health Universities Variant annotation system arm biomarker development biomedical informatics cohort computer infrastructure computer science data framework data standards data submission design exome sequencing experimental study fecal microbiome genome wide association study high dimensionality informatics shared resource member microbiome molecular pathology multidisciplinary novel protein structure public repository single cell sequencing skin microbiome success targeted exome sequencing transcriptomics wiki

项目摘要

The Data Analysis and Translational and Translational Applications Core (DATA Core) of the AACORT was established to 1) provide a core center for standardized computational and bioinformatic analysis of human high-throughput sequencing data, and 2) provide an infrastructure for the standardized annotation, storage, and sharing of high-dimensional, patient matched data. As the AACORT pursues translational research on new-onset Alopecia Areata patients, the Resource Project Members will need a standardized manner of accessing and analyzing the data to ensure efficient use of the resources. The DATA Core will provide these services, tailoring data analysis to the needs of the Research Project. It will also serve as an interface with the TRAC Core, which will primarily be responsible for the clinical aspects of patient acquisition and sample processing. Biosamples acquired through the clinical arms of the TRAC Core will be processed for corresponding sequencing services, and the data and all clinical annotations will be passed to the DATA Core for processing, storage, and subsequent analysis. Additionally, the DATA Core will collaborate with the TRAC Core in the subsequent design of pilot experiments and research projects to ensure proper experimental design that provides proper power for the computational analyses. In terms of specific services, the DATA Core and its personnel are equipped both by training and in facilities, to handle a broad spectrum of data including: genotyping/exome sequencing, transcriptomics and regulatory modeling, and immunoproteomics/protein structure analysis. This will include somatic variant identification, targeted exome sequencing, biomarker development, master regulatory analysis and network-based drug predictions. It will further include immunotyping for antigen and TCR sequencing, computational antigen predictions, and leveraging of single-cell sequencing for pathogenic immune cells. We have assembled a highly trained, multidisciplinary team of scientists and Investigators at the Columbia University Medical Campus in Systems Biology, Biophysics, and Computer Science to complement the biological, clinical and immunological expertise of the other modules of the AACORT. We further have the support of Columbia Core Facilities, as well as the extensive computational infrastructure of the Center for Computational Biology and Bioinformatics and the Department of Systems Biology to facilitate the storage and analysis of our data.

数据分析以及转化和转化应用程序的核心（数据核）建立了AAcort至1）为标准化计算和人类高通量测序数据的生物信息学分析，2）提供基础架构用于高维患者匹配的数据的标准化注释，存储和共享。作为 AACORT追求有关新发育脱发Areata患者的转化研究，资源项目成员将需要一种标准化的方式来访问和分析数据以确保有效利用资源。数据核心将提供这些服务，并将数据分析定制为研究项目的需求。它也将作为与TRAC核心的接口，将主要负责患者获取和样本处理的临床方面。通过TRAC芯的临床臂获取的生物样本将用于处理相应的测序服务，数据和所有临床注释将传递给用于处理，存储和后续分析的数据核心。此外，数据核心将与TRAC核心合作，在试点实验和研究的随后设计中项目以确保适当的实验设计，为计算提供适当的功能分析。在特定服务方面，数据核心及其人员都配备了培训和设施，处理广泛的数据，包括：基因分型/外显子测序，转录组学和调节模型以及免疫蛋白质组学/蛋白质结构分析。这将包括躯体变体识别，靶向外显子组测序，生物标志物开发，主监管分析和基于网络的药物预测。它将进一步包括用于抗原和TCR测序，计算抗原预测和利用的免疫型致病性免疫细胞的单细胞测序。我们组装了一个训练有素的，哥伦比亚大学医学校园的科学家和研究人员的多学科团队系统生物学，生物物理学和计算机科学，以补充生物学，临床和 AACORT其他模块的免疫学专业知识。我们进一步得到了哥伦比亚核心设施以及该中心的广泛计算基础设施计算生物学和生物信息学以及系统生物学系促进我们数据的存储和分析。