Bioinformatics Core

生物信息学核心

基本信息

批准号：
10733235
负责人：
Qi Long
金额：
$ 11.19万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-05 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10733235
关键词：
Address Artificial Intelligence Bioinformatics Biological Markers Biometry Cancer Center Clinical Clinical Trials Collaborations Consensus Consultations Data Data Analyses Data Storage and Retrieval Development Ensure Epidemiology Evolution Faculty Genomics Home Human Human Resources Informatics Leukemic Cell Measurement Mentors Methodology Patients Pennsylvania Phenotype Pilot Projects Productivity Proteomics Reporting Research Research Design Research Personnel Role Students Techniques Time Transplantation Tumor Volume Universities Variant Work Xenograft procedure arm biomedical informatics clinically relevant data management design experience high standard in vivo medical schools multiple omics next generation sequence data next generation sequencing novel novel strategies patient derived xenograft model phase II trial potential biomarker preclinical study professor response transcriptome sequencing tumor tumor growth

项目摘要

Summary: The Bioinformatics Core is the primary data management and analysis arm of the UP-PDTC. Of note, the Bioinformatics Core will include biostatistics, bioinformatic and data management. The Bioinformatics Core enhances the productivity of the proposed project investigators, PDX Core and, eventually the PDXNet by providing them access to a statistical/bioinformatics/data management team who possess expertise in study design and conduct, and data analysis in patient derived xenotransplantation studies including the analysis of genomic, proteomic and RNA sequencing data. Timely and in-depth collaboration ensures that the proposed studies are designed, managed, analyzed, and reported to the highest standard and provide valid and robust answers to the scientific questions that the U54 project seeks to address. Importantly, Bioinformatics Core personnel will work with other experts in PDXNet to ensure a consensus of tumor and response measurement which can be widely used across the network. The Core is located within the Department of Biostatistics, Epidemiology and Informatics, and the Institute for Biomedical Informatics (IBI) at Penn Perelman School of Medicine. The DBEI and IBI are interdisciplinary homes for faculty, staff and students specialized in biostatistics, epidemiology, and clinical/bioinformatics research on campus. Furthermore, Dr. Long is a Professor of Biostatistics and Director of the Biostatistics and Informatics Core for the Abramson Cancer Center. Through his roles, Dr. Long has substantial experience addressing clinically relevant endpoints for pre-clinical studies which will be necessary for development of XP2 trials using biomarkers to guide development of expected human Phase 2 trials. Dr. E. Paul Wileyto is an experienced biostatistician with expertise in pre-clinical study design including tumor measurements and appropriate study design. Dr. Taehyong Kim is Interim Director of Bioinformatics Core at the Penn Institute for Biomedical Informatics with extensive experience in analysis of NGS data, RNA sequencing and other omic data. This team has already contributed to definitions of tumor volume and growth in PDX models as well as to planned XP2 studies in Projects 1 and 2. Importantly, a major role of the Bioinformatics Core will be studies of tumor changes during serial transplantation. These studies will involve multi-omics analysis for Project Two and the development of novel potential biomarkers using artificial intelligence. Project One will work closely with Bioinformatics personnel to apply recently developed techniques to study leukemia cell phenotypic evolution using deconvolution of RNA seq data using CIBERSORTx. This novel approach will help define leukemic cell evolution in vivo to a degree never previously done.

概括：生物信息学核心是 UP-PDTC 的主要数据管理和分析部门。值得注意的是，生物信息学核心将包括生物统计学、生物信息学和数据管理。生物信息学核心提高拟议项目研究人员、PDX Core 以及最终 PDXNet 的生产力为他们提供拥有研究专业知识的统计/生物信息学/数据管理团队的机会患者来源的异种移植研究中的设计和实施以及数据分析，包括分析基因组、蛋白质组和 RNA 测序数据。及时、深入的合作确保了拟议的研究按照最高标准进行设计、管理、分析和报告，并提供有效和稳健的结果 U54 项目寻求解决的科学问题的答案。重要的是，生物信息学核心人员将与 PDXNet 的其他专家合作，确保肿瘤和反应测量达成共识可以在网络上广泛使用。核心位于生物统计系内，宾夕法尼亚佩雷尔曼学院流行病学和信息学以及生物医学信息学研究所 (IBI) 药品。 DBEI 和 IBI 是生物统计学专业教职员工和学生的跨学科之家，校园流行病学和临床/生物信息学研究。此外，龙博士是生物统计学教授艾布拉姆森癌症中心生物统计和信息学核心主任。龙博士通过他的角色拥有解决临床前研究的临床相关终点的丰富经验，这是必要的使用生物标志物来开发 XP2 试验，以指导预期的人体 2 期试验的开发。 E·保罗博士 Wileyto 是一位经验丰富的生物统计学家，拥有临床前研究设计（包括肿瘤测量）方面的专业知识和适当的研究设计。 Taehyong Kim 博士是宾夕法尼亚大学生物信息学核心临时主任生物医学信息学专业，在 NGS 数据分析、RNA 测序和其他组学分析方面拥有丰富的经验数据。该团队已经为 PDX 模型中肿瘤体积和生长的定义以及计划在项目 1 和 2 中进行 XP2 研究。重要的是，生物信息学核心的主要作用将是研究连续移植期间肿瘤的变化。这些研究将涉及项目二和利用人工智能开发新型潜在生物标志物。项目一将与生物信息学人员应用最近开发的技术来研究白血病细胞表型进化使用 CIBERSORTx 对 RNA seq 数据进行反卷积。这种新方法将有助于定义白血病细胞体内进化到了前所未有的程度。