Bioinformatics Core

摘要： 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、生物信息学和数据管理。生物信息学的核心 通过以下方式提高建议的项目调查员、PDX Core以及最终PDXNet的工作效率 为他们提供与拥有研究专业知识的统计/生物信息学/数据管理团队的联系 患者来源的异种移植研究的设计和实施，以及数据分析，包括分析 基因组、蛋白质组和RNA测序数据。及时和深入的协作确保拟议的 研究以最高标准进行设计、管理、分析和报告，并提供有效和可靠的 U54项目试图解决的科学问题的答案。重要的是，生物信息学核心 工作人员将与PDXNet的其他专家合作，以确保对肿瘤和反应测量的共识 它可以在整个网络中广泛使用。该中心位于生物统计系内， 流行病学和信息学，以及宾夕法尼亚大学佩雷尔曼学院生物医学信息学研究所(IBI) 医学。DBEI和IBI是生物统计学专业的教职员工和学生的跨学科之家， 流行病学和校园内的临床/生物信息学研究。此外，龙博士还是生物统计学教授 艾布拉姆森癌症中心生物统计和信息学核心主任。通过他的角色，龙博士 有为临床前研究处理临床相关终点的丰富经验，这是必要的 用于XP2试验的开发，使用生物标志物来指导预期的人类第二阶段试验的开发。E.保罗博士 Wileyto是一位经验丰富的生物统计学家，在包括肿瘤测量在内的临床前研究设计方面具有专业知识。 和适当的研究设计。金泰贤博士是宾夕法尼亚大学生物信息学核心的临时主任 对于生物医学信息学，在分析NGS数据、RNA测序和其他基因组方面具有丰富经验 数据。该团队已经对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 连续移植过程中肿瘤的变化。这些研究将涉及对项目二和 利用人工智能开发新的潜在生物标志物。项目一将与以下项目密切合作 生物信息学人员将应用最新开发的技术来研究白血病细胞表型进化 使用CIBERSORTx进行RNA序列数据的反褶积。这一新的方法将有助于确定白血病细胞 体内的进化达到了前所未有的程度。

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.