Proteogenomics of Cancer Training Program

摘要 这是我们的T32癌症蛋白基因组学培训计划（PCTP）的更新申请， 密歇根大学。国家癌症研究所在新技术方面进行了大量投资 癌症蛋白质组学平台，最近通过临床蛋白质组肿瘤分析联盟 （CPTAC）。蛋白质组是理解癌症的功能基因组学和系统生物学的关键 以及用于治疗和预防的生物标记候选物和分子靶标的发现和验证。 复杂的蛋白质组分析需要先进的信息学来处理复杂的 标本、蛋白质浓度的极端动态范围、翻译后修饰， 选择性剪接异构体，对各种干扰的反应，以及数据库和数据的差异 格式.此外，使用多组学产生的数据的整合蛋白质基因组学分析 技术（蛋白质组学、基因组学、转录组学、代谢组学等）已经成为一个强大 重建癌症靶向通路的方法。PCTP的主要目标是解决当前 缺乏科学家能够有效地生成和生物信息学分析自己的蛋白质组学数据， 利用CPTAC和其他公开可用的大规模蛋白质组学数据集， 多层次蛋白质组学数据整合。PCTP是一个真正的多学科培训计划， 非常独特，与M的U和全国。锚定在大学范围内的计算中心 医学和生物信息学，它提供了一个机会，来自不同背景的学生成为 精通PCTP的所有重点领域-癌症生物学、蛋白质组学、生物信息学和蛋白质基因组学。 PCTP要求每年7个名额，以支持博士前学员1-2年。我们拥有强大的 癌症研究人员，生物信息学家，数据科学家，统计学家和化学家的社区。我们的教师 和学生在人类蛋白质组组织的倡议，发展和全球的领导 部署数据存储库和数据分析系统，并创建新的蛋白质组算法 生物信息学和多组学数据整合。我们的学员来自国内较大的研究生课程， 密歇根大学（包括生物信息学，病理学，癌症生物学，化学和生物医学工程） 并通过课程、研讨会和 特别研讨会。PCTP强烈鼓励癌症研究人员对每位学员进行双重指导， 计算机科学家我们将进一步加强我们的培训计划， 为我们的T32学员举办蛋白质基因组学数据分析年度研讨会，利用我们学院的 参与CPTAC联盟的工作。总之，我们正在进行的NCI培训计划， 癌症蛋白基因组学培养了新一代的科学家，为独立的职业生涯做好了充分的准备， 跨学科的生物医学研究，提高教师的研究，并支持NCI的目标。

ABSTRACT This is a renewal application for our T32 Proteogenomics of Cancer Training Program (PCTP) at the University of Michigan. The National Cancer Institute has made substantial investments in new technology platforms for cancer proteomics, most recently through the Clinical Proteomic Tumor Analysis Consortium (CPTAC). The proteome is critical to understanding functional genomics and systems biology of cancers and to discovery and validation of biomarker candidates and molecular targets for therapy and prevention. Sophisticated analysis of proteomes requires advanced informatics to deal with the complexity of specimens, the extreme dynamic range of protein concentrations, post-translational modifications, alternative splice isoforms, responses to all sorts of perturbations, and differences in databases and data formats. Furthermore, integrative proteogenomics analysis of data generated using multiple omics technologies (proteomics, genomics, transcriptomics, metabolomics, etc.) has emerged as a powerful approach for reconstructing targetable pathways in cancer. The main goal of PCTP is to address the current scarcity of scientists able to effectively generate and bioinformaticly analyze their own proteomics data, to take advantage of CPTAC and other publicly available large-scale proteomics datasets, and to perform multi-level proteogenomics data integration. PCTP is a truly multi-disciplinary Training Program that is also very unique, with the U of M and nationally. Anchored in the university-wide Center for Computational Medicine and Bioinformatics, it provides an opportunity to students from diverse backgrounds to become well skilled in all PCTP focus areas - cancer biology, proteomics, bioinformatics, and proteogenomics. PCTP is requesting 7 slots/year to supports pre-doctoral trainees for 1-2 years. We have a robust community of cancer researchers, bioinformaticians, data scientists, statisticians, and chemists. Our faculty and students are in the leadership of Human Proteome Organization initiatives, development and global deployment of data repositories and data analysis systems, and creation of new algorithms for proteome bioinformatics and multi-omics data integration. Our trainees come from larger Graduate Programs within the U of M (including Bioinformatics, Pathology, Cancer Biology, Chemistry, and Biomedical Engineering) and receive training in cancer biology, bioinformatics, and proteomics through courses, seminars, and special workshops. PCTP strongly encourages dual mentorship of each trainee by a cancer researcher and a computational scientist. We will further strengthen our Training Program with an addition of a special Annual Workshop for our T32 trainees on Proteogenomics Data Analysis, taking advantage of our Faculty’s engagement in the efforts of the CPTAC consortium. In summary, our ongoing NCI training program in Proteogenomics of Cancer trains a new generation of scientists well prepared for an independent career in interdisciplinary biomedical research, enhances faculty research, and supports NCI goals.