IMAT-ITCR Collaboration: An integrated experimental and computational platform for analyzing the spatial organization of tumor clones

癌症基因组通过获得不同的DNA突变库、拷贝数 染色体畸变（CNA）和大的染色体重排，引起遗传多样性 无性系分离和量化遗传异质性和空间线索内 对于理解肿瘤进展的基础和对治疗的反应是至关重要的。 PI Chen的IMAT项目的目标是将Slide-seq开发成一个高分辨率的空间 癌症精准医疗的基因组学平台。该项目旨在开发强大的 使空间转录组学分析民主化的协议、管道和计算算法 用于临床标本，并在肿瘤类型中展示它们，直接在临床上工作， 设置. PI Raphael的ITCR项目的目标是开发一个全面的，用户友好的， 和模块化软件套件，用于跨空间的肿瘤异质性和克隆进化研究， 时间和基因组规模，使用来自批量和单细胞测序技术的数据。 在这里，我们寻求合并，我们将开发一个综合的实验和计算 该平台用于分析肿瘤样品中克隆的空间组织。这个平台将 联合收割机结合PI中正在开发的Slide-RNA-SeqV 2和Slide-DNA-seq技术 Chen的IMAT项目，采用定制的计算算法，扩展了开发的方法 在PI Raphael的ITCR项目中。

Cancer genomes evolve by acquiring a diverse repertoire of DNA mutations, copy number aberrations (CNAs), and large chromosomal rearrangements, giving rise to genetically diverse clonal lineages. Decoupling and quantifying genetic heterogeneity and spatial cues within a tumor is critical for understanding the basis for tumor progression and response to therapies. The goals of PI Chen’s IMAT project are to develop Slide-seq into a high-resolution spatial genomics platform for cancer precision medicine. This project seeks to develop robust protocols, pipelines and computational algorithms to democratize spatial transcriptomic profiling for clinical specimens and demonstrate them across tumor types, working directly in the clinical setting. The goals of PI Raphael’s ITCR project are to develop a comprehensive, user-friendly, and modular software suite for tumor heterogeneity and clonal evolution studies across space, time, and genomic scale using data from both bulk and single-cell sequencing technologies. Here, we seek to merge we will develop an integrated experimental and computational platform to analyze the spatial organization of clones in tumor samples. This platform will combine the Slide-RNA-SeqV2 and Slide-DNA-seq technologies under development in PI Chen’s IMAT project with customized computational algorithms that extend methods developed in PI Raphael’s ITCR project.