The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection

<p>This collection contains subjects from the National Cancer Institute’s <u><a href="https://proteomics.cancer.gov/programs/cptac">Clinical Proteomic Tumor Analysis Consortium</a></u> Clear Cell Renal Cell Carcinoma (CPTAC-CCRCC) cohort. CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. Radiology and pathology images from CPTAC patients are being collected and made publicly available by The Cancer Imaging Archive to enable researchers to investigate cancer phenotypes which may correlate to corresponding proteomic, genomic and clinical data.</p><p>Imaging from each cancer type will be contained in its own TCIA Collection, with the collection name "CPTAC-<em>cancertype</em>".  Radiology imaging is collected from standard of care imaging performed on patients immediately before the pathological diagnosis, and from follow-up scans where available.  For this reason the radiology image data sets are heterogeneous in terms of scanner modalities, manufacturers and acquisition protocols. Pathology imaging is collected as part of the CPTAC qualification workflow.  </p><p>All CPTAC cohorts are released as either a single combined cohort, or split into <em>Discovery</em> and <em>Confirmatory</em> where applicable.  There are two main types of proteomic studies: discovery proteomics and targeted proteomics. The term "discovery proteomics" is in reference to "untargeted" identification and quantification of a maximal number of proteins in a biological or clinical sample. The term “targeted proteomics” refers to quantitative measurements on a defined subset of total proteins in a biological or clinical sample, often following the completion of discovery proteomics studies to confirm interesting targets selected. Commonly used proteomic technologies and platforms are different types of mass spectrometry and protein microarrays depending on the needs, throughput and sample input requirement of an analysis, with further development on nanotechnologies and automation in the pipeline in order to improve the detection of low abundance proteins, increase throughput, and selectively reach a target protein <em>in vivo</em>.  Once the protein targets of interest are identified, high-throughput targeted assays are developed for confirmatory studies: tests to affirm that the initial tests were accurate. A summary of CPTAC imaging efforts can be found on the <u><a href="https://wiki.cancerimagingarchive.net/display/Public/CPTAC+Imaging+Proteomics">CPTAC Imaging Proteomics</a></u> page. </p><h3>CPTAC Imaging Special Interest Group</h3><p>You can join the <a href="https://groups.google.com/forum/#!forum/cptac-imaging-sig">CPTAC Imaging Special Interest Group </a>to be notified of webinars & data releases, collaborate on common data wrangling tasks and seek out partners to explore research hypotheses!  Artifacts from previous webinars such as slide decks and video recordings can be found on the <a href="https://wiki.cancerimagingarchive.net/display/Public/CPTAC+SIG+Webinars">CPTAC SIG Webinars</a> page. </p><p><iframe src="https://player.vimeo.com/video/390755227" frameborder="0" allowfullscreen="allowfullscreen"></iframe></p><p>On February 4, 2020 Dr. David Clarke presented the consortium's proteogenomic analyses of the CPTAC-CCRCC discovery cohort.  This deep dive into the CCRCC genomic and proteomic datasets will help researchers better understand how these can be correlated with features derived from the imaging data. (<strong><a href="https://wiki.cancerimagingarchive.net/download/attachments/52763925/200204_TCIA_ccRCC.pdf?version=1&modificationDate=1614357240790&api=v2">Download the slides</a></strong>)</p>

本集合收录了来自国家癌症研究所（National Cancer Institute）临床蛋白质组肿瘤分析联盟（Clinical Proteomic Tumor Analysis Consortium，简称CPTAC）清细胞肾细胞癌（Clear Cell Renal Cell Carcinoma，简称CCRCC）队列的研究对象。CPTAC是一项旨在通过大规模蛋白质组学和基因组分析（或称为蛋白质组学）的应用，加速对癌症分子基础的认知的国家级项目。来自CPTAC患者的放射学和病理学图像正在被收集并由癌症成像档案（The Cancer Imaging Archive）公开提供，以便研究人员研究可能与相应的蛋白质组学、基因组学和临床数据相关的癌症表型。每种癌症类型的影像资料都将包含在其独立的TCIA集合中，集合名称为“CPTAC-<em>肿瘤类型</em>”。放射学影像资料收集自患者病理诊断前的标准护理影像学检查，以及可用的随访扫描。因此，放射学影像数据集在扫描模式、制造商和采集协议方面存在异质性。病理学影像资料作为CPTAC资格流程的一部分进行收集。所有CPTAC队列均以单一综合队列或根据适用性分为<em>发现</em>和<em>验证</em>队列发布。蛋白质组学研究主要有两种类型：发现蛋白质组学和靶向蛋白质组学。‘发现蛋白质组学’一词指的是对生物或临床样本中最大数量的蛋白质进行非靶向识别和定量。‘靶向蛋白质组学’则指的是对生物或临床样本中定义的总蛋白质子集进行定量测量，通常在完成发现蛋白质组学研究后进行，以验证选定的感兴趣靶点。常用的蛋白质组学技术和平台根据分析的需求、通量和样本输入要求，包括不同类型的质谱和蛋白质微阵列。纳米技术和自动化的发展正在管道中进一步推进，旨在提高低丰度蛋白质的检测能力，增加通量，并选择性地在<em>体内</em>达到目标蛋白质。一旦确定了感兴趣的蛋白质靶点，将为验证研究开发高通量靶向检测：用于确认初步测试准确性的测试。CPTAC成像努力的总结可在CPTAC成像蛋白质组（CPTAC Imaging Proteomics）页面找到。CPTAC成像特别兴趣组（CPTAC Imaging Special Interest Group）允许成员接收网络研讨会和数据发布的通知，共同协作处理数据整理任务，并寻找合作伙伴以探索研究假设！以往网络研讨会（如幻灯片和视频记录）的资料可在CPTAC SIG网络研讨会（CPTAC SIG Webinars）页面找到。2020年2月4日，David Clarke博士在网络研讨会上展示了CPTAC-CCRCC发现队列的蛋白质组学分析。对CCRCC基因组学和蛋白质组学数据集的深入研究将有助于研究人员更好地理解这些数据如何与影像数据中提取的特征相关联。

搜集汇总

背景与挑战

背景概述

该数据集来自美国国家癌症研究所的临床蛋白质组肿瘤分析联盟（CPTAC），专注于透明细胞肾细胞癌（CCRCC），旨在通过蛋白质组学和基因组学分析加速癌症研究。它包含放射学和病理学图像，这些图像公开提供以帮助研究人员探索癌症表型与蛋白质组、基因组及临床数据的关联。图像数据来自诊断前后的标准护理和病理工作流程，因此在扫描模式、制造商和协议方面具有异质性。