PO.BCS01.16 · 生物信息与计算
Sylvester数据门户：对一个多样化临床基因组学队列的群体水平特征描述
Sylvester Data Portal: Population-level characterization of a diverse clinicogenomic cohort
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
Sylvester数据门户(SDP)由迈阿密大学(UM)Sylvester综合癌症中心开发，是一个先进的基于云的多组学平台，可简化真实世界数据和研究数据的管理。SDP提供了一个集成框架，用于管理和协调该中心由主要基因组图谱分析供应商生成的临床基因组学数据，包括Caris Life Sciences、Foundation Medicine、NeoGenomics和Guardant Health。SDP现在支持群体规模的分析，能够跨Sylvester的服务群体进行比较研究。为便于对临床和基因组数据进行安全的、基于角色的访问，SDP提供了三个结构化界面：(1)临床仪表板，汇总聚合的患者人口统计学信息和数据可用性；(2)临床浏览器，支持对去标识化的受试者水平数据进行查询和可视化；(3)临床集合，在IRB和数据经纪人批准下整合受保护健康信息与新一代测序数据。这一集成基础设施实现了对大型、多样化且不断增长的临床基因组学数据集的标准化和可重复访问，支持转化研究并促进精准肿瘤学中的公平代表性。使用这一框架，我们系统评估了Sylvester临床基因组学队列的人口统计学和分子特征，并将其与癌症基因组图谱(TCGA)进行比较。Sylvester队列包括超过30,000个样本，几乎是TCGA所报道样本数(11,387)的三倍，且主要来源于靶向panel测序而非全外显子组测序。值得注意的是，该队列中接近一半的病例(45.9%)来自自我认定为西班牙裔的患者，而TCGA中为3.52%，反映了该癌症中心独特的群体，并有助于改善癌症基因组学中一个代表性不足群体的基因组代表性。还比较了突变患病率，特别是TP53在TCGA队列中更常发生突变(36.99% vs. 26.72%)，而KRAS突变在SDP队列中更为普遍(7.5% vs. 9.81%)。
查看英文原文 English abstract
The Sylvester Data Portal (SDP), developed at the University of Miami (UM) Sylvester Comprehensive Cancer Center, is an advanced cloud-based multi-omics platform that streamlines the management of real-world and research data. SDP provides an integrated framework for managing and harmonizing the center's clinicogenomic data generated by major genomic profiling vendors, including Caris Life Sciences, Foundation Medicine, NeoGenomics and Guardant Health. SDP now supports population-scale analyses that enable comparative studies across Sylvester's catchment population. To facilitate secure and role-based access to clinical and genomic data, SDP provides three structured interfaces: (1) The Clinical Dashboard, which summarizes aggregated patient demographics and data availability; (2) the Clinical Browser, which supports query and visualization of de-identified subject-level data; and (3) Clinical Collections, which integrate protected health information with next-generation sequencing data under IRB and Data broker approvals. This integrated infrastructure enables standardized and reproducible access to a large, diverse and growing clinicogenomic dataset, supporting translational research and promoting equitable representation in precision oncology. Using this framework, the demographic and molecular profiles of the Sylvester clinicogenomic cohort were systematically evaluated and compared with those of the Cancer Genome Atlas (TCGA). The Sylvester cohort includes over 30,000 samples, almost three times the number of samples reported in TCGA (11,387), and is derived primarily from targeted panel sequencing rather than whole exome sequencing. Notably, close to half of the cases, 45.9%, within this cohort are from patients that self-identify as Hispanic, vs. 3.52% in TCGA, reflecting the distinctive population from the cancer center and contributing to improved genomic representation of an underrepresented group in cancer genomics. Mutational prevalence was also compared, in particular TP53 is more often mutated in the TCGA cohort, 36.99% vs. 26.72%, whereas KRAS mutations are more prevalent in the SDP cohort 7.5% vs. 9.81%.
利益披露 Disclosure
O. Mazariegos, None..
P. Seo, None..
F. Sotolongo, None.