Abstract 1081: Sylvester Data Portal: Streamlined access to standardized clinicogenomic data
Authors: Jeronimo I. Pissinis, Oliver Mazariegos, Marcin Pilarczyk, Michael S. Sinclair, Lukas Rupprecht, Caty Chung, Franklin Sotolongo, Gabriel Lichtenstein, Kathleen M. Jagodnik, Joanita Figueredo, Pearl Seo, Carlos J. Obregon, Marcin Blicharz, Piotr Smol, Michal Pyrkosz, Mateusz Jura, Vasileios Stathias, Stephan Schürer
Journal: Cancer Research (2025)

The Sylvester Data Portal (SDP), developed at the University of Miami (UM) Sylvester Comprehensive Cancer Center, is an advanced multi-omics platform that streamlines the management of real-world and research data. SDP facilitates the standardization and integration of data from major genomic profiling vendors, including Caris Life Sciences, Foundation Medicine, and NeoGenomics. SDP utilizes an event-driven ETL pipeline to process, validate, and standardize genomic reports (XML, PDF) and files (FASTQ, BAM, VCF, TSV) from Whole Exome Sequencing (WES), Targeted Sequencing (TS), and Whole Transcriptome Sequencing (WTS) tests. Metadata are harmonized into a unified format, enabling cross-vendor and cross-test-type queries. The platform also supports the preparation of data and metadata for submission to the AACR Project GENIE.A LIMS-like module within SDP is operationally integrated with data generation at the Onco-Genomics Shared Resource (OGSR). This module tracks sequencing workflows, performs automated quality control (QC), and manages the release of high-quality datasets to users, including their secure long-term storage. These functionalities enhance the reliability and accessibility of sequencing data for translational research. SDP also supports interactive data exploration and analysis.The platform enables containerized and reproducible bioinformatics workflows, supporting tasks like demultiplexing, as well as single-cell and bulk RNA-seq analyses. Future functionalities will include handling additional data types such as ATAC-seq and ChIP-seq, alongside integrated DNA analysis of germline and somatic variants.To ensure secure and tailored access to clinical data, SDP provides three user interfaces: (1) The Clinical Dashboard offers aggregated patient statistics, such as demographics and summaries of available data; (2) The Clinical Browser grants access to de-identified subject-level data upon institutional approval; and (3) Clinical Collections include PHI and NGS data, accessible after IRB and Data Broker approval. These interfaces facilitate data sharing within the Sylvester community, advancing translational research while adhering to data governance and regulatory policies. Citation Format: Jeronimo I. Pissinis, Oliver Mazariegos, Marcin Pilarczyk, Michael S. Sinclair, Lukas Rupprecht, Caty Chung, Franklin Sotolongo, Gabriel Lichtenstein, Kathleen M. Jagodnik, Joanita Figueredo, Pearl Seo, Carlos J. Obregon, Marcin Blicharz, Piotr Smol, Michal Pyrkosz, Mateusz Jura, Vasileios Stathias, Stephan Schürer. Sylvester Data Portal: Streamlined access to standardized clinicogenomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1081.