Soares, P. | Search bioRxiv

bioRxiv2026

COSMOS: A FAIR-aligned infrastructure for clinical trial data validation, warehousing, and interactive discovery

1.SummaryThe Clinical Omics System for Metadata and Outcome Storage (COSMOS) is an open-source, FAIR- and GCP aligned clinical trial unit (CTU) infrastructure designed to streamline the transition of academic clinical and multi-omic trial datasets into curated, analysis-ready repositories within Secure Data Environments (SDEs). By integrating an automated Data Quality and Data Validation (DQ&DV) "Trust Layer" with a relational Structured Query Language (SQL) schema, COSMOS enables programmatic and interactive data access via R Shiny applications. Dynamic integration of omics and clinical data is achieved through analytical data structures (e.g. ExpressionSet objects) linked via relational database identifiers. This lowers technical barriers for researchers and promotes governed data reuse and secondary discovery. Availability and ImplementationCOSMOS is freely available under the GPL-3.0 license at https://github.com/at2e19/SCTU_COSMOS_DQDV_Shiny Supplementary information: Supplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

Uromonitor(R) as a novel sensitive and specific urine-based test for recurrence surveillance of patients with non-muscle invasive bladder cancer

Bladder cancer is the most frequent malignancy of the urinary system and is ranked the seventh most diagnosed cancer in men worldwide. About 70-75% of all newly diagnosed patients with bladder cancer will present disease confined to the mucosa or submucosa, the non-muscle invasive bladder cancer (NMIBC) subtype. Of those, approximately 70% will recur after transurethral resection (TUR). Due to this high rate of recurrence, patients are submitted to an intensive follow-up program that should be maintained throughout many years, or even throughout life, resulting in an expensive follow-up, with cystoscopy being the most cost-effective procedure for NMIBC screening. Currently, the gold standard procedure for detection and follow-up of NMIBC is based on the association of cystoscopy and urine cytology. As cystoscopy is a very invasive approach, over the years, many different non-invasive (both in serum and urine samples) assays have been developed in order to search genetic and protein alterations related to the development, progression and recurrence of bladder cancer. TERT promoter mutations and FGFR3 hotspot mutations are the most frequent somatic alterations in bladder cancer and constitute the most reliable biomarkers for bladder cancer. Based on these findings, an ultra-sensitive assay called Uromonitor(R) was developed that corresponds to a urine-based assay capable of detecting trace amounts of the two most common alterations in NMIBC, TERT promoter and FGFR3 mutation, in urine samples. The Uromonitor(R) test was performed in a cohort of 72 patients, firstly diagnosed with bladder cancer and under surveillance for NMIBC, to access its sensitivity and specificity in the detection of NMIBC recurrence. Uromonitor(R) was shown to be highly sensitive and specific in detecting recurrence of bladder cancer in patients under surveillance of non-muscle invasive bladder cancer.

cancer biology↗