Tumor Genomic and Transcriptomic Analysis Integrated With Liquid Biopsy ctDNA Monitoring: Analytical Validation and Clinical Insights.

ABSTRACT:

Background

Comprehensive genomic profiling (CGP) is a time- and tissue- efficient method to help guide precision oncology. To enhance the clinical utility of CGP, we investigated the performance of a novel strategy integrating tumor DNA and mRNA profiling, together with liquid biopsy ctDNA monitoring.

Methods

Genomic DNA and mRNA simultaneously extracted from 604 archived tissue samples of 12 cancer types were used. Tumor DNA was subjected to targeted sequencing using a 504-gene panel with high-density probes (HDP), and shallow whole genome sequencing to profile genomic biomarkers. mRNA transcriptome profiling was performed to further capture fusion variants, and to predict tissue of origin (TOO) using our ensemble model OriCUP, an algorithm trained on 9889 samples and indep

SUBMITTER: Tran NHB 

PROVIDER: S-EPMC12685469 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature