Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methods.

ABSTRACT: Gene expression profiling in precision oncology is increasing with uncertain validity across platforms. In this study, we examined the application of PurIST, a molecular subtyping algorithm for pancreatic ductal adenocarcinoma (PDAC), across different platforms. We compared PurIST calls between matched samples processed by whole transcriptome and commercial exome capture RNA-seq. In parallel, we compared subtypes between matched samples processed by NanoString and whole transcriptome RNA-seq from the PANCREAS trial (NCT04683315). Between whole transcriptome and exome capture, subtype agreement was 81% with significant increase in basal-like subtype with exome capture. Differences in overall survival in patients with basal-like tumors compared to classical tumors did not reach statistical s

SUBMITTER: Lee JJ 

PROVIDER: S-EPMC12819530 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature