Identification of actionable targets using DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded tissues followed by shallow whole-genome sequencing.

ABSTRACT: Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent precious resources for clinical genomic profiling studies, especially when coupled with comprehensive medical records. Even though next-generation sequencing (NGS) is an effective tool to detect somatic mutations and somatic copy number alterations (sCNA), the biggest challenges in unlocking clinically translatable genomic information from FFPE tissue are low DNA yields and degraded DNA, affected by variable formalin fixation. Another issue is that the proportion of carcinoma and other noncarcinoma cells is variable and can be confounded by intratumoral heterogeneity. To explore these challenges, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolati

SUBMITTER: Nteliopoulos G 

PROVIDER: S-EPMC12699240 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature