Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

ABSTRACT:

Background

Formalin-fixed paraffin embedded (FFPE) samples suffer from the degradation of nucleic acids, a problem that becomes particularly acute with samples stored for extended periods. It remains challenging to profile FFPE using high-throughput sequencing technologies including RNA-sequencing, and the resulting FFPE RNA-seq (fRNA-seq) data has a high rate of transcript dropout, a property shared with single cell RNA-seq. Transcript counts also have high variance and are prone to extreme values, together making downstream analyses extremely challenging.

Methods

We introduce the PaRaffin Embedded Formalin-FixEd Cleaning Tool (PREFFECT), a probabilistic framework for the analysis of fRNA-seq data. PREFFECT uses generative models to fit distributions to observed expression

SUBMITTER: Mucaki EJ 

PROVIDER: S-EPMC12486589 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature