biostudies-literatureMucaki EJNatural Sciences and Engineering Research Council of CanadaCanadian Institutes of Health Research (CA)Canada Foundation for InnovationCanadian Institutes of Health Research1023https://www.ebi.ac.uk/biostudies/studies/S-EPMC12486589biostudies-literatureUnknown23(1)<h4>Background</h4>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.<h4>Methods</h4>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 Journal of translational medicineGenerative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.PMC12486589RGPIN-2018-05039168243481Mucaki EJZhang WSaha ADumeaux VTrebinjac SRakovitch EHallett MTNofech-Mozes SfalseGenerative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.<h4>Background</h4>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.<h4>Methods</h4>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 2025-01-01T00:00:00Z2025 Sep2026-06-04T01:27:03.089Z2026-05-03T03:14:12.241ZS-EPMC124865894102982210.1186/s12967-025-07031-y