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Updated: Jan 16, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

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

Eliseos J Mucaki¹, Wenhan Zhang¹, Aryamaan Saha²

¹Department of Biochemistry, Western University, 1151 Richmond St., London, ON, N6A 3K7, Canada.

Journal of Translational Medicine

|October 1, 2025

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This summary is machine-generated.

PREFFECT is a new computational framework that improves RNA sequencing analysis for degraded formalin-fixed paraffin-embedded (FFPE) samples. It accurately imputes missing data and adjusts for batch effects, enhancing downstream analysis for clinical studies.

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Formalin-fixed paraffin-embedded (FFPE) samples exhibit nucleic acid degradation, complicating high-throughput sequencing.
FFPE RNA-sequencing (fRNA-seq) data presents challenges like transcript dropout and high variance, hindering downstream analysis.

Purpose of the Study:

To introduce PREFFECT, a probabilistic framework for analyzing fRNA-seq data.
To address the challenges of data quality and analysis in fRNA-seq datasets.

Main Methods:

PREFFECT employs generative models to fit expression count distributions, adjusting for technical and biological variables.
It leverages matched tissue profiles for stabilization and imputation, and utilizes sample-sample adjacency networks with graph attention mechanisms.

Keywords:

Formalin fixed paraffin embedded Generative modeling Graph attention networks RNA-sequencing

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Published on: June 8, 2020

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Last Updated: Jan 16, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

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Published on: August 21, 2016

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Main Results:

The negative binomial distribution was identified as the best fit for fRNA-seq transcript counts.
PREFFECT accurately imputes missing values, adjusts for batch effects, and enhances sample clustering when using adjacency networks and multiple tissues.

Conclusions:

PREFFECT offers improved and specific model fits compared to generic bulk RNA-seq tools, especially with matched profiles.
The framework's transformed data is compatible with existing tools, supporting clinical biomarker discovery and diagnostics.