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Formalin Fixed Paraffin Embedded Tissue

Applications, Advantages and Advancements in Analysis

Formalin-Fixed Paraffin-Embedded (FFPE) biosamples are invaluable resources in biomedical research due to their ability to preserve cellular and molecular structures for long periods. These samples are obtained by fixing tissues with formalin, which prevents decomposition and maintains the tissue architecture, followed by embedding the tissue in paraffin wax. 

"Fixation stabilizes and preserves the tissue, preventing degradation and allowing for long-term storage."

FFPE biosamples offer several advantages for scientific research. Formalin fixation prevents cellular structure degradation and preserves tissue morphology, while paraffin embedding provides a stable environment for long-term storage. Samples can be stored at room temperature, which makes them easy to handle and transport, reducing the need for specialized storage facilities. Due to their stability, they can be archived for several years, allowing researchers to access valuable historical data and compare the progression of diseases over time. The formalin fixation and paraffin embedding process are inexpensive, making it an affordable option for large-scale sample collection and storage.

Another benefit of FFPE tissues is that they can be quickly processed and analyzed using various techniques, allowing researchers to examine the expression of specific proteins or genes within the tissue samples and providing insight into the molecular mechanisms underlying different diseases and conditions. Tissues are processed using the following downstream applications:


FFPE samples are widely used for histopathological examinations, which help diagnose diseases and study tissue morphology. Hematoxylin and eosin (H&E) staining is often used to visualize the cellular structure and arrangement.

Immunohistochemistry (IHC)

Used to detect specific proteins, antigens, or other molecules within tissue sections. This technique relies on antibodies that bind to specific targets, which are then visualized using various detection methods.

In Situ Hybridization (ISH)

Allows researchers to detect specific DNA or RNA sequences within a tissue section. This technique can be used to study gene expression patterns, detect viral or bacterial infections, and identify chromosomal abnormalities. 

Tissue microarrays (TMAs)

Enable a high-throughput approach that allows researchers to analyze multiple FFPE samples simultaneously. TMAs can be used to study various diseases and conditions, providing insights into disease pathology and identifying potential biomarkers.

Molecular profiling

Researchers can extract DNA, RNA, and proteins from FFPE samples for various molecular analyses, such as gene expression studies, genotyping, and identifying mutations in oncogenes and tumour suppressor genes.

Next-generation sequencing (NGS)

NGS technologies, including whole-exome, whole-genome, and targeted gene panel sequencing, can be applied to FFPE samples to identify genetic alterations and gain insights into disease pathogenesis, progression, and potential therapeutic targets.


FFPE tissue samples can be used to perform proteomic analysis, which involves identifying and quantifying proteins within a biosample. This can provide valuable information about cellular processes, signalling pathways, and potential disease biomarkers.

Recent advancements in FFPE tissue analysis have opened up new avenues for researchers to analyze and understand the molecular changes in diseases and conditions. These advancements below have improved the quality of data obtained from FFPE biosamples, increased the range of molecular analysis techniques available, and provided new insights into disease pathology.

Improved sample preparation techniques

Recent advancements in sample preparation techniques, such as more gentle fixation methods and improved antigen retrieval techniques, have improved the quality and reliability of data obtained from FFPE biosamples.

Single-cell analysis

One of the most significant recent advancements in FFPE tissue analysis is the ability to perform single-cell analysis. Single-cell analysis techniques, such as single-cell RNA sequencing, allow researchers to study individual cells within FFPE samples, providing insights into the heterogeneity of the disease and identifying rare cell populations.

Imaging mass spectrometry (IMS)

A technique that allows researchers to analyze the molecular composition of FFPE samples at a spatial resolution. This technique provides insights into the molecular changes that occur in specific regions of tissue samples and can be used to identify biomarkers and potential drug targets.

Digital pathology

Requires digitizing FFPE slides and analyzing them using computer algorithms. This technique allows for a more accurate and precise analysis of tissue samples and can improve disease diagnosis and patient outcomes.

Machine learning (ML) and artificial intelligence (AI)

ML and AI algorithms have provided new insights into disease pathology and improved the accuracy and speed of molecular analysis in FFPE samples. These techniques can be used to identify new biomarkers and potential drug targets, leading to the development of new treatments and therapies.

FFPE samples have been a cornerstone of tissue preservation in the fields of pathology, oncology, and molecular biology for decades. Recent advancements in FFPE tissue analysis have expanded the range of molecular analysis techniques available to researchers, providing new insights into disease pathology and potential treatment options. Single-cell analysis, NGS, IMS, digital pathology, TMAs, improved sample preparation techniques, and machine learning and AI algorithms have all contributed to the improved analysis of FFPE biosamples. As these techniques evolve and improve, FFPE biosamples will continue to be an essential tool for medical research.

Please click on the links below to inquire about the Compare Biomarket® range of clinical biospecimens and services suitable for your unique human health research needs.

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