FFPE vs. Fresh Frozen Tissue: Which is Better For Your Research?

When it comes to preserving biological samples for research and diagnostics, two common methods stand out: FFPE (formalin-fixed, paraffin-embedded) and fresh frozen tissue. Both approaches have their own advantages and limitations, making them suited for different types of studies. FFPE tissue is well-known for its long-term stability, allowing researchers to store samples for decades. In contrast, fresh frozen tissue excels at preserving nucleic acids and proteins in their natural state. But when choosing between these methods, how do you know which is better for your research or clinical needs? In this blog, we’ll compare FFPE vs. fresh frozen tissue, exploring its uses, benefits, and limitations to help you make an informed decision.

What is FFPE Tissue?

FFPE or formalin-fixed paraffin-embedded tissue is preserved by a process that includes formalin fixation and paraffin wax embedment to maintain the biospecimen’s original quality. The process starts when a patient donates human biospecimen samples during a biopsy, and they can be sourced from donors with diseased, cancerous, or normal tissue. After collecting the tissue, it’s then fixed in a solution of 10% formalin, which cross-links protein structures and pauses biological and chemical processes. After being preserved in formalin for about 18–24 hours, the biospecimen is dehydrated using ethanol to prepare it for paraffin wax. The tissue sample is then embedded in paraffin wax, protecting the biospecimen from environmental degradation due to elements like light, temperature, or touch. Paraffin embedment also makes cutting the tissue samples into sections or slides easier for microscopic analysis.

FFPE tissue samples can be stored at room temperature for extended periods, making them a convenient and cheap option for research purposes.

What FFPE Tissue is Used For

When comparing FFPE vs. fresh frozen tissue, it may depend on what you’re using the biospecimens for. Formalin-fixed paraffin-embedded tissue can be more accessible to collect, faster to process, cheaper, and more stable than fresh frozen biospecimens.

FFPE samples are used for various purposes, including:

Oncology: One of the most popular areas of FFPE tissue application is oncology, which is the study of cancer. Biopsies can help researchers stage and characterize several types of cancer, helping them study biospecimens under microscopy and gain monumental insights into the pathology. Since FFPE tissues are more stable than fresh samples and preserve structural integrity for an extended period, they are ideal for this purpose. Often, researchers utilize FFPE tissue to search for particular proteins, which can be used for further diagnosis and determining whether a therapeutic antibody could be helpful for treatment.
Immunohistochemistry (IHC): As mentioned above, FFPE tissue samples are commonly used in a technique called immunohistochemistry (IHC), in which biospecimens are mounted on a microscopic slide, bathed in a solution to bind antibodies to proteins, and studied by researchers. The antibody solution helps detect and measure particular molecules, like proteins, in a sample. IHC is often used in oncology to identify tumors and can be used to help doctors check for signs of other illnesses, such as Alzheimer’s disease or autoimmune disorders.
Molecular and Genetic Studies: FFPE tissues are used for DNA, RNA, and protein extraction to study genetic mutations, gene expression profiles, and protein markers. This is essential for understanding genetic disorders and their variations and creating treatment plans. However, DNA can become degraded in FFPE tissue, sometimes leading to unreliable and inaccurate results.

Pathology and Histology: Researchers use FFPE tissues in pathology labs to prepare biospecimen sections for microscopic examination. The study of FFPE tissue samples in microscopy helps doctors diagnose a range of conditions, from inflammatory diseases to metabolic illnesses.

What is Fresh Frozen Tissue?

The main distinction between FFPE vs. fresh frozen tissue is how they’re preserved. Fresh frozen tissue is dipped in liquid nitrogen during “flash freezing.” The biospecimens are stored in an ultra-frigid freezer at less than -80℃. While FFPE tissue samples have been the preferred preservation method for clinical analysis, frozen biospecimens are becoming more popular due to the various advantages they offer researchers.

The downside of fresh frozen tissue vs. FFPE biospecimens is that they’ll quickly degrade at room temperature and not maintain their quality when stored in a more standard food or household freezing environment. Researchers must freeze tissue as soon as possible and keep it frigid to maintain quality. This can be difficult for biopsy tissue since surgeons don’t always have access to liquid nitrogen to flash-freeze the tumor material. Additionally, fresh frozen tissue samples may not maintain their quality if technicians leave the biospecimens on the counter or neglect to close the freezer door fully. Since frozen tissues require immense care and caution, biobanks generally store a smaller collection of these biospecimens than FFPE samples.

What Fresh Frozen Tissue is Used For

Fresh frozen tissue samples allow researchers to access and study genetic material in its purest form, helping them obtain more accurate results compared to those collected from FFPE biospecimens.

Researchers use fresh frozen tissue samples for the following purposes:

DNA and RNA Extraction: Frozen tissue is preferred for DNA and RNA extraction since it preserves nucleic acids in their natural, intact form. This makes frozen biospecimens suitable for sequencing studies, gene expression analysis, and other molecular biology strategies, such as RNA-Seq and microarray testing.
Cryosectioning: Fresh frozen tissue can be cut into thin slices or cryosectioned to prepare biospecimens for immediate microscopic analysis. This can be extremely necessary and beneficial in surgical settings, helping to guide doctors in their decisions during cancer surgeries and more.
Proteomics: Since frozen tissue preserves proteins in their natural conformation, they are commonly used for mass spectrometry-based proteomic analyses. There’s broad concern that in FFPE tissue samples, proteins can become denatured during the preservation process from formalin and ethyl alcohol exposure. This can lead to worries since it can result in proteins not binding to the same antibodies they would in their organic, living biological area. Fresh frozen tissues help identify and quantify proteins, study post-translational modifications, and understand protein interactions in health and illness.

Fresh Frozen Tissue vs. FFPE: Which is Best For You?

Both fresh frozen tissue and FFPE biospecimens have advantages and specific uses in research. Deciding which is the better option for you depends on your research and the resources you have to preserve tissue samples.

FFPE tissue samples are best for those who’d like the convenience and affordability of storing biospecimens at room temperature for extended periods. Once prepared, FFPE tissue can last for decades. FFPE tissue is ideal for those using it for oncology, IHC, pathology, and histology. The availability of FFPE biospecimens in biobanks makes it easy to secure several tissue types for various studies. However, it may not be suitable for analyzing native proteins and is generally not the best option for genetic analysis, such as PCR or next-generation DNA sequencing.

On the other hand, frozen tissue preserves DNA, RNA, and native proteins exceptionally well. However, frozen tissue samples must be stored in a frigid environment and maintained correctly. Frozen tissue archives can quickly degrade due to power outages, mechanical failures, or lack of quality control in laboratories. Frozen tissue samples aren’t as popular or common in pathology, and pathologists are often more comfortable using FFPE biospecimens for microscopic analysis and diagnoses.

Obtain High-Quality FFPE Tissue From Superior BioDiagnostics

You can choose from countless biobanks to obtain FFPE tissue samples. Superior BioDiagnostics is ideal if you’re looking for the highest quality FFPE tissue samples from almost every anatomical site. Our biobank collects normal, malignant, and disease-positive tissue samples for researchers, labs, and scientists and has been a trusted FFPE tissue sample provider for the better part of a decade.

Superior BioDiagnostics’ tissue samples are delivered with known diagnoses, tumor type identification (if applicable), TNM stages, and histological grades. Order your FFPE human tissue samples today to receive the biospecimens you need to further your research.