Advantages and Drawbacks of Paraffin and Frozen Tissues

Paraffin and Frozen tissues

Formalin-fixed paraffin embedded (FFPE) and frozen tissues are widely used histology methods for assessing tissue samples. Depending on the downstream applications of the study, one histology method may have better advantages to the other. This article will cover both advantages and drawbacks of both histology methods to help identify which route will best reveal the tissues properties on various situations.

Formalin-Fixed Paraffin Embedded (FFPE) Tissue
FFPE involves the process of dehydrating and the infiltration of paraffin into the tissue. This tissue is then encased in paraffin to create the tissue block and thin sections are sliced with a microtome. Paraffin sections are more physically stable than frozen sections and better at preserving tissue morphology with less injury. However, owing to the process of paraffin infiltration, paraffin sections are not optimal for all staining procedures.
Advantages of FFPE include better preservation of tissue architecture, capability for long-term storage, easily obtainable for research, compatible with immunohistochemistry (IHC), and cost-effectiveness. Drawbacks of FFPE include degradation of DNA and RNA, difficulty extracting high-quality and intact nucleic acids for next-generation sequencing (NGS) or gene expressing profiling, and the processing time for preparing FFPE tissue.

Frozen Tissue
Frozen tissue processing involves embedding tissue in a medium such as OCT. Frozen tissue sections are then cut using a cryostat. However, we need to remember that frozen tissues are divided into two categories, “Fresh Frozen” and “Fixed Frozen”. Although frozen sections are less physically stable than paraffin sections, they are preferable in terms of antigenicity and lipid retention. Freezing also destroys the viability of the cells, but necessarily the function of the proteins.

For fresh frozen samples, advantages include better preservation of the native biological state, higher quality biomolecules, flexibility in downstream applications, facilitate dynamic time-course studies, and wider availability and sampling options compared to fixed frozen tissue. Disadvantages of fresh frozen tissue include tissue degradation over time, requires rapid processing, inconsistent sample quality and variability, lack of long-term preservation, and ethical considerations with human tissue samples.

Advantages for fixed frozen include the ability for long-term preservation, resource efficiency, allows for longitudinal studies, diagnostic accuracy, and compatibility with various analytical techniques. Drawbacks for fixed frozen include artifacts and tissue alterations, variability in fixation protocols, loss of cellular viability, storage and logistical challenges, and ethical considerations with human tissue samples.

Plan Ahead
Ideally before you collect tissue, you should plan and determine the end goal of your study to determine which method best suits your needs. The table below illustrates few of the best uses and compatibility of each tissue type for various studies. If you are still unsure which is the best method for you contact or call 604-822-1595 to speak to an associate.

Formalin-Fixed Paraffin-Embedded Fixed Frozen Fresh Frozen
Histopathological analysis Disease diagnosis and classification Molecular profiling
Immunohistochemistry (IHC) Biobanking and archival storage Drug discovery and development
Tissue archives and retrospective studies Comparative studies and cohort analyses Translational research
Tumor bank and retrospective studies Quality control and assay optimization Biomarker discovery

  It is crucial to note that the above benefits and drawbacks may vary based on the individual study objectives, methodology, and resources available. These variables should be carefully considered by researchers when deciding on the best sample type for their investigations.