FFPE Tissue Sections

Introduction

FFPE is an acronym that stands for Formalin Fixed Paraffin Embedded. It refers to a method of preservation of cell tissues majorly used for profiling gene expression and help in the study of various diseases. Samples of FFPE can be stored at room temperature to avoid complexities. This proves to be cost effective and therefore convenient. These samples work well for immunohistochemical staining and analysis of morphology. Due to FFPE being widespread, there exist many archives of its specimen thus giving users a range of samples to select from.

Important Tips

FFPE tissue sections can be used as an ideal way of quickly identifying cellular location of RNA and proteins. These tissues in human beings may include adult & fetal tissues and diseased & tumor tissues. In animals they could comprise tissues of animals like mice, rats and monkeys. These tissues sections could be as small as five micro-millimeters in thickness and are best when placed on positively charged glass slides.

Process

Sample fixation, quantitation and DNA isolation are some of the pre-analytical processes. In each of these stages, minor differences like instrumentation, methodology and operator to operator sample handling could lead to unreliable results and questionable DNA quality. The widespread application of Formalin fixation is due to its ability to cross-link proteins. The only problem is that it induces methylol changes and acid-mediated hydrolysis which could mix up genotyping analysis. Extraction is however done through commercially available kits from a variety of manufacturers. Quantitation helps to make sure that DNA isolates meet basic concentration required for trial. Low sample yields and sample fragmentation can confound measurement systems.

Limitations of FFPE and Solution

Low availability of quantities of DNA archives, makes amplification of the samples necessary to solve this problem. It’s however challenging to amplify the FFPE tissues sections primarily because of damaged templates that result from the archiving process. Formalin is toxic, and fixation & embedding procedures are time consuming which makes FFPE tissue sections unsuitable for molecular analysis. FFPE protocols used are not standardized thus it’s not guaranteed that different samples were prepared in the same way. This may render the final results bias. These limitations have given access to break through of using frozen samples to replace FFPE. Freezing process is relatively fast compared to FFPE preparation, and samples made from freezing are well suited for molecular analysis. However freezing has a short coming too. Frozen samples deteriorate rapidly at room temperature thus the samples should be frozen immediately after collection.

Advantages of FFPE

A lot of time and cost required to pile up the number of required samples is alleviated, the way of sampling and the protocol of storage is well formed. In addition, the follow up activities that connect the samples to clinical outcomes have already been done. This has helped to archive FFPE samples which await analysis not only in the clinical field, but also in plant and insect biology. This bridges a big gap in mind that it’s difficult to preserve plant and insect sections in frozen state.

FFPE has contributed to break-through tests in clinical researches. It always leads to the best outcomes when used alongside frozen samples.