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FFPE: The Foundation of Clinical Genomics Research

Formaldehyde fixation has been the gold standard for tissue preservation for decades, and for a good reason. Formalin-Fixed Paraffin-Embedded (FFPE) tissues store at room temperature and have impressive long-term storage capabilities, allowing researchers to keep samples without concern for degradation for years. This blog will delve into the discovery, preparation and applications of FFPE and how it became a staple of research and therapeutic applications.

Preparing an FFPE sample

Adding to its allure, creating an FFPE sample is surprisingly simple and involves submerging the clinical sample into formaldehyde. Once this initial step is complete, the technician embeds the sample into paraffin wax and allows it to set before storing.

With the FFPE process, various tissue sample banks can be stored for extended periods and remain intact. This extensive collection allows researchers to continuously explore novel ideas that could shape our world as we know it today. Easy access to these preserved libraries also allows us more time to make technological advancements that produce valuable diagnostic data.

Uncovering their Applications

Although histologists and immunohistochemists traditionally utilise these samples, they are steadily earning their place in the field of genetics. Researchers have also begun to note the rich resource FFPE samples represent for clinical genomics studies.

With the ability to identify a pair of tissue samples from identical sources, oncologists can accurately analyse and compare an initial tumour with more distant metastatic tumours within one patient. This provides both patients and physicians alike with invaluable resources for genomics research. Whilst this technology is constantly progressing and improving, it is essential to note that certain conditions such as age, fixation techniques or inhibitors may affect DNA quality extracted from FFPE samples, ultimately impacting genomic analysis results.

In addition to providing a more precise overview of a patient's genomic map, FFPE samples have therapeutic applications. formalin-fixed and paraffin-embedded specimens are most commonly used to investigate the characteristic morphologies preserved tumour tissues exhibit. As articulated by BioChain, "Researchers often use FFPE tissue to look for specific proteins. The presence of these proteins can diagnose and assess whether a therapeutic antibody is useful for treatment. "FFPE tumour tissues should have a minimum tumour content of 60% unless indicated otherwise."

Next-Generation Sequencing

One of the most momentous transformations that FFPE has brought to us is in the realm of Next Generation Sequencing (NGS). To guarantee the most accurate results for Next-Generation Sequencing (NGS) tests, it is necessary to use the highest quality FFPE DNA extractions possible. Any pre-processing inconsistencies can cause mutation detection discrepancies, and both the method and sample quality need careful optimisation. ATOM-Seq possesses the unique capability to correct errors while minimising any additional errors during processing, improving the reliability of the results.

As modern technologies continue to emerge, FFPE samples remain an invaluable asset for clinical genomics research. The valuable data sources they provide offer us the opportunity to formulate new therapies that can even help improve patient care. As such, FFPE samples will continue to be indispensable in advancing our understanding and treatment of various diseases.

To learn more about how ATOM-Seq can work with FFPE samples, head to our website or check out the additional resources below.


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