Quality Innovation Starts with Careful Tissue Preservation Processes

By Natasha Kuzmova, Head of Histology, Reference Medicine

When it comes to molecular research and clinical diagnostics, the quality of a tissue sample can make or break the success of DNA and RNA analysis. And while advances in sequencing technology and testing methods have brought precision medicine breakthroughs closer to reality, the integrity of the samples these innovations rely on is dependent upon steps taken well before they arrive at the lab bench.

Pre-analytic processes—including handling, processing, and preservation—are critical in ensuring tissue samples meet the rigorous demands of modern molecular applications. Yet several common missteps in these processes frequently compromise sample quality, leading to wasted time, money, and opportunities to glean actionable insights for patient care or research.

Why Pre-Analytic Quality Matters

Histology (the study of tissues and their structure) has long been central to laboratory-developed test (LDT) development and patient diagnoses. However, today’s research and clinical labs demand much more from tissue specimens. Beyond morphological analysis, samples are now used for immunohistochemistry, protein studies, and increasingly, DNA and RNA testing for molecular and genetic profiling.

This evolution means that the steps taken immediately after tissue extraction—collectively referred to as pre-analytic processes—are more important than ever. These pre-analytic processes must preserve not only the structural integrity of the tissue but also the quality of its nucleic acids. Without careful attention, degradation and contamination can render a sample unsuitable for downstream testing.

Let’s explore the three most common pre-analytic errors that undermine DNA and RNA preservation—and the steps researchers can take to avoid them.

1. Improper Handling: The Clock Is Ticking

Once tissue is removed from the body, the race against time begins. Without proper stabilization, cellular degradation starts immediately, affecting the quality of DNA and RNA. Improper handling—such as delays in fixation, exposure to suboptimal temperatures, or allowing tissues to dry out—can irreparably harm samples.

Handling errors often stem from the chaotic environment of surgical suites or pathology labs, where immediate preservation may not always be prioritized. Tissue may sit on a surgical table or cart for extended periods, or it might be transported under unsuitable conditions.

When tissues aren’t stabilized quickly, nucleic acids begin to degrade. Even brief exposure to room temperature can compromise molecular integrity. Drying out or excessive exposure to air further exacerbates the problem, leading to inconsistent results in downstream analyses.

The solution:

• Expedite fixation by placing tissue in an appropriate fixative (e.g., 10% neutral buffered formalin) as soon as possible.
• Train surgical and pathology staff to recognize the importance of prompt stabilization for molecular testing applications.

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2. Delayed Processing: Finding the “Goldilocks Zone”

Proper preservation doesn’t end with prompt fixation; what happens next is equally critical. Delayed processing—whether by leaving tissue in a fixative for too long or waiting too long to start processing—can also lead to significant quality issues.

Fixatives like formalin preserve tissue by crosslinking proteins and halting decomposition. However, over-fixation forms a crosslinked mesh that can hinder DNA and RNA extraction. Conversely, under-fixation fails to stabilize the tissue adequately. Without clear timelines, samples are often left sitting too long or not long enough.

DNA and RNA quality suffer when tissue is fixed for less than six hours or more than 48 hours. Extended fixation creates barriers to molecular testing, while under-fixation can lead to incomplete stabilization, leaving nucleic acids vulnerable to degradation.

The solution:

• Standardize fixation times based on tissue type and size. Small biopsies may require only six hours, while larger specimens may need up to 48 hours.
• Document and monitor cold ischemia time—the interval between tissue removal and fixation—to ensure it remains under one hour.

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3. Unsuitable Preservation Methods: One Size Does Not Fit All

While formalin is the most widely used fixative, it’s not always the right choice for every application. Inadequate quality checks for reagents, reliance on outdated practices, or use of inappropriate preservation methods for specific tissue types can lead to poor outcomes.

Preservation techniques optimized for morphological studies don’t always align with the needs of molecular testing. For example, hydrochloric acid-based decalcification methods destroy DNA, while frozen-section techniques degrade tissue when samples are later thawed and processed. Additionally, fixatives with incorrect pH levels or insufficient reagent freshness can negatively impact nucleic acid preservation.

These types of inconsistent preservation methods can lead to degraded or unusable DNA and RNA. Such failures can result in repeated experiments, wasted sequencing reagents, and delays in research or patient diagnosis.

The solution:

• Ensure fixative penetration by "bread-loafing" thicker tissue samples to expose more surface area. Specimen slices should not exceed 5mm in thickness.
• Regularly check reagent quality and replace alcohols or other chemicals that degrade over time or through exposure to humidity.

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A Call for Uniform Standards

Despite decades of progress in histological and molecular testing, a lack of uniform standards for pre-analytic tissue processing for DNA and RNA applications remains a significant challenge. While organizations like the College of American Pathologists (CAP) have issued guidelines, these remain recommendations rather than requirements, leading to variability in practices across institutions.

The absence of mandatory documentation also compounds the problem. Researchers often receive samples without critical information such as fixation duration or cold ischemia time, leaving them to piece together the sample’s pre-analytic history.

Adopting universal standards would reduce variability, improve sample quality, and save time and resources for researchers and clinicians alike.

Best Practices for Quality Control

At Reference Medicine, we understand that a well-preserved sample is the foundation for reliable molecular testing. That’s why our approach includes:

• Comprehensive quality checks: Reviewing pathology reports for pre-analytic details, measuring tissue dimensions, and assessing tumor cell percentages.
• DNA quality control (QC): Testing the DNA quality of samples to ensure they meet the stringent requirements of molecular assays.
• Feedback loops: Providing detailed reports to pathology departments to highlight preservation issues and recommend process improvements.

Such measures not only reduce waste but also help researchers achieve more consistent results, saving valuable time and resources and ensuring that innovations make it to the patients who need them.

Unlocking the Potential of Innovation

The path from biopsy to breakthrough starts with proper tissue preservation. By addressing common pre-analytic errors in handling, processing, and preservation, researchers can unlock the full potential of DNA and RNA testing.

As molecular diagnostics continue to evolve, so too must the practices supporting them. By adopting rigorous quality controls and advocating for standardized processes, we can ensure that every tissue sample serves as a reliable gateway to discovery.

Don’t settle for "the way we’ve always done it." The future of research and patient care depends on it.