Introduces FFPE-Compatible Barcoding Innovation Enabling Whole Transcriptome Single-Cell Analysis
Parse Biosciences, a subsidiary of QIAGEN and a recognized leader in scalable single-cell sequencing technologies, has announced the commercial launch and immediate availability of its Evercode™ Whole Transcriptome FFPE kits. This new product represents a major technological advancement in the field of transcriptomics, enabling researchers for the first time to perform true whole transcriptome single-cell RNA sequencing (scRNA-seq) on formalin-fixed, paraffin-embedded (FFPE) samples.
With this launch, Parse Biosciences is addressing one of the most persistent technical barriers in molecular biology and translational research. FFPE samples, which are widely used in clinical and research settings due to their long-term stability and ease of storage, have historically been difficult to analyze at the single-cell level. RNA degradation and fragmentation inherent to the FFPE preservation process have limited researchers to targeted gene panels, restricting the ability to capture the full complexity of gene expression.
The introduction of Evercode Whole Transcriptome FFPE kits changes this paradigm by unlocking the potential of FFPE samples for comprehensive single-cell analysis. Researchers across multiple disciplines—including oncology, neuroscience, and translational medicine—can now access unbiased, genome-wide transcriptomic data at single-cell resolution, even from archived tissue samples that may have been stored for years or decades.
Overcoming Longstanding Challenges in FFPE Analysis
Formalin fixation and paraffin embedding have been a gold standard for tissue preservation in pathology laboratories worldwide. These samples represent one of the largest repositories of clinically annotated biological material, often linked with detailed patient histories, treatment outcomes, and longitudinal data. However, the same chemical processes that preserve tissue morphology also degrade RNA, making it difficult to extract high-quality genetic information.
Traditional single-cell RNA sequencing methods rely on intact RNA molecules to generate accurate transcriptome profiles. In FFPE samples, RNA fragmentation disrupts this process, forcing researchers to rely on predefined gene panels that target only a subset of genes. While useful, these panels inherently limit discovery by excluding unknown or unexpected transcripts, alternative splice variants, and regulatory RNA species.
Parse Biosciences’ new solution directly addresses these limitations through a combination of innovative chemistry and advanced barcoding technology. By enabling whole transcriptome analysis, the Evercode platform allows researchers to move beyond targeted approaches and explore the full breadth of gene expression within individual cells.
Innovative Technology Driving the Breakthrough
At the core of the Evercode Whole Transcriptome FFPE solution is a proprietary split-pool combinatorial barcoding approach. This method allows for the labeling of individual cells without the need for physical isolation, enabling massively scalable single-cell analysis. The approach is particularly advantageous for FFPE samples, where cell integrity may be compromised and traditional microfluidic techniques are less effective.
In addition, Parse has developed a specialized reverse transcription-based RNA capture chemistry optimized for degraded RNA. This chemistry is designed to efficiently capture fragmented RNA molecules and convert them into complementary DNA (cDNA) suitable for sequencing. By tailoring the chemistry specifically to the challenges of FFPE samples, the platform ensures high sensitivity and accuracy in transcript detection.
The result is a system that is not only capable of analyzing degraded RNA but also delivers unbiased, species-agnostic, and exponentially scalable transcriptomic data. Researchers can now perform comprehensive single-cell profiling across a wide range of sample types, including human clinical specimens and preclinical models.
Unlocking the Value of Archived Tissue Samples
One of the most significant implications of this technology is its ability to unlock the vast potential of archived FFPE tissue collections. Hospitals, research institutions, and biobanks around the world house millions of FFPE samples, many of which are associated with valuable clinical metadata. Until now, these samples have been largely inaccessible for high-resolution transcriptomic analysis.
With Evercode Whole Transcriptome FFPE kits, researchers can revisit these archives and extract new insights that were previously unattainable. For example, cancer researchers can analyze tumor heterogeneity at the single-cell level, identifying rare cell populations that may drive disease progression or treatment resistance. Neuroscientists can study cellular diversity in preserved brain tissues, gaining insights into neurodegenerative diseases and developmental processes.
In translational research, the ability to link molecular data with clinical outcomes opens new avenues for biomarker discovery and precision medicine. By analyzing patient samples collected over time, researchers can better understand disease trajectories and identify factors that influence therapeutic response.
Expanding Opportunities in Oncology and Beyond
The launch of Evercode Whole Transcriptome FFPE kits is particularly impactful for oncology research, where FFPE samples are extensively used. Tumor biopsies are routinely preserved using FFPE methods, creating a rich repository of samples that reflect diverse cancer types, stages, and treatment histories.
With single-cell resolution, researchers can now dissect the tumor microenvironment in unprecedented detail, examining interactions between cancer cells, immune cells, and stromal components. This level of insight is critical for developing next-generation immunotherapies and targeted treatments.
Beyond oncology, the technology has broad applications across multiple fields. In neuroscience, FFPE samples can be used to study cellular organization and gene expression patterns in the brain. In infectious disease research, archived tissues can provide insights into host-pathogen interactions. In drug development, the ability to analyze historical samples can inform target validation and mechanism-of-action studies.
Leadership Perspective on the Innovation
Charlie Roco, Ph.D., Co-founder and Chief Technology Officer of Parse Biosciences, emphasized the significance of this advancement in expanding the boundaries of single-cell analysis. He noted that FFPE samples represent the largest reservoir of clinically annotated tissue in the world, yet have remained largely inaccessible for comprehensive transcriptomic studies.
According to Roco, the launch of Evercode Whole Transcriptome FFPE kits eliminates the trade-off that researchers have traditionally faced between preserving valuable samples and obtaining complete biological insights. With this new solution, scientists can achieve both—leveraging precious, often irreplaceable specimens while capturing the full complexity of gene expression.
Integration with QIAGEN’s Broader Portfolio
As part of QIAGEN, Parse Biosciences benefits from the global reach and infrastructure of a leading provider of molecular diagnostics and life sciences tools. The integration of Evercode technology into QIAGEN’s portfolio further strengthens the company’s position in the rapidly growing field of multiomics and single-cell analysis.
QIAGEN’s established customer base and distribution network are expected to facilitate widespread adoption of the new kits, enabling researchers around the world to access this cutting-edge technology. The collaboration also underscores the strategic importance of single-cell sequencing in advancing precision medicine and biomedical research.
Availability and Industry Engagement
The Evercode Whole Transcriptome FFPE kits are now commercially available and shipping to customers, marking the beginning of a new era in FFPE analysis. Researchers interested in learning more about the technology and its applications can engage directly with the Parse Biosciences team at upcoming scientific events.
Notably, the company will showcase its latest innovations and datasets at the AACR Annual Meeting, one of the premier gatherings in cancer research. Attendees visiting the Parse booth will have the opportunity to explore real-world applications of the technology and gain insights into how it can be integrated into their research workflows.
A Transformative Step Forward
The launch of Evercode Whole Transcriptome FFPE kits represents a transformative step forward in the field of single-cell genomics. By overcoming the longstanding challenges associated with FFPE samples, Parse Biosciences has opened new possibilities for discovery and innovation across a wide range of scientific disciplines.
This breakthrough not only enhances the utility of existing sample repositories but also accelerates the pace of research by enabling more comprehensive and unbiased analyses. As scientists continue to explore the complexities of biology at the single-cell level, technologies like Evercode will play a critical role in shaping the future of biomedical research.
In conclusion, Parse Biosciences’ latest innovation stands as a powerful example of how advances in technology can unlock previously inaccessible data and drive meaningful progress in science and medicine. With the ability to perform whole transcriptome single-cell RNA sequencing on FFPE samples, researchers are now better equipped than ever to uncover the molecular underpinnings of disease and develop more effective therapies for patients worldwide.
About Parse Biosciences
Parse Biosciences, a QIAGEN company, is a global life sciences company whose mission is to accelerate progress in human health and scientific research. Empowering researchers to perform single cell sequencing with unprecedented scale and ease, its pioneering approach has enabled groundbreaking discoveries in cancer treatment, tissue repair, stem cell therapy, kidney and liver disease, brain development, and the immune system.
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