PacBio And Covaris Launch New FFPE Genomics Workflow For HiFi Cancer Sequencing

PacBio, a company known for developing highly accurate long-read sequencing technologies, and Covaris, a PerkinElmer company specializing in sample preparation solutions, have announced the development of a joint workflow designed to enable robust HiFi sequencing of formalin-fixed, paraffin-embedded (FFPE) tissue samples. The workflow will be formally presented at the upcoming American Association for Cancer Research (AACR) Annual Meeting.

The new solution integrates Covaris’ truXTRAC® FFPE extraction technology with PacBio’s Kinnex™ library preparation method and sequencing on the Revio system. Together, these technologies create an end-to-end workflow that improves the usability of FFPE samples, which are widely available in clinical and research settings, particularly in oncology.

FFPE tissues are among the most commonly stored biological samples in cancer research because they preserve tissue architecture for long periods. However, the chemical fixation process typically damages and fragments DNA, making it difficult to use these samples for advanced long-read sequencing approaches. The combined workflow is designed to overcome these limitations by improving DNA recovery and enabling high-quality sequencing output from previously challenging archived samples.

A key component of the workflow is Covaris’ Adaptive Focused Acoustics (AFA)-based truXTRAC FFPE extraction method, which helps recover longer DNA fragments of up to approximately 5,000 base pairs from FFPE material. These fragments are then processed using PacBio’s Kinnex library preparation system, which concatenates DNA fragments into longer molecules suitable for HiFi sequencing. This approach improves both sequencing efficiency and data quality.

In performance studies conducted across brain, kidney, and uterine tumor samples, the workflow generated more than 100 million HiFi reads per sample, with average read lengths ranging from 750 to 1,500 base pairs. The resulting data enabled the identification of over 11,000 structural variants and more than 5 million small variants per sample. Approximately 60% of these variants were successfully phased into haplotypes, allowing researchers to better understand how genetic variations are organized on individual chromosomes.

For comparison, conventional short-read sequencing of FFPE samples typically identifies around 3,000 to 7,000 structural variants per sample. The lower yield is largely due to the inability of short reads to effectively span complex genomic rearrangements and repetitive regions. While short-read methods can detect a similar number of small variants, they generally struggle with direct haplotype phasing, often requiring statistical inference or additional specialized methods. In this context, the roughly 60% direct phasing achieved by the PacBio–Covaris workflow represents a significant improvement, offering potentially more accurate and biologically meaningful insights into tumor genomics.

Annemarie Watson, Chief Executive Officer of Covaris, said the collaboration reflects a shared commitment to advancing genomic research through integrated and innovative technologies. She emphasized that combining Covaris’ AFA-based extraction methods with PacBio’s sequencing platform allows researchers to access valuable genomic information from difficult FFPE samples, ultimately supporting new discoveries in cancer biology and other disease areas.

Dave Miller, Vice President of Global Marketing at PacBio, noted that the workflow opens access to large collections of archived clinical samples for HiFi sequencing on platforms such as Revio and Vega. He also highlighted that with improvements in cost efficiency, including SPRQ-Nx enabling lower per-genome sequencing costs, researchers can revisit these archived samples to study structural variation, phased mutations, and complex genomic regions that were previously difficult to analyze using short-read sequencing.

Overall, the collaboration demonstrates consistent performance across different tissue types and varying DNA quality. By enabling high-quality sequencing from FFPE samples, PacBio and Covaris are expanding the use of archived clinical material, supporting deeper genomic analysis and helping generate richer datasets that can contribute to oncology research and AI-driven biological discovery.