PacBio and Covaris Develop Workflow for Sequencing FFPE Tumor Samples

Integrating Covaris' acoustic-based extraction technology with PacBio's Kinnex library preparation opens up freezers full of banked clinical samples to long-read sequencing.

PacBio and Covaris have codeveloped a workflow to enable long-read sequencing from formalin-fixed, paraffin-embedded (FFPE) tumor tissue, the companies announced on April 15.

The workflow combines Covaris’ truXTRAC FFPE extraction technology with PacBio’s Kinnex library preparation and sequencing on the Revio instrument. It is designed to address longstanding limitations in applying long-read sequencing to FFPE material, where DNA damage and fragmentation caused by the fixation process have hindered compatibility.

FFPE tissue represents one of the largest and most clinically relevant archives of biological material in oncology research, but accessing high-quality sequencing data from these samples has remained technically difficult.

“We are enabling researchers to unlock valuable insights from even the most challenging FFPE samples, helping accelerate discoveries in cancer biology and beyond,” Annemarie Watson, CEO of Covaris, said in a statement.

Dave Miller, Vice President of Global Marketing at PacBio, added that the workflow “opens up vast archives of banked samples for HiFi sequencing. Clinical researchers can revisit these samples to uncover structural variation, phase mutations, and resolve complex genomic regions that have remained out of reach with short-read sequencing.”

The Covaris extraction method uses Adaptive Focused Acoustics (AFA) technology to recover DNA fragments up to 5,000 bp from FFPE tissue. PacBio’s Kinnex library preparation step then concatenates those fragments into longer molecules for HiFi sequencing.

In studies across brain, kidney, and uterine tumor samples, the workflow produced more than 100 million HiFi reads per sample, with mean read lengths of 750 bp to 1,500 bp. It detected more than 11,000 structural variants and more than 5 million small variants per sample, with approximately 60 percent of variants phased directly into haplotypes.

That structural variant yield compares favorably with short-read sequencing of FFPE tissue, which typically detects 3,000 to 7,000 structural variants per sample, the partners said. While short-read approaches produce comparable small variant counts, their read lengths generally limit direct haplotype phasing, often requiring statistical inference or specialized library methods.

The workflow showed consistent performance across diverse tissue types and varying DNA quality. The protocol will be presented at the upcoming American Association for Cancer Research Annual Meeting. Financial and other terms of the collaboration were not disclosed.

Covaris is a subsidiary of PerkinElmer.