PacBio, Covaris Launch FFPE Workflow Yielding 100M HiFi Reads and 5,000bp Fragments
PacBio and Covaris’ workflow combines truXTRAC FFPE extraction with PacBio’s Kinnex prep on Revio, recovering fragments up to 5,000 bp. Across brain, kidney and uterine samples it produced over 100 million HiFi reads per sample, detecting 11,000 structural and 5 million small variants with 60% phasing.
1. Workflow Integration
PacBio and Covaris have integrated Covaris’ truXTRAC® FFPE extraction technology with PacBio’s Kinnex™ library prep and sequencing on the Revio system. This end-to-end workflow streamlines sample processing from extraction through HiFi long-read sequencing, targeting highly fragmented DNA from formalin-fixed, paraffin-embedded tumor tissues.
2. Sequencing Performance
In validation tests using brain, kidney and uterine tumor samples, the combined protocol recovered DNA fragments up to 5,000 base pairs and generated over 100 million HiFi reads per sample. Mean read lengths ranged from 750 to 1,500 base pairs, enabling comprehensive coverage of genomic regions previously inaccessible to short-read methods.
3. Variant Detection Gains
The workflow delivered detection of more than 11,000 structural variants and 5 million small variants per sample, with approximately 60% of variants directly phased. By comparison, short-read sequencing of FFPE samples typically uncovers only 3,000–7,000 structural variants and lacks direct phasing capability.
4. Research and Clinical Implications
By unlocking vast FFPE archives for high-quality long-read sequencing, this collaboration could accelerate discoveries in oncology and other fields. Lower cost per genome with SPRQ-Nx and robust performance across diverse sample types position this solution to expand use of PacBio’s Revio and Vega platforms in clinical research.