How Covaris and PacBio Make FFPE Long-Read Sequencing Possible
Watch On-Demand: Unlocking FFPE Tumor Samples: A Novel Covaris and PacBio Workflow for HiFi Long-Read Sequencing
FFPE tumor samples are one of the richest available resources in cancer genomics and are often linked to pathology data, treatment history, and clinical outcomes, but formalin fixation damages DNA in ways that have historically kept these samples out of reach for long-read sequencing. This presentation introduces a new workflow that changes that, combining Covaris truXTRAC® extraction with PacBio’s HiFi long-read sequencing and Kinnex library prep to make FFPE long-read sequencing possible for the first time.
The talk, led by PacBio’s Deborah Moine, walks through how Covaris addresses DNA quality and fragment length recovery from FFPE tissue, while PacBio’s amplification and Kinnex concatenation steps generate the long molecules HiFi sequencing requires. Using kidney, uterine, and brain tumor FFPE samples starting from just ~50 nanograms of input DNA, the workflow delivered over 100 million reads per sample, identified roughly 11,000 structural variants and 5 million+ SNPs per sample, and successfully phased HLA loci — demonstrating that comprehensive variant detection and phasing are achievable directly from FFPE-derived DNA.