Scientific posters

Rapid whole genome sequencing (rWSG) can help accelerate genomic insights in time-critical settings. Here, we developed and assessed an accelerated HiFi WGS workflow on the Revio system with SPRQ-Nx chemistry, designed to reduce turnaround time while preserving accuracy for comprehensive variant detection across diverse specimen types.

Read-to-consensus divergence rates obtained from HiFi sequencing data provide a scalable foundation for measuring repeat instability. Repeat-specific models of baseline repeat instability allow identification of abnormally unstable alleles, enabling genome-wide studies of repeat instability and prioritization of potentially pathogenic repeats.

We present isocall, an efficient multi-sample isoform detection tool, together with workflows to enable population-scale full-length RNA analysis.

PureTarget enrichment combined with PacBio HiFi sequencing enables comprehensive characterization of clinically relevant genomic regions within a single workflow.

This comparison illustrates the flexibility of PacBio’s HiFi sequencing ecosystem and quantifies trade-offs among quality results, input requirements, cost, and workflow simplicity. This study provides researchers with a practical framework for selecting the optimal PacBio workflow to suit their needs.

HiFi long-read sequencing provides highly accurate reads of fragments from 500 bp to 25,000 bp in length. These long reads offer an agnostic measure of sequence length and enable structural variant detection, phasing, and direct methylation analysis. However, FFPE tissue has been difficult for HiFi sequencing because extraction often yields short, damaged fragments and fixation crosslinks DNA which disrupts long-read sequencing. This poster demonstrates a workflow that can be used to extract longer DNA fragments from FFPE-preserved tissue to realized the benefits of HiFi sequencing for FFPE DNA.

Microsatellite instability (MSI) is a key biomarker of mismatch repair deficiency and response to immunotherapy, yet most existing genomic detection methods are optimized for short-read sequencing and rely on small panels of homopolymer markers, limiting the ability to characterize genome-wide and motif-specific patterns of instability. Here we present Owl, a bioinformatic tool for quantifying MSI from PacBio HiFi whole- genome data.

PureTarget enables PCR-free investigation of SNVs, repeat expansions, paralogous genes, and structurally complex disease loci. PureTarget overcomes limitations of PCR- and short-read-based assays, enabling comprehensive CFTR interrogation with high accuracy, phasing, and epigenetic context.

Non-invasive sample types such as saliva, buccal, and dried blood spots (DBS) are essential for scaling genomic research. However, conventional extraction workflows often yield fragmented, low- input DNA — limiting their suitability for HiFi long- read sequencing, which requires high-quality, high- molecular-weight DNA. Optimized workflows enable high-quality HMW DNA recovery from saliva and buccal samples, supporting robust HiFi long-read WGS and PureTarget targeted sequencing.

The Dennis Lab at UC Davis has developed the CiFi method (McGinty et al., 2025) on human and insect samples. They adapted the CiFi protocol using the Arima CiFi kit to plant species of different size and complexity. The resulting matrices are comparable to the ones generated with Hi-C data. CiFi libraries can be sequenced with the HiFi library in the same SMRT cell.

Evaluated three PacBio workflows: standard HiFi library preparation, the Ampli-Fi protocol, and the seqWell LongPlex3 PCR+ method on representative genomic DNA samples including plant, microbial isolates, and metagenomic samples. Libraries were sequenced on the PacBio Revio and/or Vega systems.

Here, we demonstrate an approach to detect strand-specific 5hmC in PacBio whole genome sequencing.

Targeted long-read sequencing enables efficient characterization of tandem repeats, structural variants, and copy number variants that currently require non-NGS assays like rpPCR, MLPA, long range PCR, and Sanger sequencing. Here we demonstrate that our PCR-free Cas-9 target enrichment panels can resolve these variants in clinically- relevant regions of the genome.

Selecting the appropriate genomic coverage for reference-based variant detection requires balancing sequencing cost with accuracy. While 30x coverage is the standard for comprehensive variant detection with short-read technologies, it remains unclear whether this benchmark applies to long-read sequencing, which offers improved coverage uniformity, access to challenging genomic regions, and haplotype resolution. To address this, we analyzed a 40x HiFi dataset of HG002 generated on a single Revio SMRT Cell using PacBio’s new SPRQ chemistry. We downsampled the data to simulate varying coverage levels and assessed small and structural variant calling accuracy against Genome in a Bottle (GIAB) benchmarks.

Saliva stabilized in Oragene devices and extracted with Nanobind kits is a convenient sample type for HiFi long-read sequencing and broadly applicable to large-scale genomic studies. WGS from saliva samples show optimal HiFi performance with 20-fold to 40-fold coverage sufficient for comprehensive variant detection and methylation analysis. PureTarget from saliva samples enables characterization of complex genes for carrier screening using an accessible sample type.