GenomOncology & PacBio Unify Long-Read Sequencing and Reporting

CLEVELAND, OH – July 30, 2026 – GenomOncology, a leader in precision oncology software, has announced a significant collaboration with PacBio to launch an integrated, end-to-end workflow for somatic whole-genome sequencing (WGS) in cancer research and diagnostics. The new solution combines PacBio’s high-fidelity (HiFi) long-read WGS secondary analysis pipeline with GenomOncology’s Pathology Workbench (PWB) platform. This partnership aims to solve a persistent operational challenge for clinical laboratories: translating the vast, complex data from long-read sequencing into standardized, clinician-ready reports that can inform patient care.

Long-read WGS technology holds immense promise for providing a more comprehensive view of a tumor's genetic and epigenetic landscape from a single assay. However, the sheer volume and complexity of the data have historically created a bottleneck between the sequencer and the clinical report. This integrated workflow is designed to break down that barrier, creating a streamlined, automated path from raw sequencing data to actionable intelligence for pathologists and oncologists.

Bridging the Data-to-Diagnosis Gap with an End-to-End Workflow

The power of the newly announced solution lies in its seamless connection of two best-in-class components. The first is the PacBio Somatic WGS RUO analysis pipeline, which handles the crucial secondary analysis stage. This pipeline processes raw sequencing output to produce aligned reads and comprehensive variant calls, identifying everything from small nucleotide variants to large structural changes. The second component is GenomOncology’s Pathology Workbench, a sophisticated tertiary analysis platform that ingests the processed data and provides the tools for final interpretation and reporting.

Within the Pathology Workbench, laboratories can manage run-level and sample-level quality control, review variant calls with a built-in BAM pileup viewer, and leverage an automated variant interpretation algorithm that boasts high concordance with manual expert review. The platform’s integrated knowledge base, which is continuously updated with FDA approvals, NCCN guidelines, and clinical trial information, provides critical context for every finding. The end result is a configurable, comprehensive genomic report designed for clinical utility.

"Translating long-read WGS data into reports that pathologists and oncologists can act on requires more than a sequencing pipeline. It requires a system that understands the clinical context of each result," said Matthew Stachowiak, PhD, Vice President of Innovation at GenomOncology. "This integrated workflow gives laboratories a structured, scalable path from instrument output to clinical report, with the flexibility to support the reporting programs they actually run."

Unlocking a Deeper View of the Cancer Genome

The primary driver for this integration is the unique power of PacBio's HiFi long-read sequencing technology. Unlike traditional short-read methods, which analyze DNA in small fragments, long-read sequencing provides a much more complete and accurate view of the cancer genome, uncovering critical alterations that are often missed.

One of the most significant advantages is the superior detection of complex structural variants (SVs)—large-scale insertions, deletions, inversions, and translocations that are known drivers in many cancers. "Short-read sequencing gave us a book with missing pages and jumbled chapters," explained one genomic scientist not affiliated with the companies. "Long-read WGS gives us the complete manuscript, allowing us to see how everything is connected." This capability is crucial for identifying gene fusions that can be targeted with specific drugs or large deletions that inactivate tumor suppressor genes.

Furthermore, the technology enables accurate haplotype phasing, which determines whether multiple variants lie on the same copy of a chromosome. This is essential for understanding their combined effect. Perhaps most powerfully, PacBio HiFi sequencing allows for the direct detection of DNA methylation from the same sequencing run. This provides a simultaneous view of both the genetic sequence and its epigenetic regulation, offering multi-omic insights from a single assay without the need for separate, labor-intensive bisulfite sequencing. This integrated genomic and epigenomic data can be critical for tumor classification and predicting response to therapy.

A Practical Solution for the Modern Clinical Laboratory

While the technology is advanced, the integrated workflow is designed for practical implementation in today's clinical laboratories. A key feature is the modular reporting architecture within the GenomOncology Pathology Workbench. This allows a lab to perform comprehensive WGS upstream but generate tailored, histology-specific reports downstream. For example, from a single WGS run, a lab can produce a focused myeloid panel, a comprehensive genomic profiling report, or other sub-panels aligned with specific tumor types and clinical programs. This flexibility allows labs to standardize their sequencing process while customizing outputs to meet clinical and potential reimbursement needs, avoiding the inefficiency of building separate pipelines for each indication.

Deployment is also flexible, with the workflow capable of running in on-premises data centers or on major public cloud platforms. This gives laboratories control over their data while enabling rapid implementation without requiring specialized infrastructure. The platform’s ability to integrate seamlessly with existing Laboratory Information Systems (LIS) and Electronic Health Record (EHR) systems further lowers the barrier to adoption, ensuring that genomic insights can be incorporated directly into established clinical workflows.

Navigating the Path to Clinical Adoption

The workflow's components, including the PacBio pipeline, are initially designated as Research Use Only (RUO). This means that for diagnostic use, a clinical laboratory must validate the entire process as a Laboratory Developed Test (LDT), taking on the responsibility for its analytical and clinical performance under CLIA regulations. While this is a standard path for introducing cutting-edge diagnostics, it represents a significant consideration for labs.

However, the integrated and validated nature of this end-to-end solution provides a robust foundation for labs undertaking this LDT validation. By offering a standardized process from sequencer to report, the workflow helps ensure the consistency and reproducibility required for clinical use. As the body of evidence for the clinical utility of long-read WGS in oncology grows, this workflow positions labs at the forefront of precision medicine, ready to generate the comprehensive data that could lead to improved patient outcomes and, eventually, broader reimbursement.

Professionals attending the Cancer Genomics Consortium (CGC) Annual Meeting in Houston from August 1-5, 2026, can learn more about this integrated workflow and see a demonstration at the GenomOncology poster presentation.