The solution combines long-read whole-genome sequencing with standardized clinical reporting for pathology laboratories.
GenomOncology and PacBio announced an integrated end-to-end workflow for somatic whole-genome sequencing (WGS) in oncology. The solution combines the PacBio HiFi WGS research-use-only secondary analysis pipeline with the GenomOncology Pathology Workbench platform to provide standardized, clinician-ready reporting for laboratories using long-read sequencing technology, according to a press release from GenomOncology.
Long-read WGS allows for the simultaneous detection of small and large variants, haplotype phasing, and methylation calling within a single assay. The integrated workflow aims to address the operational challenge of translating these sequencing outputs into structured reports for clinicians.
The workflow connects two primary components. The PacBio somatic WGS RUO analysis pipeline manages secondary analysis from raw sequencing data to aligned reads and variant calls. The GenomOncology Pathology Workbench provides tertiary analysis, including quality control review, variant interpretation, and the generation of configurable genomic reports.
A modular reporting architecture within the Pathology Workbench allows laboratories to create histology-specific sub-panels from the WGS data. This supports reporting for specific tumor types, genomic profiling, and myeloid-focused panels. This approach enables labs to standardize sequencing while tailoring outputs to clinical or reimbursement requirements without developing separate pipelines for each indication, according to the company.
“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. 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,” says Matthew Stachowiak, PhD, vice president of innovation at GenomOncology, in a release.
Validation testing using control and reference samples confirmed the workflow produces aligned BAM and VCF outputs for clinical review. The system provides visibility into quality control metrics, coverage, phased variants, and methylation-derived data tracks. The workflow can be deployed on-premises or via public cloud platforms.
The PacBio HiFi WGS pipeline is a research-use-only assay and is not intended for use in diagnostic procedures.
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