Webinar: Oncomine Precision Assay—Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA

In this OncomineWorld webinar, Dr. Ting Chan, PhD, Curation Scientist, Centre for Cancer Research at the University of Melbourne, assessed the feasibility and performance of a decentralized liquid biopsy workflow using circulating tumor DNA (ctDNA) as part of a Japanese national AI hospital initiative at the Japanese Foundation for Cancer Research.

The evaluation focused on an automated sequencing workflow combining the Ion Torrent Genexus Integrated Sequencer with the Oncomine Precision Assay, with the goal of addressing common limitations of liquid biopsy studies, including workflow variability, reliance on centralized testing, and sensitivity constraints. Due to its short fragment length and rapid turnover, ctDNA provides a dynamic representation of tumor-derived genomic material and supports longitudinal genomic characterization through minimally invasive sampling.

Analytical assessment demonstrated high sensitivity and reproducibility for detecting low-frequency single-nucleotide variants and indels down to approximately 0.2% variant allele frequency, as well as reliable detection of gene fusions, using cfDNA inputs as low as 10 ng. The workflow was further evaluated using 298 plasma samples across multiple cancer types, achieving a sequencing success rate of 99%, which exceeded that observed in matched tissue-based sequencing.

Genomic alterations were identified in approximately half of the samples analyzed, with detection frequencies varying by tumor type in a manner consistent with prior studies. Variants with established biological or therapeutic relevance were observed in 29% of samples, with higher prevalence in breast, gastrointestinal, and lung cancer cohorts.

Comparative analysis between plasma- and tissue-derived sequencing data showed an overall concordance of 72%, with agreement strongly influenced by variant class and clonal representation. Small sequence variants exhibited substantially higher concordance than copy number alterations, which required higher tumor DNA fractions or amplification levels for consistent detection. These findings highlight the impact of tumor heterogeneity and molecular abundance on ctDNA detectability.

Overall, the results support the use of a fully automated, decentralized ctDNA sequencing approach as a robust research tool that complements tissue-based analyses and enables scalable, time-efficient genomic profiling in precision oncology studies.