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Updated: Mar 8, 2026
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic
Aino Paasinen-Sohns1, Viktor H Koelzer2, Angela Frank1
1Cantonal Hospital Baselland, Institute of Pathology, Mühlemattstrasse 11, CH, 4410 Liestal, Switzerland.
Abstract:
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology.
Insights
The Oncomine Focus Assay (OFA) provides rapid, reliable next-generation sequencing (NGS) for detecting cancer gene alterations. This validated assay is suitable for routine diagnostics and precision oncology, even with archival samples.
Area of Science:
- Molecular Oncology
- Genomic Diagnostics
- Cancer Genomics
Background:
- Companion diagnostics are crucial for targeted cancer therapy, relying on genomic testing to identify actionable molecular alterations.
- Next-generation sequencing (NGS) offers a powerful approach for comprehensive genomic profiling in oncology.
- Clinical validation of commercially available NGS assays is essential for routine diagnostic application.
Purpose of the Study:
- To clinically apply and validate the Oncomine Focus Assay (OFA) for targeted next-generation sequencing (NGS) in routine cancer diagnostics.
- To assess the workflow, turnaround time, feasibility, and reliability of the OFA using both fresh diagnostic and archival tumor samples.
- To evaluate the OFA's potential as a tool for precision oncology.
Main Methods:
- The Oncomine Focus Assay (OFA), a commercially available NGS panel, was used to detect variants in 52 therapeutically relevant cancer genes.
- Two patient cohorts were analyzed: 59 routine diagnostic samples and 39 archival melanoma samples (up to 15 years old).
- Libraries were sequenced on the Ion Torrent PGM, and data analyzed using Ion Reporter software; results were validated by orthogonal methods.
Main Results:
- The OFA successfully detected single nucleotide variants, insertions/deletions, copy number variations, and gene rearrangements in both cohorts.
- Sequencing results were consistent with published variant frequencies, demonstrating reliability with archival formalin-fixed, paraffin-embedded material.
- A 100% concordance was observed between OFA and established orthogonal assays, with a turnaround time of 3.5 days.
Conclusions:
- The Oncomine Focus Assay (OFA) is a convenient, fast, and reliable tool for targeted NGS in routine cancer diagnostics.
- The assay demonstrates broad applicability and cost-effectiveness, with strong potential for precision oncology.
- OFA provides accurate genomic profiling, even from challenging archival samples, supporting clinical decision-making.
