NGS data to verify high-quality results across the Oncomine assay portfolio
Genetic profiling of FFPE cancer tissue samples by targeted next-generation sequencing (NGS) is becoming a daily routine in oncology clinical research. Due to handling in the preanalytical phase, the fixation process, and size limitations, samples can pose a challenge for molecular genetic methods.
Ion Torrent NGS platforms combined with Ion AmpliSeq technology, optimized for oncology clinical research in the form of Oncomine Assays, have demonstrated robust performance even with very limited FFPE samples such as fine needle aspirates (FNA).
See results for:
NCI-MATCH Trial Assay & Ion Torrent platforms ›
Oncomine Focus Assay & Ion PGM System ›
Oncomine Focus Assay & Ion S5 System ›
NCI-MATCH Trial Assay on Ion Torrent platforms—performance verification results
The NCI-MATCH Trial Assay* is based on the 143-gene Oncomine Comprehensive Assay. In performance verification studies, the NCI-MATCH Trial Assay demonstrated high-reproducibility, sensitivity, and specificity across 455 sequencing runs.
At the outset of this verification study, data was generated using the Ion PGM System across four testing sites. All four sites increased throughput by switching to the Ion S5 XL System to complete the analysis more quickly. Based on the observed data, assay performance was consistent across both platforms at all four sites.
*The information presented summarizes data generated in the NCI-MATCH Clinical Trial. The NCI and collaborating laboratories associated with the NCI-MATCH program make no specific endorsement of the Oncomine Comprehensive Assay in reporting these results.
| Sensitivity | Specificity | LOD | |
| SNVs | 99.02% | 99.99% | 2.80% |
| Indels | 95.00% | 99.98% | 10.50% |
| Large indels (gap > 4 bp) | 97.50% | 100% | 6.80% |
| CNVs | 92.50% | 100% | 4 copies |
| Gene fusions | 97.67% | 99.99% | N/A |
| Combined overall | 96.98% | 99.99% | N/A |
Table 1. Performance evaluation of the NCI-MATCH Trial Assay as completed on the Ion PGM System using a modified version of the Oncomine Comprehensive Assay. Data represents 455 sequencing runs.
Oncomine Focus Assay on the Ion PGM System—performance verification results
The performance verification of the 52-gene Oncomine Focus Assay on the Ion PGM System demonstrates that it is a precise, reproducible, sensitive, and accurate NGS assay for the detection of somatic genetic variants from FFPE tissue.
A performance study of the Oncomine Focus Assay was completed in our laboratories, and the results were published in a white paper entitled " An approach for establishing Oncomine Focus Assay performance".
| Sensitivity | PPV (Specificity) | Reproducibility | |
|---|---|---|---|
| SNVs | 99.39% | 100% | 98.70 |
| Indels* | 100% | 100% | 100% |
| CNVs | 90% | (100%) | 100% |
| Gene Fusion | 93.33% | 96.60% | 91.70% |
| Combined Overall | 99.31% | 99.95% (100%) | 97.6% |
*All indels are >4bp
Table 2. DNA sequencing performance analysis, Oncomine Focus Assay on Ion PGM System.
Oncomine Focus Assay on the Ion S5 System—performance results
The Oncomine Focus Assay on the Ion S5 System achieves similar performance when the same assay is run on the Ion PGM System, demonstrating high sensitivity, specificity, and reproducibility. Performance was assessed using the Ion Chef System for automated template preparation and chip loading.
A performance study of the Oncomine Focus Assay was completed in our laboratories, and the results can be reviewed in a presentation entitled " Oncomine Focus Assay on Ion S5 System— Analytical Performance".
| Sensitivity | PPV (Specificity) | Reproducibility | |
| SNVs | 98.77% | 99.63% | 99.6% |
| Indels | 100% | 100% | 100% |
| CNVs | 96.42% | 100% | 96.42% |
| Gene fusion | 100% | 100% | 100% |
| Overall | 98.70% | 99.67% | 99.01% |
Table 3. Sensitivity, specificity, and reproducibility across variant types using the Oncomine Focus Assay on the Ion S5 System.
For Research Use Only. Not for use in diagnostic procedures.