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
SNVs 99.02% 99.99% 2.80%
Indels 95.00% 99.98% 10.50%
Large indels
(gap > 4 bp)
97.50% 100%
CNVs 92.50% 100% 4 copies
Gene fusions 97.67% 99.99%
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)
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.

  See the detailed data from the evaluation study ›