The Oncomine BRCA Research Assay is now able to detect large indels and exon or whole gene deletion or duplication events

The Oncomine BRCA Research Assay now uniquely empowers laboratories to detect all classes of mutations in one NGS workflow, removing the need to employ multiple technologies.

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The Oncomine BRCA Research Assay was evaluated by 22 laboratories during early-access program. Downoload a poster with data from this evaluation that was presented at the European Congress of Pathology in September 2016.

The Oncomine BRCA Research Assay enables robust performance and reliable, rapid, and consistent high-quality results from every sample.

  • Based on proven Ion AmpliSeq technology
  • Fully qualified on clinical research samples
  • Requires as little as 10 ng DNA input
  • Enables 100% exonic coverage, superior uniformity, and high reads (average is >600)
  • Detects 5% and below minor-allele frequencies
  • Flexible workflow enables full automation

Oncomine BRCA Research Assay workflow

The Oncomine BRCA Research Assay workflow is flexible in allowing manual or automated template preparation followed by sequencing using the Ion PGM™ or Ion S5™ systems.

Sequencing data are analyzed using Ion Reporter™ Software, a tailored bioinformatics solution that enables easy implementation and use in every laboratory.

Figure 1. Oncomine BRCA Research Assay workflow.

Oncomine BRCA Research Assay performance

The associated figures demonstrate the superior performance of the Oncomine BRCA Research Assay. All exons are 100% covered, with an average of 64 bases of flanking sequence into the introns upstream and downstream of each exon, allowing for over 99% confidence of detecting 5% somatic variants. The uniformity and high read  counts ensure high sensitivity and accuracy of both somatic and germline mutation detection, demonstrated with different workflows (templating and sequencers). The performance has been verified for use on the Ion 318 and Ion 530 chips.

Figure 2. 100% exon coverage across both BRCA 1 and BRCA 2 genes, with high uniformity and read counts across all exons, allowing for over 99% confidence of detecting 5% somatic variant.

gDNA  variants   Platform Library & templating SNV Indel
Sensitivity PPV Sensitivity PPV
5% allele frequency Ion PGM™ System/
Ion 318™ Chip
Ion Chef 100 99 99 98
Ion S5™ System/
Ion 530™ Chip
Ion Chef 100 92 99 99
50% and 100% allele frequency Ion PGM System/
Ion 318 Chip
Ion Chef 100 100 100 99
Ion S5 System/
Ion 530 Chip
Ion Chef 100 100 100 100

Figure 3. Superior accuracy in detecting somatic and germline variants that is highly consistent and independent of workflow. At 5% allele frequency, >1,000 SNV and >600 indel variants measured. At 50%, 100% allele frequency, >4,000 SNV and >200 indel variants measured. Positive predictive value (PPV) = true positives/total number of positives. Sensitivity = true positive/(true positives + false positives).

Figure 4. Relative abundance of BRCA exons are plotted. The sample has a deletion in BRCA1 (red) of exons 4–9 (green circle). BRCA2 (blue) has no CNV. The green plot indicates the sample ID amplicons used for normalization.