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Oncomine BRCA Research Assay
Detect large indels and exon or whole gene deletion or duplication events
The Oncomine BRCA Research Assay uniquely empowers laboratories to detect all classes of mutations in one NGS workflow, removing the need to employ multiple technologies.
The Oncomine BRCA Research Assay was evaluated by 22 laboratories during an early-access program.
Download a poster from the 2016 European Congress of Pathology with data from this evaluation ›
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
- Provides 100% exonic coverage, including flanking intronic sequences (average of 64 bases in either direction), superior uniformity, and high reads (average is >600)
- Detects 5% and below minor-allele frequencies
- Flexible workflow enables full automation
- Detects large indels and exon or whole gene deletion or duplication events
White Paper: Evaluation of the Oncomine BRCA Research Assay for variant detection by next-generation sequencing
Learn how the Oncomine BRCA Research Assay offers sensitive, specific detection of SNVs, MNVs, indels, and whole-exon, multiple-exon, or entire-gene aberrations.
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.
Click image to enlarge
Click image to enlarge
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.
For Research Use Only. Not for use in diagnostic procedures.