Oncomine BRCA Assay | Thermo Fisher Scientific

Enabling large genomic rearrangement detection in BRCA 1 and BRCA 2 genes in as little as 24 hours

The Oncomine BRCA Assay 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 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 only 20 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
Detect large genomic rearrangement, such as large insertions and deletions (indels), and exon-level duplication and deletion

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.

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Oncomine BRCA Assay workflow

The Ion Torrent Oncomine BRCA Assay is now available for use on the Ion GeneStudio systems with the Ion Chef Instrument or for use on the Ion Torrent Genexus System.

Figure 1. Ion Torrent Next Generation Sequencing systems

Oncomine BRCA Assay performance

The associated figures demonstrate the superior performance of the Oncomine BRCA 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 (and sequencers). The performance has been verified for use on the Ion 530 chips on GeneStudio system and GX5 chip on Genexus system.

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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.

Control sample variants	Platform	Library	SNV		Indel
Control sample variants	Platform	Library	% Sensitivity	% PPV	% Sensitivity	% PPV
5% allele frequency	GeneStudio S5 System	Manual	100	98	98	92
	GeneStudio S5 System	Chef	100	92	99	99
	Genexus System	Genexus	100	100	98	100
50%, 100% allele frequency	GeneStudio S5 System	Manual	100	100	100	100
	GeneStudio S5 System	Chef	100	100	100	100
	Genexus System	Genexus	100	100	94	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.z

For Research Use Only. Not for use in diagnostic procedures.