Visualize the BRCA report

Some Oncomine™ assays used with Ion Reporter™ Software include BRCA1 and BRCA2 amplicons that enable detection and visualization of whole exon and multiple exon deletion in BRCA1 and BRCA2 genes in somatic and germline samples with high sensitivity.

In the Analysis Results screen, click Visualize, then select the BRCA tab.

When you open a visualization for a panel that contains amplicons that target the BRCA1 and BRCA2 genes, you can view a BRCA Report that shows a boxplot of read counts of each BRCA1 and BRCA2 exon that are normalized to the Oncomine BRCA DNA Baseline. The Post-Corrected view is shown by default. Click Pre-Corrected to view the uncorrected raw data.

Note: For brevity, only genes from the HRR pathway are shown. Consequently, the figures cannot be used to interpret gain-of-function or loss-of-function from these genes.

Figure 1. Normal sample, no BRCA whole-gene or exon deletion

Figure 2. Tumor sample with BRCA exon deletion
(Optional) To download the figures as PNG files, click Download Results.

A ZIP file containing the PNG files for the graphs is downloaded.
Click the IRGV & Generate Report tab to view exon deletions or duplications on chromosomes 13 and 17.
1. Click to open the Sample Analysis Summary in a separate browser window
2. Zoom in and zoom out for the selected chromosome
3. Click to select and view a chromosome
4. Slide the MAPD filter to adjust the threshold value. This filter applies to the entire sample. If the reported MAPD value is higher than the selected MAPD filter value, no CNVs are shown in the BRCA Report.
5. Scroll down in this section to see more of the alignments or hotspots.
6. Oncomine BRCA Expanded designed BED file alignment. This IRGV track shows the alignment of the amplicons to the reference sequence.
Click IRGV Export & Preferences to open the visualization in IGV, export the whole genome view or the IRGV tracks to a PNG file, or show IRGV preferences.