Visualize the BRCA report

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.

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

Example post-correction boxplot (Figure 1 a) of a tissue normal sample without whole-gene or exon deletions in either the BRCA1 or BRCA2 genes. The data have less variability relative to the pre-corrected view (Figure 1 b).

In Ion Reporter™ Software 5.16 or later, the Post-Corrected view normalizes the abundance of the amplicons in BRCA1 and BRCA2, bringing the median coverage of amplicons in BRCA1 and BRCA2 to comparable values. This correction is used to detect exon deletions in the BRCA1 or BRCA2 genes (Figure 2). As a result the Post-Corrected view does not show any whole-gene deletions or duplications in BRCA1 or BRCA2 (for example, somatic CNVs). This behavior is different than in the earlier version of Ion Reporter™ Software (5.14), where whole-gene deletions were visible in the Post-Corrected view. To view whole-gene deletions or duplications, review the Pre-Corrected view (Figure 3) or the IRGV & Generate Report tab.

Figure 2. Tumor sample with BRCA exon deletion

Example Post-Corrected boxplot of a tumor sample with an exon deletion in the BRCA2 gene.

Figure 3. Tumor sample with BRCA2 whole-gene deletion

Example Pre-Corrected boxplot (Figure 3 a) of a tumor sample with a whole-gene deletion in the BRCA2 gene. The whole-gene deletion is not visible in the Post-Corrected view (Figure 3 b).