View BRCA analysis results
The Oncomine™ BRCA Research Assay that is used with Ion Reporter™ Software enables 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 Analyses tab, click Overview.
- Click the hyperlink for the analysis of interest to open a table of BRCA analysis results.
The following data for the BRCA results is available in the Analysis Results screen:
- A summary of called variants and their genotypic and functional properties, and sort and select variants of interest. Variants that are listed include SNVs, InDels, long exon deletions, duplications, and whole gene deletions and duplications.
- Metrics and information at the top of the screen.
The name of the analysis.
The MAPD (Median of the Absolute values of all Pairwise Differences) metric is an estimate of coverage variability between adjacent amplicons. The default threshold is 0.5. As a result, sample results with a MAPD above this value should be viewed with lower confidence.
- Click Summary to view a summary of the called variants. Select a classification from the dropdown list to assign a classification to a variant. The following variant types are available for a BRCA analysis.
Deletion of at least one exon
Duplication of at least one exon
Whole BRCA1/BRCA2 gene deletion or duplication
Read count differs from baseline by non-integer amount; evidence for a BigDel or BigDup call is weak
Read count matches reference baseline
Single nucleotide substitution
Multiple nucleotide polymorphism at adjacent nucleotide positions
Single or multiple nucleotide insertion or deletion
- Click Functional to view other functional annotations and use the annotations to classify, sort, and filter variants.
- Click Pharmacogenomics to view the ClinVar column. Click the link in the ClinVar column for a selected variant to open an NCBI ClinVar website where information about the ClinVar variant annotation is available.