View Oncomine™ BRCA analysis results
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 Analyses tab, click Overview.
- Search, sort, or filter the Analyses table to find the sample result of interest.
- In the Analysis column, click the hyperlink for the analysis of interest to open Analysis Results screen for the BRCA analysis.
- 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. 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.
- 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.
Type
CNV Subtype
Description
CNV
BigDel
Deletion of at least one exon
BigDup
Duplication of at least one exon
GeneCNV
Whole BRCA1/BRCA2 gene deletion or duplication
NOCALL
Read count differs from baseline by non-integer amount; evidence for a BigDel or BigDup call is weak
REF
Read count matches reference baseline
LongDel
—
A specific 40 bp deletion in BRCA1 (c.1176_1214del)
SNV
—
Single nucleotide substitution
MNP
—
Multiple nucleotide polymorphism at adjacent nucleotide positions
INDEL
—
Single or multiple nucleotide insertion or deletion
Click Functional to view other functional annotations and use the annotations to classify, sort, and filter variants.
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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.
- Click Visualize to view a BRCA Report that shows read counts of BRCA1 and BRCA2 exons that are normalized to the Oncomine BRCA DNA Baseline. For more information, see Visualize the BRCA report.