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.

  1. In the Analyses tab, click Overview.
  2. Search, sort, or filter the Analyses table to find the sample result of interest.
  3. In the Analysis column, click the hyperlink for the analysis of interest to open Analysis Results screen for the BRCA analysis.
  4. 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.

      Item

      Description

      Analysis Name

      The name of the analysis.

      Cancer Type

      The type of cancer, as defined by the sample attribute in Torrent Suite™ Software, if sample data are transferred by Torrent Suite™ Software.

      MAPD

      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.

      BRCA CNV QC

      A quality control score that is based on the MAPD threshold, and quality scores for the percent of non-zero amplicons, total number of reads, and the number of calls. BRCA CNV QC is PASSED or FAILED. If the BRCA CNV QC fails, a reason is provided.

      Sample ID

    • 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.

    • 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.

  5. 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.