View analysis results for a single sample

Use this procedure to view and manage the extended analysis results of a single sample.

Note: Analyses that are performed as described in this procedure generate a variants table that does not have optimized TagSeq specific filters applied. These filters are applied only when you generate results analysis as described in Visualize identified variants in an Oncomine analysis from a TagSeq analysis workflow.

  1. Click the Analyses tab, then click Overview.
  2. In the Analyses screen you can:

    To

    Action

    Select an analysis

    Enable the checkbox.

    Open an Analysis Results screen.

    Click the hyperlink (in the Analysis column).

    View details

    Click anywhere in the analysis' row, except on the hyperlink.

    Sort

    Click column headings to sort the analyses based on the column contents.

    1. Select analysis

    2. Open Analysis Results screen

    3. View details

    4. Sort a column

  3. To view and manage the extended Oncomine™ Cell-Free Research Assay results, use the available filters to limit the list of analyses (for example, select your analysis workflow from the Workflow list), then click the hyperlink in the Analysis column.
  4. In the Analysis Results screen, sort or filter the data using the Oncomine™-specific annotations. See the software help menu for more options.
  5. Review the results in the Median Read Cov, Median Mol Cov, and LOD % columns.

    Column

    Description

    Median Read Coverage

    Reports median coverage across targets. Median Molecular Coverage reports median number of individual interrogated DNA molecules across targets.

    Median Molecular Coverage

    Directly influences the limit of detection in a sample run. We always require two independent molecular families to identify a variant for it to be called. Lower median molecular coverage values result in less sensitive detection of variants at 0.1% frequency, although still sufficient for sensitive detection of variants with higher frequency. For example, Median Molecular Coverage of 700 is sufficient for accurate detection of variants at 0.5% frequency.

    LOD %

    A segment (e.g., 0.02−0.03) where 0.02 represents the median value across all targets, and 0.03 represents the limit of detection (LOD) for the 80th percentile targets. If both numbers are ≤0.1% then the sequencing run is of acceptable quality for 0.1% LOD.

    For sensitive variant detection down to 0.1% frequency, we see optimal results when targeting a Median Read Coverage >25,000, Median Molecular Coverage >2,500, and both numbers of the LOD % segment are ≤0.1.

  6. In the Liquid Biopsy tab, view Mol Depth, Mol Counts, and other columns.

    Column

    Description

    Molecular Depth

    Reports number of interrogated DNA molecules containing target. It defines limit of detection at hotspot position in a particular run and sample. For instance, if molecular depth is ≥1,500, you can have high confidence that no variant is present at 0.2%. If molecular depth is ≥2,500, you can have high confidence that no variant is present down to 0.1% LOD.

    For reference calls, Molecular Depth provides measurable metric that serves as confirmation for variant absence among a large number of interrogated molecules.

    Molecular Counts

    Reports the number of detected DNA molecules containing variant allele.

  7. In the Oncomine tab, click the column headings to sort the list of variants by Oncomine Variant Class and Oncomine Gene Class.

    Reference calls display chromosomal position with empty value in the Amino Acid Change column.

  8. In the Ontologies tab, click the column headings to sort the list by variant Type or Genes to analyze your results.