Create an analysis workflow that contains a copy number baseline

Ion Reporter™ Software provides a workflow bar to guide you through the process to create an analysis workflow that contains a CNV baseline workflow preset. However, we recommend that you copy an existing predefined analysis workflow, then add the CNV baseline workflow preset to the new analysis workflow.

  1. In the Workflows tab, click the Overview screen, then select an appropriate Oncomine™ analysis workflow.
  2. Click Actions > Copy, then click Next .
  3. In the Reference step, ensure that hg19 is the selected Reference, then select Target Regions, Hotspot Regions, and Fusions BED files, then click Next.
  4. In the Annotation step, select an Annotation Set from the dropdown list, then click Next.
  5. In the Filters step, select a Filter Chain from the list, then click Next.
  6. Select the baseline that you want to use from the Baseline dropdown list.
  7. Click Next.
  8. In the Plugins step, ensure that all In-Analysis plugins are deselected, then click Next.
  9. In the Final Reports step, select a Final Report Template from the list, then click Next.
  10. In the Parameters tab, review the default settings, then click Next.

    Note: Although Read Mapping parameters are exposed when you create a CNV baseline analysis workflow, it is not necessary to change any settings.

  11. In the Confirm tab, enter a Workflow Name and description, then click Save Workflow.

You can now use the analysis workflow to launch an analysis. For more information, see Launch an analysis. You can also optionally download the analysis results and view them visually in the cn_results.png.

These example analysis results shows a plot with log2 ratios across the genome and highlights panel CNV IDs, in this case gene symbols, to aid in verifying calls made by the CNV detection algorithm. The alternating gray and black dot color is used to distinguish between adjacent amplicons in the CNV IDs. The outliers in the data are drawn as small circles. The numbers on the X axis are the chromosomes numbers. The CNV ID names and the mean copy number call for each CNV ID are indicated above the chromosomes at their approximate location. This example has copy number gains on chromosomes 13 and 20, and deletion of a portion of chromosome 9, and possibly other subchromosomal events. The MAPD value of 0.2781 for the sample is displayed at the top of the plot and is a QC metric measuring the noisiness of the sample. A low MAPD is good. MAPD at or above 0.5 is considered to fail QC. Log2 ratios of 0 are equivalent to a copy number call of 2 (normal for autosomes and female X). If the sample is for a male, you would expect to see the log ratio equivalent to a copy number of 1 on chromosome X.