Improve detection of small segmental CNV events

You can improve the detection of small segmental CNV events if you adjust the CNV Transition Penalty parameter in Ion ReproSeq™ analysis workflows for use with aneuploidy research. The CNV Transition Penalty parameter establishes the trade-off between false-positive and false-negative rates. The transition penalty is a probability that the copy-number state changes for any given random tile. A smaller probability results in calling of only larger CNV segment sizes, or calling of only segments that include greater support for the changed state, that is, a greater difference in copy number value from the current ploidy state.

Low sensitivity results in fewer false positives, but more false negatives. High sensitivity results in fewer false negatives, but more false positives. High sensitivity is required to make segmental aneuploidy calls of ~20 Mbp. Custom CNV Sensitivity allows you to change the CNV Transition Penalty parameter to detect even smaller segmental CNV events more sensitively.

IMPORTANT! Do not change parameters from the default settings unless you understand how the change can affect your analysis.

You can change the CNV Transition Penalty parameter to any value that does not exceed the highest allowable for this parameter:

  • −1.05 for nonmosaic analysis workflows

  • −2.31 for mosaic analysis workflows

  1. In the Workflows tab, click Overview.
  2. In the list of analysis workflows, select Aneuploidy from the Research Application list, select the software version that you use, then sort the list by predefined analysis workflows.
  3. Select the analysis workflow of interest, such as the Ion ReproSeq™ PGS analysis workflow, then in the Workflows tab, click Overview, then in the Workflows table, click the row for an analysis workflow that you want to copy, then click  (Actions) > Copy.
  4. In the Create Workflow screen, advance to the Parameters step, then click the Cnv Finding link. In the Analysis section Main tab, change the CNV Sensitivity setting to Custom, then enter new values for the parameter.
  5. Click Advanced, scroll to the CNV Transition Penalty parameter, then enter the desired value.

    The approximate recommended values are:

    • -2.33 for mosaic ploidy calling

    • -15 for low sensitivity

    • -5 for medium sensitivity

    • -2.0 for nonmosaic ploidy calling

    • -3.0 for high sensitivity in mosaic and nonmosaic analysis workflows

  6. In the Confirm step, click Save Workflow.

    The following results show a sample analyzed twice with two customized workflows—one with the CNV Transition Penalty parameter set to -3, and a second with the parameter set to -2.

    In this visualization, a 7.9‑Mb deletion that is called on chromosome 6 is visible with the slightly higher transition penalty.