Create a custom analysis workflow for mosaicism, No Gender, or different tile sizes

To create a new analysis workflow for use with Ion ReproSeq™ aneuploidy research, you can copy and edit a predefined analysis workflow.

Mosaicism detection, a software setting that allows non-integer ploidy calls and reports a CNV event as a decimal ploidy value instead of an integer value, is enabled by default in the Mosaic aneuploidy analysis workflows. For each tile that is shown in analysis results, the algorithm fits the data to all ploidy with a step of 0.05.

You can decrease tile size to further improve sensitivity to detect small segmental CNV events. This adjustment must be accompanied by selection or creation of a CNV Baseline with a corresponding smaller tile size. CNV baselines that correspond to smaller tile sizes are included in Ion Reporter™ Software and are ready to copy and edit to create custom aneuploidy analysis workflows.

You can further customize mosaicism detection if you use a filter chain that includes the Expected Normal Ploidy Buffer (ENPB) filter.

For example, you can copy the Ion ReproSeq™ No Gender PGS w1.1 analysis workflow, which has mosaicism detection that is enabled by default, and improve the detection of small segmental CNV events if you adjust the CNV Transition Penalty parameter. For more information, see Improve detection of small segmental CNV events. You can also select a baseline to increase sensitivity through tile sizes.

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

The CNV Gender Caller Enable Flag parameter value can be set to True in only the Ion ReproSeq™ No Gender PGS w1.1 analysis workflow. You cannot enable gender hiding in other Ion ReproSeq™ analysis workflows because the Hide called gender parameter is locked as False. That is, gender is called in analyses that use other Ion ReproSeq™ analysis workflows.

  1. In the Workflows tab, click Overview.
  2. In the list of analysis workflows, select Aneuploidy from the Research Application list to narrow the list of analysis workflows. Select the Ion ReproSeq™ No Gender PGS w1.1 analysis workflow, then click  (Actions) > Copy.
  3. To change the default sensitivity of 2-Mbp tile size, browse to the Baseline step, then select one of the following:
    • Ion ReproSeq Low-Coverage Whole-Genome Baseline 1 Mbp,

    • Ion ReproSeq Low-Coverage Whole-Genome Baseline .5 Mbp,

    • or a custom baseline to increase sensitivity for tile sizes in analysis results.

  4. Click Next .
  5. In the Confirm step, enter a name and an optional description for the new analysis workflow, then click Save Workflow.

    The custom analysis workflow is added to the list of available analysis workflows. To see a visualization of analysis results for which a custom analysis workflow for use with aneuploidy research was used, see Smoothing, no gender, and mosaicism results in IRGV.