Visualize aneuploidy analysis results

You can view interactive aneuploidy analysis results and customize visualizations in the Ion Reporter™ Genomic Viewer (IRGV). With this viewer, you can visualize multiple analyzes at once, zoom in on chromosomes of interest, generate reports of the data that you view,

You must have IRGV set as the default viewer for this procedure. For more information, see Set IRGV or IGV as the default viewer.

  1. Under the Analyses tab, click Overview.
  2. Select the Workflow filter and enter ReproSeq to find analyses that used a ReproSeq analysis workflow, or select a specific analysis workflow filter, such as ReproSeq No Gender PGS w.1.1.
  3. Select one or more analyses then click Visualize.

    The Analysis Visualization screen opens in the IRGV tab.

  4. Use the interactive view to customize the visualization and generate reports, as needed.
    Figure 1. Aneuploidy analysis results
    1. Analysis whole genome view. Provides a genome-wide perspective of the sample data. A chart or graph is shown for each selected analysis. Click on the chart to zoom in on a region of the genomic data, or a chromosome, and view more information about your selection throughout the visualization.
    2. Click on thisIRGV track to view details about the selected chromosome and view more information about the chromosome in the tracks below. Or, select data in the whole genome view or Karyogram to view data reflected in each track below.
    3. Click Shift and drag across the x-axis of the ploidy scale to zoom in on a region of the scale and change the other data in the visualization to reflect the selection.
    4. Adjustable ploidy scale for selected chromosomes or chromosome regions. Change the track name or track height for the histogram, or hide the track. See Adjust (IRGV) BAM tracks for more information.
    5. Adjustable Reference and Preferred Transcript tracks. Change the BAM track name, track height, and track color, or collapse, squish or expand the track. See Adjust (IRGV) BAM tracks for more information.
    6. Click in a row of the Gains/Losses table to open a detailed view of a single sample visualization. See View single sample aneuploidy details for more information.
    7. Zoom in and out of the chromosome Karyogram, and click Reset to return to the default chromosome view.
    8. Enter a set of chromosomal coordinates in the Search field to zoom into chromosome data, or click on a chromosome in the Karyogram to view its chromosomal coordinates. Or, view the chromosomal coordinates when you change the selections in the whole genome chart, IRGV, or Karyogram.
    9. Chromosome Karyogram.
    10. Adjust the MAPD filter.
    11. Select a filter chain to apply filters to the data.

      Note: If you select multiple analyses generated from analysis workflows with different filter chains that use different confidence settings, the software will apply the filter chain with the lowest confidence setting to all selected analyses.

    12. View the filter change, or filter chain query that is applied to the visualization.
    13. View details about the filter chain, or filter chain query, the total number of genes, and the variants that were filtered in.
    14. Export the visualization, or change the IRGV preferences. See Set IRGV preferences for more information.