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.

When you use aneuploidy analysis workflows, if there are not enough mapped reads to calculate Called Gender, the analysis will complete successfully and the sample coverage section in the analysis.log file contains information on why the gender calling failed.

  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 & Generate Report 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 this IRGV 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. Hover over a tile in the visualization to get the following information.

      • Start: Start coordinate for the copy number call region.

      • End: End coordinate for the copy number call region.

      • Ploidy: Called ploidy value.

      • Expected value: Expected ploidy value for this chromosome. The value is 2 for autosomes and chrX for females. It is 1 for chrX and chrY for males.

      • Start: Start position of the selected tile.

      • End: End position of selected tile.

      • Ploidy: The actual calculated ploidy value of the tile.

      • Cytobands:The cytoband range of the tile.

    5. 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.

    6. 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.

    7. 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.

      The Gains/Losses table shows the following information.

      CID (Couple ID): An identifier for the parents of an embryo.

      EID (Embryo ID): An identifier for the embryo biopsied and run through the ReproSeq workflow)

      Cell# (Cell Num): The number of cells in the sample, if known.

      MA: A calculated result the ratio of Mitochondrial DNA and Autosomal DNA.

      An: Aneuploidy, shown as An(+) for a copy number gain, and An(-) for a copy number loss. The affected chromosomes are shown in a comma-separated list.

      MAPD (Median Absolute Pairwise Difference): An estimate of coverage variability between adjacent amplicons.

      WaveSD (Waviness Standard Deviation): Standard deviation of all log2 read count ratios after subtraction of the contribution of pairwise differences.

    8. Zoom in and out of the chromosome Karyogram, and click Reset to return to the default chromosome view.

    9. 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.

    10. Chromosome Karyogram.

    11. Adjust the MAPD filter.

    12. Select a filter chain to apply filters to the data. 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.

    13. View the filter change, or filter chain query that is applied to the visualization.

    14. View details about the filter chain, or filter chain query, the total number of genes, and the variants that were filtered in.

    15. Export the visualization, or change the IRGV preferences. See Set IRGV preferences for more information.