Smoothing, no gender, and mosaicism results in IRGV

Figure 1. Example of a mosaic sampleThe following Ion Reporter™ Genomic Viewer(IRGV) plot shows non-integer ploidy for the short arm of chromosome 9, indicating that the sample is mosaic.

This image shows five analyses run with various Ion Reporter™ Software aneuploidy analysis workflows that show how smoothing, no gender, and mosaicism appear in IRGV visualizations. Visualization of aneuploidy detection is enhanced by tile-by-tile data points that appear as easier-to-see circles in the whole‑genome views. All results from IRGV aneuploidy analysis workflows use this enhanced view.

Note: Analyses 2 through 5 have smoothing of the discrete tile data turned on by default. Smoothing of the discrete data have no effect on the calls that are made by the aneuploidy pipeline in the software. Smoothing can be turned on or off in any analysis workflow.

Figure 2. Examples of smoothing, No Gender and mosaicism
  1. An analysis launched with the Ion Reporter™ Software 5.2 version of the Low Pass Whole‑Genome Aneuploidy analysis workflow and the Demo Aneuploidy sample that is available in the software, with a loss of one copy of chr13 and single copy gains of chrs 14 and 15. This analysis was run with an Ion Reporter™ Software 5.2 analysis workflow version that does not include smoothing of the discrete tile data.

  2. An analysis launched with the default ReproSeq analysis workflow and the Demo Aneuploidy sample in Ion Reporter™ Software.

  3. An analysis launched with the ReproSeq No Gender analysis workflow and the Demo Aneuploidy sample. Use of the no gender analysis workflow generates analysis results that do not record or show the called gender of the sample in the software or in data files. Instead, a called gender value of SxChrNrml is given when the sample is either a normal XY male or a normal XX female with no sex chromosome aberrations. A gender call is SxChrAbnrml when the sex chromosomes deviate from normal male or normal female by either whole-chromosome or subchromosomal aneuploid events. Aneuploidies on autosomes do not affect the called gender value, and can be present in samples with normal sex chromosomes.

  4. An analysis launched with the ReproSeq Mosaic analysis workflow and the Demo Aneuploidy sample. Some chromosomes can look like they were called aneuploid if the copy number is called as CN loss = ploidy 1.95, or CN Gain = ploidy 2.05 (as shown in this example on chr1), and on the Y chromosome as a slight ploidy gain. Gain or Loss events with ploidy very near expected normal ploidy can be a result of slight differences in normalization instead of true biological ploidy changes.

  5. An analysis of a spiked‑in sample that was mixed to have a chr9p event of relative copy number ploidy of 2.5 and analyzed through the ReproSeq Mosaic analysis workflow. The two mixed samples consisted of one male and one female, one of which had an integer copy number gain of ploidy=3 for chr 9, although the other sample was normal ploidy=2 for chr 9. The mixing of two samples of different genders can be seen in the observed ploidies of the X and Y chromosomes.