Smoothing, no gender, and mosaicism results in IRGV

This image shows five aneuploidy analyses run in various Ion Reporter™ Software aneuploidy analysis workflows that show how smoothing, no gender, and mosaicism appear in Ion Reporter™ Genomic Viewer (IRGV) visualizations. Visualization of aneuploidy detection is enhanced by tile-by-tile data points that are displayed 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 has no impact on the calls that are made by the aneuploidy pipeline in the software. Smoothing can be turned on or off in any analysis workflow.

  1. An analysis performed 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 of the Demo Aneuploidy sample run through the default ReproSeq analysis workflow in Ion Reporter™ Software.

  3. An analysis of the Demo Aneuploidy sample run through the ReproSeq No Gender analysis workflow. Use of the no gender analysis workflow generates analysis results that do not record or display the called gender of the sample in display 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 of the Demo Aneuploidy sample run through the ReproSeq Mosaic analysis workflow. Note that 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 close to 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, while the other sample was normal ploidy=2 for chr 9. The mixing of two samples of different gender can be seen in the observed ploidies of the X and Y chromosomes.