Use gender to call gains from expected copy number changes

You can use the following approach to call gains from expected copy number changes with analyses that are performed on Oncomine™, Ion AmpliSeq™, or Ion AmpliSeq™ HD cancer research panels that use analysis workflows that include the Variability Correction Informatics Baseline (VCIB).

A copy number baseline has a gender, either male or female. A sample also has a gender: male, female, or unknown (unknown is interpreted as female). Expected genomic copy number regions for these genders are defined in the ploidy files that are supplied by Ion Reporter™ Software within analysis workflows.

For example, create a copy number baseline with "male" normal human samples and chromosome X non-Pseudo Autosomal Regions (non-PAR) amplicons in the panel. The baseline copy number for the non-PAR chromosome X amplicons is expected to be 1. If a male sample is run using this baseline the relative copy number to the baseline should be 1:1 and is expected (normal) and should be reported accordingly. A female sample using this baseline should have a relative copy number of 2:1 as is expected (normal) and should be reported accordingly. Using a ploidy file, each amplicon is assigned to the baseline expected copy number found in the baseline ploidy file (male), in this example non-PAR chromosome X amplicons would have a copy number of 1. Running a sample with a female ploidy file, the non-PAR chromosome X amplicons has a copy number of 2, so the final copy number relative to the baseline is adjusted appropriately.

More precisely, if for amplicon *, expected baseline copy number = B, and expected sample copy number = S, after variability corrections, set l2r = log2 ratio of sample observation to the baseline.

Final CN = 2**(lrr) * B

For purposes of reporting at the CNV_ID level, S and B are used to determine how different Final CN is from expected for that sample. The actual algorithm is proprietary.

Note: Analyses results in Ion Reporter ™ Software reflect the following:

  • FASTA files in Torrent Suite™ Software hard mask all Psuedo Autosomal Region (PAR) region values in chromosome Y for hg19 and GRch38 reference genomes. The hard mask removes the PAR for the Y chromosome to improve variant calling in Ion Reporter™ Software.
  • The variantCaller plugin in Torrent Suite™ Software defaults to use only reads that include mapping quality value scores >0, that is, reads that map to only one location in the reference. When FASTA files originate in Torrent Suite™ Software, Ion Reporter™ Software removes the PAR from chrY to prevent the reads that map to the PAR in chrX from mapping to both the chrY and chrX locations. As a result, all reads in the chrX PAR that do not also map to yet another location will be included for making variant calls.
  1. Create a normal male and chrX PAR CNV baseline.

    For more information, see Create a copy number baseline workflow preset.

  2. Add the CNV baseline to an Oncomine™, Ion AmpliSeq™, or Ion AmpliSeq™ HD analysis workflow.

    For more information, see Apply a baseline workflow preset to an analysis workflow.

    Note: The name of the target regions BED file in the CNV baseline must match the target regions BED file that is used in the analysis workflow.

  3. Launch the analysis.

    For more information, see Launch an analysis.

  4. Visualize the analysis.

    For more information, see IRGV tab or Visualize analysis results with Ion Reporter Software.

Copy number gains are reported on the Analysis Results screen and the Analysis Visualization screen, Variant Matrix tab. For more information about the results, see Reasons for NOCALL in a gene-level CNV.