Genomic segmentation analysis results

The Ion Reporter™ Software can detect heterozygous population SNPs to determine ploidy levels of genomic segments, when some IR analysis workflows are used, such as the Oncomine™ Comprehensive Assay Plus, DNA. The genome is divided into contiguous segments of similar ploidy levels using a circular binary segmentation (CBS) algorithm. Log odd ratios for variant allele frequency of observed population SNPs (by TVC) and copy-number (CN) ratios (by CNV pipeline) for each segment are calculated. Log odd ratio and CN ratios are then used to infer:

  • Tumor cellularity percentage (percentage of tumor cells in the sample)

  • Loss-of-heterozygosity (LOH) for each genomic segment. Segment level LOH events are intersected with targeted gene boundaries to determine LOH events in selected genes. Segment level LOH events are also aggregated to determine genomic (%LOH).

To download the results, see Download filtered variants

Related Topics
Parent topic: Visualize analysis results with Ion Reporter™ Software
Child Topics
Visualization of genomic segmentation analysis, Allele Specific Copy Number plots