Copy Number Variant detection

There are known sources of variability in analysis results, including pool imbalance (if an assay has more than one pool of amplicons), total number of reads and per-amplicon attributes of GC proportion. In practice, other variability exists that is not associated with known attributes, yet is systematic.

A copy number baseline, when added to an analysis workflow can correct the variability. Copy number baselines can be added only to assays that support CNV detection.

A copy number baseline is a set of control samples that are used to create a baseline for the detection of copy number variants (CNVs). CNV analysis is based on reads counts for each amplicon. Copy number estimates are made using a proprietary algorithm.

Analysis workflows that use baseline controls allow you to determine copy number changes in the sample of interest, without the use of a matched control.

In Ion Reporter™ Software, copy number baseline workflow presets are the components that you can add to analysis workflows as baseline controls. There are 6 types of copy number baselines in the software. The Baseline Type is based on the type of libraries that you use.

  • AmpliSeq—Use to create copy number baselines for Ion AmpliSeq™ and Oncomine™ libraries (not Exome).

  • AmpliSeq HD—Use to create copy number baselines for Ion AmpliSeq™ HD libraries.

  • AmpliSeq Exome—Use to create copy number baselines for Ion AmpliSeq™ Exome libraries.

  • TagSeq—Use to create copy number baselines for Ion TagSeq libraries.

  • TargetSeq-Exome—Use to create copy number baselines for Ion TargetSeq™ Exome or other targeted libraries.

There are 2 algorithms that detect CNVs in the software for Ion AmpliSeq™ and Ion AmpliSeq™ HD custom panels. You can select a CNV Detection Type based on the types of variants that the panel detects. The CNV Detection Type that you select applies a CNV detection algorithm to the analysis workflow, based on the panel that you use.

  • The Somatic (CNV VCIB) detection type is designed for use with panels used to detect somatic variation. The Somatic (CNV VCIB) detection type is recommended for use with somatic variant detection.

  • The Germline (CNV Informatics Baseline) is designed for use with panels and samples used to detect germline variation.

Samples are added to the baseline, based on recommended guidelines. For more information, see CNV Informatics Baseline workflow presets and Variability Correction Informatics Baseline (VCIB) baseline workflow presets.

Administrators and Analyze users can create new copy number baselines, create copies of existing copy number baselines, and augment existing copy number baselines. When a baseline is augmented, an existing copy number baseline is copied and saved with a new name. More samples can then be added to the new baseline.