VCIB baseline workflow presets

In Ion AmpliSeq™, Ion AmpliSeq™ HD, and Oncomine™ assays, somatic copy number estimates are made when Ion Reporter™ Software counts reads for each amplicon, and makes adjustments to account for specific types of variability. The software then compares the read counts to expected counts for the amplicons in a normal sample, that is a sample without known copy number variants, then makes further adjustments.

Known sources of variability include pool imbalance (when the assay has more than one pool of amplicons), total number of reads, and per amplicon attributes of GC proportion, and length of the amplicon insert. In practice, we observe other variability that does not associate with known attributes yet is systematic. The method that is used by the software to identify copy number variations is based on many diverse samples, captures systematic effects, and encodes the samples into a file that comprises the baseline.

You can create a Variability Correction Information Baseline (VCIB) baseline to detect copy number variation in samples. To try to get improved results with a baseline, you can create a custom baseline that uses your samples, or you can augment an existing baseline, with samples. The VCIB baseline must include a minimum of 48 samples, and at least 6 of the samples must be normal.

When a baseline is augmented with samples, new samples are run, the size of each systematic effect that is encoded in the baseline is estimated, and a correction is applied to remove the effect. The added samples must be diverse to capture likely systematic variation. The samples do not need to be normal.

To use a VCIB baseline that is included in Ion Reporter™ Software, you can select the baseline preset when you create an analysis workflow. For more information, see Apply a copy number baseline workflow preset to an analysis workflow.