CNV and aneuploidy detection

The CNV detection that is used in all predefined low-pass whole genome detection analysis workflows, including Ion ReproSeq™ analysis workflows for single-sample and two-sample Ion AmpliSeq™ panels, call copy number results down to the gene and subgene-level ploidy variants.

These predefined analysis workflows support chromosome and subchromosome-level aneuploidy detection down to submegabase resolution.

These low-pass whole genome detection aneuploidy detection analysis workflows that are intended for Pre-Implantation Genetic Testing (PGT) based on low-pass whole genome preparation contain a CNV detection module, and correct read coverage for GC bias. Corrected coverage is compared to a baseline coverage from control samples of regions with known expected normal ploidy. That is, 2 on autosomes and X in females, and 1 on sex chromosomes in males.

The following information applies to the predefined analysis workflows for CNV aneuploidy detection and custom analysis workflows that you create from the predefined analysis workflows:

• The input data are only a test research sample. A control research sample is not necessary, because a precomputed Informatics Baseline Control is used as a copy number reference.

• The input sample is from a whole genome amplified library.

• The volume of the sample can be small.

• The average coverage can be small, in the order of 0.01x.

• These analysis workflows identify regions of the genome that are duplicated or deleted. The variant length detectable is typically from ~10 Mb up to a whole chromosome.

• These analysis workflows overcome the variations in coverage that are typical with amplified data.

• With these analysis workflows, the coverage is typically too low to call SNPs or INDELs.