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CNV Detection by Ion Semiconductor Sequencing application note

Copy number variation

Copy number variations (CNVs) represent of class of variation in which segments of the genome can be duplicated (gains) or deleted (losses). Research of inherited de novo CNVs (up to ~10 Mb) have been associated with many disease conditions, including cancer, and inherited disorders.

Why copy number matters

CNVs can lead to a variety of phenotypic impacts: deletions can unmask recessive mutations, duplications and deletions can alter the copy number of dosage-sensitive genes, deletions can result in position effects that alter the expression or regulation of genes, and selection of duplicated regions containing gain-of-function driver mutations can occur in cancer.

Inherited and de novo CNVs of chromosomal regions have been associated with many debilitating diseases, including birth defects and cancer, and have been associated with hemizygous or homozygous gains or losses of chromosomal material.

Single workflow for the detection of CNVs

There are multiple default research workflows in Ion Reporter Software for single samples or paired samples when using Ion AmpliSeq gene panels that simultaneously detect copy number variation, SNPs, and indels in a single run. The workflows are easily customizable and have 3 sensitivity settings to allow flexibility in experimental design. All use a Hidden Markov Model (HMM) algorithm for copy number detection.

Copy Number Variants can be now be detected using ready-to-use and custom Ion AmpliSeq panels and the Ion Reporter Software.

Examples of custom and ready-to-use panels:

To browse complete list of ready-to-use panels, or to place an order:

1. Visit Ion AmpliSeq Designer at ampliseq.com and sign in. If you do not have an account, follow the registration process to create a new account.
2. After signing in, go to "Fixed Panels" located in the top navigation to find your panel of interest.

View the AmpliSeq CNV application note.

To design a custom Ion AmpliSeq DNA panels which will robustly detect CNVs, visit Ion AmpliSeq Designer and select the Made-to-Order Panel design workflow.

1Design custom panel

Ion AmpliSeq Designer

2Run sequence

Ion Torrent NGS sequencers

3Analyze data

Ion Reporter Software


Single, paired, or tumor/normal samples


Copy number


Interpretive report

Figure 2. An easy-to-implement, cost-effective, scalable targeted DNA sequencing workflow for the Ion PGM System, with a rapid workflow from library to variant-called results. Following library construction, using the Ion AmpliSeq Library Kit, template preparation and 200-base sequencing runs using the Ion 314 or Ion 318 Chip. Primary data analysis is performed using Torrent Suite software, and SNP, indel, and CNV polymorphisms are determined using Ion Reporter Software.




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For Research Use Only. Not for use in diagnostic procedures.