Ion Reporter™ Software Copy Number Variation Analysis
See changes in both gene sequence and gene abundance
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). Inherited de novo CNVs (up to ~10 Mb) have been associated with many disease research conditions, including cancer research, and inherited disorders research.
Why copy number matters
CNVs 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 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.
- Ion AmpliSeq™ Exome Panel
- Ion AmpliSeq™ Cancer Hotspot v2 Panel
- Ion AmpliSeq™ Comprehensive Cancer Panel
- Ion AmpliSeq™ Inherited Disease Panel
- Ion AmpliSeq™ Colon and Lung Cancer Panel
View the AmpliSeq™ CNV application note.
For designing custom AmpliSeq™ DNA panels, which will robustly detect CNVs, please see the AmpliSeq.com website, under the "My Designs" tab.
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.
Ordering information for Ion Reporter™ Server and Software
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For Research Use Only. Not for use in diagnostic procedures.