Archer® Analysis tool: CNV Visualization in v5.1

By Kiri Burrow, Ph.D. on Tue Sep 12, 2017

CNV visualization tool highlights:

  • Dynamic and interactive
  • Customizable sensitivity settings
  • Identify copy gains and losses with exon-level resolution
  • Quickly export images and PDF reports
  • Track reported CNVs within your own database

Archer® Analysis offers multiple tools to help you analyze your samples to the fullest extent. These tools enable you to accurately detect and characterize the following:

  • Gene fusions
  • Isoforms
  • Single-nucleotide polymorphisms (SNPs)
  • Insertions/deletions (indels)
  • Copy number variations (CNVs)
  • Internal tandem duplications (ITDs)
  • RNA expression patterns
  • Immune repertoire profiling

Here we highlight one of these analysis features: CNV visualization. Detecting CNVs for cancer genome analysis is essential, given the frequent occurrence of these aberrations during carcinogenesis. See the poster for more information on driver detection rate.

The CNV visualization tool is user friendly, dynamic and customizable to maximize your analytic capabilities. It was designed to not only determine relative copy number per locus but also sub-gene events in which partial gains and losses are detected with exon-level resolution.

The CNV visualization tool is accessed from the Sample Details page by selecting a sample and clicking on the CNV link in the upper left-hand corner.

From the Sample Details page, click on CNV in the upper left-hand corner to acces the tool.

CNV visualization plot features:

  • All CNVs in your sample are arranged by chromosome on the X-axis and relative copy number on the Y-axis
  • Each dot represents a gene-specific primer 2 (GSP2), color-coded by gene
  • Each gene is listed to the right of the plot
  • Click on a gene-of-interest to see only CNVs located on that gene
  • Hover the cursor over any data point for more information, including the relative copy number, Z-score, gene and primer(s) from which it originated
  • A global scope of the plot is located below the X-axis with toggle bars situated on either side for zooming in or out
Dynamic and interactive CNV plot

Signal vs Noise

The CNV visualization tool allows users to determine the sensitivity based on assay requirements. In the CNV plot screenshot, both the purple- and orange-highlighted genes passed the threshold for strong evidence of copy number gains. By default, if a gene has three or more adjacent primers indicating a CNV with a p-value ≤0.01, it is determined there is strong evidence for a copy number gain or loss. The analysis tool aggregates those data points to generate the copy number score. The default settings are based on typical sensitivity versus specificity requirements for analyzing FFPE samples; however, these setting can be easily adjusted based on the needs of a particular assay. For example, a user may want to increase the sensitivity settings when working with ctDNA samples.


A user may also want to adjust the sensitivity settings based on how results will be normalized. If tumor samples are run in pairs with normal controls, a high threshold may not be necessary. However, if less-sensitive controls are in place, such as a Genome in a Bottle (NIST) or simply a large batch of tumor samples to be normalized against each other, more stringent thresholds may be required.

CNV visualization table

Directly below the CNV plot is a table containing a detailed report of your CNV results. The default fields are those determined to be of interest to any user; however, these fields can be personalized and saved for future analyses.

  • By clicking on the “Edit Columns” button, fields can be rearranged, added and/or deleted from the table
  • Drag and drop columns to change the table
  • Hover the cursor over a specific field or abbreviation for an information box
  • Results can be filtered by field and/or value by clicking on the drop-down menu next to the default filters
  • Create your own customized filters
  • Any number of unique filter sets can be created, named and saved for future analyses
  • To quickly filter by a specific field, click on the filter icon within that column
  • Easily export your data set as a CSV file
  • Create a CNV report (more information below)
  • Make and read comments about each sample and track its history
  • If you suspected the data point was a technical artifact, you can mark it as such
Personalize the CNV table and easily create reports and export data

Notable fields

Report: By checking the box under the “Report” column, the row becomes highlighted in green (see the two genes listed in the CNV table screenshot) and can be included in the CNV report (more information below). This CNV mutation will also be annotated on the sample summary page, allowing the user to see all relevant information about a given sample in one place.

Rept: This is the total number of times a CNV has been reported for a given gene within the system. Any time “Report” is marked by a user, this number will increment. This allows for any user to collect knowledge about a CNV and have confidence when making calls. This number can also be found on the CNV report (see below for more information on CNV reports).

Tier: This field further categorizes a CNV by allowing a user to note why a particular CNV was reported. This four-tiered system is in accordance with The Association for Molecular Pathology (AMP) guidelines for standardizing the interpretation and reporting of sequence variants in cancer:

  • Tier I = pathogenic
  • Tier II = likely pathogenic
  • Tier III = unknown
  • Tier IV = benign or likely benign

CNV report

Another element of the CNV visualization tool is the CNV report. A CNV report includes the overall sample frequency and provides a list of all samples in which it was reported. If a sample originated from another user’s library, the URL will not be available for privacy reasons; however, the copy number score will be listed. To generate a CNV report, click on the action icon next to the gene of interest.

CNV report


The CNV visualization tool within Archer Analysis was designed to maximize analytical capabilities for a variety of NGS library preparations. By giving the user the ability to customize the sensitivity settings based on assay and normalization requirements, copy number gains and losses, in addition to novel variants, can be detected with exon-level resolution and effortlessly tracked within the database.

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About Kiri Burrow, Ph.D.

Kiri earned her Ph.D. in Behavioral Genetics and Neuroscience from the University of Colorado at Boulder. Her research involved identifying novel genetic mutations associated with addictive behaviors. Her interest in cancer genomics led her to join the ArcherDX team in May, 2017. In her free time, Kiri enjoys hiking with her dog, Frankie, and spending time with her family.

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