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:
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.
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.Normalization
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.
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.Features:
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:
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.
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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