SureSelect Cancer CGP wizard:

Add/Review Content

The Add/Review Content step consists of a series of selections that allow you to add content (i.e. probes organized into probegroups) to your design, define certain parameters, and review the content of the design. The advanced wizard lets you repeat the Add/Review Content step multiple times to continue adding more content to the design.

Each time you begin this step, you must first select a method for adding content. The SureSelect Cancer CGP wizard offers several methods for adding content, which are described in detail below.

Select Add Content Method

Select the method you want to use for adding probes to your design:

·        Select Targets from Pre-defined Cancer Genes - This method allows you to select from a pre-set list of cancer-related genes. For each gene you select, the wizard then prompts you to select which types of variants you want to be able to detect in your sequencing assays. After you make your selections, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add/Review Content > Pre-defined Cancer Genes for instructions.

·        Enter Custom Targets/Regions - This method allows you to select the desired target genes or genomic regions for each type of variant (SNV/indel, copy number variant, and translocation). After you make your selections, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add/Review Content > Custom Targets/Regions for instructions.

·        Include genome-wide backbone - Select this option to add a 100-kb probegroup to the design. This probegroup adds a probe approximately every 3 Mb across the genome. Inclusion of this backbone probegroup is not required for SureSelect Cancer CGP protocols. To add this probegroup to the Probegroup Summary table, select the option and click Next. The name of the probegroup is Agilent CGP CNV Backbone 100Kb. Note that the backbone probegroup does not contribute to the exonic content needed for TMB calculation.

·        Select probes from an existing Design or Probegroup - This method allows you to add probes by selecting an existing SureSelect Cancer CGP probegroup or design and then selecting probes from that design/probegroup to include in the new design. If you choose this method, you must include all the probes in the selected design or probegroup. See Add/Review Content > Select Existing Probes for instructions.

OR

·        Finalize this Design - This option only appears if you have already added at least one probegroup to the design. When you are finished adding probes to the design, and are satisfied with the probegroups in the Probegroup Summary, select this option to exit the Add/Review Content step and proceed to finalizing the design.

Once you have made a selection, click Next to continue.

Possible warning messages when finalizing a design

·        If TMB Calculation was marked on the Define Design screen, SureDesign checks if the design covers at least 1 Mb of exonic content and displays a warning message if the exonic content is insufficient.

·        If the genome-wide backbone probegroup (Agilent CGP CNV Backbone 100Kb) is included in the design, SureDesign checks if the design covers any CNV targets and displays a warning message if no CNV targets are found.

Probegroup Summary

This table only appears if you have already added at least one probegroup to the design.

The Probegroup Summary table displays the probegroups that are currently included in the design.

 NOTE  If you marked the MSI Detection check box on the Define Design screen, then the Probegroup Summary table automatically includes the Agilent MSI Probegroup. This probegroup contains probes to capture MSI sites.

The columns of the Probegroup Summary are described in the table below.