The functionality described in this topic is only available when you mark Show Advanced Options.

CGH advanced wizard:

Add/Review Content

Once you have completed the CGH advanced wizard: Define Design step, you will be directed to the Add/Review Content step. Repeat the Add/Review Content step multiple times to continue adding more content to your design.

Select a method to add content to your design. The method options are:

·        Select Probes from Agilent High Definition Database - Use Agilent's high definition (HD) probe database to locate the probes for your design. The options are:

·        Select probes for specific genes or regions - Add probes by defining targets that you want to cover. See Add/Review Content > Select probes from Agilent HD Database for instructions.

·        Select probes by Probe ID - Add probes by listing the Probe IDs for the desired probes. See Add/Review Content > Select probes from HD database > Select probes by Probe ID.

·        Select Probes from SNP - Select probes from the selected SNP probe database that cover your specified chromosomes of interest. This method is only available if you selected CGH+SNP as the Application on the Define Design step of the wizard.

·        Select probes from an existing Design or Probegroup - Add probes by selecting a subset of probes from an existing probegroup or design (custom or catalog) to include in the new design. You must specify if want to select the subset of specific probes from the existing design/probegroup. The options are:

·        Select all probes - to select all the probes in the selected design or probegroup. See Add/Review Content > Select Probe Source.

·        Select probes by Probe ID - to select probes from the selected design or probegroup that cover specific Probe IDs. See Add/Review Content > Select Existing Probes > Select Probe Source.

·        Select probes for specific genes or regions - to add probes from the selected design or probegroup by defining targets that you want to cover. See Add/Review Content > Select Existing Probes > Select probes for specific genes or regions.

·        Upload probes - This method allows you to upload probes that you designed with your own algorithms. See Add/Review Content > Upload Probes for instructions.

·        Design new probes by tiling genes or regions - This method follows the same workflow as that used in the standard design wizard, but with some additional probe selection parameters. After you define the targets and set the parameters, 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 > Tile Genes or Regions for instructions.

·        Fill with Genome-Wide Backbone - This option fills the remaining capacity on the array with the probes from the Genome-Wide Backbone. SureDesign creates a backbone probegroup containing the probes.

To use the Fill with Genome-Wide Backbone option:

1. Select Fill with Genome-Wide Backbone, then click Next to submit the probe selection job.
   A warning message opens to notify you that you cannot add, remove, or modify the contents of the design after creation of the backbone probegroup unless you first remove the backbone probegroup from the design. Note that at least 5% of the available features must be available in order to use the Fill with Genome-Wide Backbone option.

2. Click Continue in the warning message.
   Another message box opens. This message box indicates the e-mail address where Agilent will contact you when the probe selection job is complete. If desired, you can enter additional e-mail addresses into the provided field.

3. Click OK in the message box to submit the probegroup to SureDesign.
   Your submission is placed in the SureDesign job queue to await probe selection. The new probegroup for the backbone probes appears in the Probegroup Summary table. The # Targets column of the table lists Processing until the probe selection job is complete. Click the refresh icon to see updates to this column. You receive an e-mail from Agilent SureDesign notifying you when your job is complete. In order to finalize the design, you must wait until your probe selection job is complete.

·        Finalize this Design - This option only appears if you already have at least one probegroup in the design, or have a probegroup in processing status. 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.

Select the method you want to use for adding probes to your design, and click Next to continue.

When you select Finalize this Design and click Next, SureDesign performs a check of the design and opens a warning message if it identifies any issues with the design. Agilent recommends addressing these issues before finalizing a design.

Probegroup Summary

This table only appears if the design contains at least one probegroup, or has a probegroup in processing status.

The Probegroup Summary table displays the probegroups that are currently included in the design. You can adjust the replication number of each probegroup or remove probegroups from the design. For probegroups added from the High Definition Database or from tiling, you can modify the probes in the probegroup by redoing the probe selection process.

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