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

CGH advanced wizard:

Add/Review Content

Select Probes from SNP

 

This option is only available if you selected CGH+SNP as the Application on the Define Design step of the wizard.

Once you have chosen Select Probes from SNP from the CGH advanced wizard: Add/Review Content  step, you will be directed to the following Define Targets step. Complete the fields and selections on this screen to define the desired genes or genomic regions that you want covered in the design. When you submit the probe selection job, SureDesign searches the probes in the selected SNP probe database to locate the ones that cover your specified chromosomes of interest.

Follow the steps below to define your targets.

  1. In the SNP Probes drop-down list, select the probegroup that you want SureDesign to use to as the probe source of SNP probes for the design. These are Agilent-designed probes that are evenly spaced across the genome. The options are:

·        Genomic_SNP_100k - contains 100,000 SNP probes; available for array formats  2 x 400 K and 1 x 1 M

·        Genomic_SNP_60k - contains 60,000 SNP probes; available for array formats 1 x 1 M, 2 x 400 and 4 x 180 K

·        Genomic_SNP_30k - contains 30,000 SNP probes; available for array formats 8 x 60 K and 4 x 180 K

·        Genomic_SNP_15k - contains 15,000 SNP probes; available for array format 8 x 60 K

  1. In the Probegroup Name field, type a name for the probegroup that will be created from the probe selection job.

  2. Select check boxes to indicate chromosomes you want included in the SNP probe selection. Click Select All to mark the check boxes for all chromosomes, or Deselect All to clear all check boxes.

 

To submit the design for probe selection:

  1. Click Begin Probe Selection.

    A message box opens indicating 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.

  2. Click OK in the notification message to submit the design to SureDesign.

    Your submission is placed in the SureDesign job queue to await probe selection.

    The wizard takes you to the Add/Review_Content screen. The new probegroup 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.

    Agilent SureDesign will notify you by email when your job is complete. In order to finalize the design, you must wait until your probe selection job is complete.