Example of an HD probe search

This example shows you how to set up and submit one type of probe search for high density CGH probes. For general information and instructions on how to do HD probe searches, see What is a High Density (HD) Search?, and Perform a High Density (HD) Search.

In this specific example, you set up a search for HD probes that are associated with several breast cancer-related genes in the human genome. Further, you wish to retrieve a maximum of 500 probes for these genes and make sure that the probes do not have significant cross-hybridization problems with secondary sites in the genome.

Click the Workspace tab (or enter a collaboration).
Set the application type to CGH.
In the Probe tab, select HD Probe Search.

The HD Probe Search pane appears. Standard HD probe search is selected by default.
In Select HD Search by, select Gene Annotations.
Set the following search parameters.

Parameter	Instructions/Details
Job Information
Search Name	Type Breast Cancer
Species	Select H. sapiens Information about the current human genome build appears in Build Number.
Probe Options
Filters	Select Total Probes, then type 500 in the box that appears. This parameter sets the search to return a total of 500 probes.
Prefer Catalog Probes	Keep this option marked. This gives preference to Agilent catalog probes in the probe selection process if two probes are close to each other for a given probe interval.
Use TM Filter	For HD-CGH Searches, the program always applies this filter for genomic intervals searches.
Similarity Filter	Select Similarity Score Filter. This filter filters out all probes with secondary genomic alignments that could potentially impact probe performance.
Interval Options
Select HD Search by	Keep this parameter set to Gene Annotations.
Extended Interval Boundary	Leave both 5' Base Pairs and 3' Base Pairs set to 0.
Gene Annotations	Type BRCA1\|BRCA2\|ATM\|P53\|P65 These are the breast cancer-related genes for which you want to find HD probes. Be sure to separate the gene names with pipe "\|" characters as shown. eArray resolves these gene names to genomic intervals before it starts your search.
Include Regions	Leave All selected.
Standard Exclusion Interval	Leave this option cleared.
Custom Exclusion Interval	Leave this option cleared.

Click Search.

eArray begins the HD search. A message tells you that your search has been submitted.
Click OK.

The HD Probe Search page displays your HD search in the Search Results pane at the bottom of the page with a status of Not Started. As eArray performs your HD search, the status of the search changes to Searching, and then to Complete. Click Refresh to view the current status. In the Job Position column, you can track the position of the HD probe search job in the queue. eArray sends you an e-mail when it finishes your search.

When the status of the search is Complete, you can take several actions from the search results pane:
- View the results of the search – In the Actions column, next to the desired search, click View. See View the High Density (HD) search results. When you view the results, you can also download them and create a probe group with them.
- Delete the search – In the Actions column, next to the desired search, click Delete. See Delete HD probe search job.
- View the search criteria for the search – In the Actions column, next to the desired search, click Search Criteria. See View the search criteria for HD searches.