Example of a SNP probe search

This topic gives an example of a SNP probe search by genomic interval. For general instructions on all types of SNP probe searches in eArray, see Search for SNP Probes.

In this example, you use a SNP probe search to retrieve Agilent SNP probes that are designed to several genomic intervals in the human genome. This search would be useful if you already have a CGH probe group with probes that are designed to the same intervals, and you want to create the corresponding SNP probe group. You could then combine these two probe groups in a CGH+SNP microarray design.

Further, in this search, you limit the results to the best 3,000 SNP probes that match the search criteria, and you also exclude any regions of known copy number variation (CNV) from the search.

Click the Workspace tab, or enter a collaboration.
Set the application type to CGH.
Click the Probe tab.

A search page appears.
At the top of the page, select SNP Probe Search.

The SNP Probe Search page appears.
In Select SNP Probes by, select Genomic Interval Search.

A new search page appears
Enter the following parameters. Leave all other parameters as they are.

Parameter	Instructions/Details
Job Information
Search Name	Type Example Search Later, you will identify the probe search results by this name.
Species	Select H. sapiens.
Probe Options
Filters	Select Total Probes, then type 3000 in the box that appears. This limits the total number of probes that the SNP probe search collectively returns for all specified genomic intervals to the 3,000 best available SNP probes. To find the best probes, the search considers empirically-determined probe scores. These scores reflect the likelihood that each given probe will produce a good log ratio response when it is used on the Agilent CGH+SNP platform. SNP probe scores are not available for download.
Interval Options
Select SNP Probes by	Keep this parameter set to Genomic Interval Search. The other options select different types of SNP probe searches.
Genomic Intervals	Type this text in the box: chr1:1-100000000\|chr2:1-80000000\|chr3:1-50000000 These are the genomic intervals for which probes will be retrieved.
Standard Exclusion Interval	Mark this option. CNV is selected by default in the box that appears. This excludes regions of copy number variation from the search.

Click Search.

eArray creates a SNP Probe Search job with the name Example Search. A job with this name appears in the Search Results pane at the bottom of the page. The current status of the job appears in the Status column. eArray does not automatically update the list of jobs. To update the list of jobs, click Refresh. eArray also sends an e-mail that tells you that the search is complete. When the status of the job is Complete, you can view and take action on the results.
In the Actions column in the Search Results pane, in the row of Example Search, click View.

The SNP search results appear in a new window in three separate tabs. For details, see View SNP probe search results.

From these results, you can create a SNP probe group, download the search results as a BED format file, and other tasks.