Search for SNP probes

An SNP probe search returns Agilent SNP probes from the eArray probe database, and is only available for the CGH application type. See What is a SNP probe search. These types of SNP probe searches are available:

Entire Agilent SNP Probe Set Search
Genomic Interval Search
Probe ID Search
SNP ID Search

Agilent Probe Set Search

This type of SNP probe search returns Agilent SNP probes from across the genome. You can filter this probe set in several ways, as described in Probe Options in the table of search parameters in step 5 below.

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. Entire Agilent SNP Probe Set Search is the default type of SNP probe search in eArray.
Enter the following parameters. Some parameters are read-only and do not require you to enter any information.

Parameter	Instructions/Details
Job Information
Search Name	Type a name for the SNP probe search job. The program uses this name to identify the job, and to identify the search results when they are available.
Species	Select the desired species. The search returns Agilent SNP probes only for the selected species. Currently, eArray supports human SNP probes.
Build Number	(Read-only) The genome build of the selected species to which SNP probes are designed.
SNP Version Number	(Read-only) The version of the SNP database for the selected species to which SNP probes are designed.
Probe Options
Use Only One Probe per SNP	(Optional) Most SNPs are represented by two probes, one for each DNA strand. To return only the best probe for each SNP, mark this option. To select the best probe, the search selects the probe with the higher empirically-determined probe score. This probe score reflects the likelihood that a 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.
Minimum MAF value	Type the desired value in the box. The minimum MAF can be a value from 0 to 50. The search returns probes for SNP sites whose MAFs are at least the entered value. To return probes without regard to MAF, enter a value of 0. The MAF (minor allele frequency) is the percentage of the total alleles in the population for a given SNP site that are the less common allele. Because the minor allele is present in the population, the MAF is always greater than 0%. Also, because the minor allele is the less common allele, the MAF is less than 50%.
Remove doubly cut SNPs from selected reference samples	When you use Agilent Genomic Workbench to analyze CGH+SNP array data, the program excludes data from SNP sites in which all of the alleles in the reference sample are cut by the Alu I/Rsa I enzyme mixture during the sample preparation process. These data are excluded because “cut” alleles generate essentially no signal, and the reported log ratio value [log (sample/reference)] would involve division by a very small number. This would cause an extremely high, spurious log ratio value to be reported. This option lets you exclude the SNP probes from your design that are associated with these "doubly cut” reference SNP sites. The data from these probes would be excluded from the analysis anyway. eArray currently supports five HapMap reference samples. By default, the program selects all five references, which excludes such probes that are found in any of the references. However, you have other options: If you intend to use a custom genotyped reference when you analyze the CGH+SNP microarray data, clear the check box. This returns probes without regard to their association with doubly cut SNP sites in the standard HapMap references. To select a single reference, keep the check box marked, then click the name of the desired reference. After you select a single reference, to select additional reference(s), control-click their names. Note: If you mark the check box, you must select at least one reference sample.
Interval Options
Select SNP Probes by	Keep this parameter set to Entire Agilent SNP Probe Set Search. The other options select different types of SNP probe searches.

Click Search.

eArray creates an SNP Probe Search job. A job with the search name that you entered 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. See What can be done with SNP probe search results.

Genomic Interval Search

This type of SNP probe search returns Agilent SNP probes that are associated with genomic intervals that you enter or upload. You can extend the entered genomic regions to capture additional probes that lie immediately outside the regions that you enter. You can also exclude standard or custom sets of intervals from the search. In addition, you can filter the returned set of probes based on several criteria. See the table of search parameters.

You can type the desired genomic intervals and exclusion intervals on the search page. However, if you have many intervals to enter, it can be easier to upload lists of Genomic Intervals or Custom Exclusion Intervals. Prepare these files before you begin the search. Create plain text files with an extension of *.txt, and put one interval on each line. Do not include headers.

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. Some parameters are read-only and do not require you to enter any information.

Parameter	Instructions/Details
Job Information
Search Name	Type a name for the SNP probe search job. The program uses this name to identify the job, and to identify the search results when they are available.
Species	Select the desired species. The search returns Agilent SNP probes only for the selected species. Currently, eArray supports human SNP probes.
Build Number	(Read-only) The genome build of the selected species to which SNP probes are designed.
SNP Version Number	(Read-only) The version of the SNP database for the selected species to which SNP probes are designed.
Probe Options
Filters	Select one of these options: Total Probes – Type the desired number of probes in the box that appears. This limits the total number of probes that the SNP probe search collectively returns for all specified genomic intervals. Example: If you type 2000 in Filter Value, the search returns the 2,000 best SNP probes that match the other search criteria. 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. Total SNPs – Type the desired number of SNPs in the box that appears. This limits the total number of SNP sites that the search considers. Example: If you type 2000 in Filter Value, the search considers only the 2,000 best SNP sites, and returns the SNP probes that are associated with those sites. To find the best SNP sites, the search considers the empirically-determined scores for the corresponding SNP probes. A probe score reflects the likelihood that a 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. No Filter – No limit is applied, either to the total number of returned SNP probes or to the number of SNPs that are considered by the search.
Use Only One Probe per SNP	(Optional) Most SNPs are represented by two probes, one for each DNA strand. To return only the best probe for each SNP, mark this option. To select the best probe, the search selects the probe with the higher empirically-determined probe score. This probe score reflects the likelihood that a 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.
Minimum MAF value	Type the desired value in the box. The minimum MAF can be a value from 0 to 50. The search returns probes for SNP sites whose MAFs are at least the entered value. To return probes without regard to MAF, enter a value of 0. The MAF (minor allele frequency) is the percentage of the total alleles in the population for a given SNP site that are the less common allele. Because the minor allele is present in the population, the MAF is always greater than 0%. Also, because the minor allele is the less common allele, the MAF is less than 50%.
Remove doubly cut SNPs from selected reference samples	When you use Agilent Genomic Workbench to analyze CGH+SNP array data, the program excludes data from SNP sites in which all of the alleles in the reference sample are cut by the Alu I/Rsa I enzyme mixture during the sample preparation process. These data are excluded because “cut” alleles generate essentially no signal, and the reported log ratio value [log (sample/reference)] would involve division by a very small number. This would cause an extremely high, spurious log ratio value to be reported. This option lets you exclude the SNP probes from your design that are associated with these "doubly cut” reference SNP sites. The data from these probes would be excluded from the analysis anyway. eArray currently supports five HapMap reference samples. By default, the program selects all five references, which excludes such probes that are found in any of the references. However, you have other options: If you intend to use a custom genotyped reference when you analyze the CGH+SNP microarray data, clear the check box. This returns probes without regard to their association with doubly cut SNP sites in the standard HapMap references. To select a single reference, keep the check box marked, then click the name of the desired reference. After you select a single reference, to select additional reference(s), control-click their names. Note: If you mark the check box, you must select at least one reference sample.
Interval Options
Select SNP Probes by	Keep this parameter set to Genomic Interval Search. The other options select different types of SNP probe searches.
Extended Interval Boundary	Type the number of 5' base pairs and 3' base pairs by which you want to move out the start and end points of all of your genomic intervals. This can help retrieve additional probes that lie outside your initially defined regions. For example, if you type 500 in 5' base pairs and 300 in 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300.
Genomic Intervals	(Required) Type either a chromosomal region or a cytoband in the box. You can enter multiple intervals separated by pipe "\|" characters, but all of the intervals must be of the same type. See Genomic interval formats. To upload a file of chromosomal locations or cytobands, click Upload. See Upload data for probe searches.
Standard Exclusion Interval	Currently, Agilent provides a set of standard exclusion intervals, based on known human copy number variation (CNV) regions. To ignore these genomic regions in the search, mark this option. CNV is selected by default in the box that appears. During a SNP probe search, no probes are returned for these regions.
Custom Exclusion Interval	To ignore particular genomic intervals in the search, mark this option, then type the desired intervals in the box. Separate multiple entries with pipe "\|" characters. During a SNP probe search, no probes are returned for these regions. To ignore the genomic intervals that are defined in a file of genomic intervals, click Upload Interval File. See Upload data for probe searches.

Click Search.

eArray creates a SNP Probe Search job. A job with the search name that you entered 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. See What can be done with SNP probe search results.

Probe ID Search

This type of SNP probe search returns Agilent SNP probes that have the exact probe IDs that you enter or upload. This type of search is best when you have a well-defined list of Agilent SNP probes that you want to include on an array. For example, if you have a list of Agilent SNP probes from an existing probe group or design, and you edit the list offline based on one or more criteria, use a Probe ID search to retrieve the probes in your edited list, and create a new probe group with them.

You can enter the desired probe IDs on the search page. However, if you have many IDs to enter, it can be easier to upload a list. Before you begin the search, create a plain text file with an extension of *.txt, and put one probe ID on each line. End each line with a new line (return) character. Do not use pipe "|" characters to separate entries, and do not include headers.

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 Using, select Probe ID Search.

A new search page appears
Enter the following parameters.

Parameter	Instructions/Details
Search Name	Type a name for the SNP probe search job. The program uses this name to identify the job, and to identify the search results when they are available.
Select SNP Probes by	Keep this parameter set to Probe ID Search. The other options select different types of SNP probe searches.
Probe ID	In the box, type the probe ID(s) of the desired Agilent SNP probe(s). Use pipe "\|" characters to separate multiple entries. eArray returns the Agilent SNP probes whose IDs are an exact match with your entries. Example: A_20_P00100032\|A_20_P00100039\|A_20_P00100046 If you prepared a file of probe IDs, you can upload it here. To upload the file, click Upload. See Upload data for probe searches. The uploaded IDs appear in the box.
Species	Select the desired species. The search returns Agilent SNP probes only for the selected species. Currently, eArray supports human SNP probes.

Click Search.

eArray creates an SNP Probe Search job. A job with the search name that you entered 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 you an e-mail when the search is complete. When the status of the job is Complete, you can view and take action on the results. See What can be done with SNP probe search results.

SNP ID Search

This type of SNP probe search returns Agilent SNP probes that are associated with the SNPs whose IDs you enter or upload. You can limit the returned probes in several ways, as described in Probe Options in the table of search parameters below in Step 6.

You can type the desired SNP IDs on the search page. However, if you have many IDs to enter, it can be easier to upload a list. Prepare the file before you begin the search. Create a plain text file with an extension of *.txt, and put one ID on each line. End each line with a new line (return) character. Do not use pipe "|" characters to separate entries, and do not include headers.

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 Using, select SNP ID Search.

A new search page appears
Enter the following parameters. Some parameters are read-only and do not require you to enter any information.

Parameter	Instructions/Details
Job Information
Search Name	Type a name for the SNP probe search job. The program uses this name to identify the job, and to identify the search results when they are available.
Species	Select the desired species. The search returns Agilent SNP probes only for the selected species. Currently, eArray supports human SNP probes.
Build Number	(Read-only) The genome build of the selected species to which SNP probes are designed.
SNP Version Number	(Read-only) The version of the SNP database for the selected species to which SNP probes are designed.
Probe Options
Use Only One Probe per SNP	(Optional) Most SNPs are represented by two probes, one for each DNA strand. To return only the best probe for each SNP, mark this option. To select the best probe, the search selects the probe with the higher empirically-determined probe score. This probe score reflects the likelihood that a 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.
Minimum MAF value	Type the desired value in the box. The minimum MAF can be a value from 0 to 50. The search returns probes for SNP sites whose MAFs are at least the entered value. To return probes without regard to MAF, enter a value of 0. The MAF (minor allele frequency) is the percentage of the total alleles in the population for a given SNP site that are the less common allele. Because the minor allele is present in the population, the MAF is always greater than 0%. Also, because the minor allele is the less common allele, the MAF is less than 50%.
Remove doubly cut SNPs from selected reference samples	When you use Agilent Genomic Workbench to analyze CGH+SNP array data, the program excludes data from SNP sites in which all of the alleles in the reference sample are cut by the Alu I/Rsa I enzyme mixture during the sample preparation process. These data are excluded because “cut” alleles generate essentially no signal, and the reported log ratio value [log (sample/reference)] would involve division by a very small number. This would cause an extremely high, spurious log ratio value to be reported. This option lets you exclude the SNP probes from your design that are associated with these "doubly cut” reference SNP sites. The data from these probes would be excluded from the analysis anyway. eArray currently supports five HapMap reference samples. By default, the program selects all five references, which excludes such probes that are found in any of the references. However, you have other options: If you intend to use a custom genotyped reference when you analyze the CGH+SNP microarray data, clear the check box. This returns probes without regard to their association with doubly cut SNP sites in the standard HapMap references. To select a single reference, keep the check box marked, then click the name of the desired reference. After you select a single reference, to select additional reference(s), control-click their names. Note: If you mark the check box, you must select at least one reference sample.
Interval Options
Select SNP Probes Using	Keep this parameter set to SNP ID Search. The other options select different types of SNP probe searches.
SNP ID	Type a SNP ID, or multiple IDs separated by pipe "\|" characters. Example: rs7172939\|re6549950\|rs4490399 If you prepared a file of SNP IDs, you can upload it here. To upload the file, click Upload. See Upload data for probe searches.

Click Search.

eArray creates an SNP Probe Search job. A job with the search name that you entered 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 sends you an e-mail when the search is complete. When the status of the job is Complete, you can view and take action on the results. See What can be done with SNP probe search results.