FGSR Targeted Genotyping Services
Affymetrix Targeted Genotyping arrays provide a more focused approach to large-scale genotyping. These arrays contain between 3,000 and 20,000 SNPs that have been chosen to be biologically meaningful. There are several options available:
- Human 10K cSNP: Contains a large variety of validated public SNPs that code for functional changes (Data Sheet)
- Human 20K cSNP: Contains an additional 10,000 validated SNPs that code for functional changes (Data Sheet)
- Mouse Mapping 5K SNP: Designed to contain 1500 meaningful SNPs for every cross of 20 of the most common strains of mice (Data Sheet)
- Human Immune and Inflammation 9K SNP: Contains markers for 1,000 genes that are thought to be involved in the inflammation response and related to the genetics of immunobiology
- Custom SNP Kits: Can contain between 3,000 and 20,000 SNPs of your choosing. As your experiments progress, you can add additional SNPS (1,000 at a time to a total of 20,000). Contact Affymetrix to begin the customization process
The raw image of a TG array. Image courtesy Affymetrix
Targeted Genotyping Software
As with all Affymetrix data, your starting point for software will be the Gene Chip Operating Software, or GCOS. This software will allow you to import, organize, and view your data, and is required for any other Affymetrix analysis software. You can download GCOS from Affymetrix. Please be aware that this software is Windows-only, and will require Administrator access to install
To view and analyze Targeted Genotyping data, you must install the GeneChip Targeted Genotyping Analysis Software, or GTGS. This software will allow you to perform the actual genotyping as well as view quality control metrics for your data. You can download GTGS from Affymetrix.
Targeted Genotyping Data
The FGSR will provide the raw data to your experiment in an archive called a DTT. This archive can be imported into your copy of GCOS using the Affymetrix Data Transfer Tool (included with GCOS 1.4, or available from Affymetrix). Data produced before 2006 was exported in CAB format, which can be imported with the same tool. Before you can import data for an array, you must install the Library file for that array.
If you have a large amount of data, your DTT may be broken into several pieces with extensions like DTT, D02, D03, etc. You must have all of the files for a single set in order to read any of the data in them. If you do not have GCOS, you can still extract the individual files in these archives. First, you must rename the files. If you have only a DTT file, rename it to .ZIP. If you have several files for a single archive, rename the last file to .ZIP. That is, if you have three files in your set, rename .D03 to .ZIP. Then proceed through the remaining files - .DTT should become .Z01, .D02 should become .Z02, and so on until you have renamed all of the files. You can now open the .ZIP file with any compressed file software, and you should see the following eight files for each sample:
- samplenamechannel.DAT: The raw image of the microarray for each of the four channels (one per nucleotide)
- samplenamechannel.CEL: The probe-level data for the array for each channel. These are the files most commonly used as "raw data" by analysis packages
In addition to providing the DTT file, the FGSR will provide the Sample Plate File and Assay Panel File. These files will need to be imported into GTGS in order to perform any analysis, see the GTGS User Guide for details.
The FGSR will also provide the genotype calls made by GTGS. These will be in a tab-delimited text file that can be easily opened in Excel.
