5. Import and Apply Marker Map

Genetic marker maps contain chromosome and position data for individual genetic data relative to some common coordinate system, as well as other annotation information for each genetic marker (if available). Most often marker map information is provided in a separate file than the genetic data. SVS allows you to either convert a text file with map information to a marker map file (*.dsm), download an Affymetrix annotation file using the integrated NetAffx service from Affymetrix, or download a marker map from Golden Helix’s data repository.

1. To access the marker map manager, from the Project Navigator, go to Tools > Manage Marker Maps.

   Click the Convert Text File button to convert a text file to a marker map. Figure 6 provides an example of a marker map text file.

   Once you choose the file you want to convert and click OK, the text marker map will be scanned and the Choose Columns to Use dialog will appear. Columns for the marker name, chromosome and position must be specified at minimum, although additional columns can be imported from the marker map as well. Clicking OK will convert the text marker map file into a *.dsm file for use in any project.

   

   Figure 6. Text marker map file opened in Excel

   See Convert Text File into Marker Map DSM Format for more information.

2. For Affymetrix customers, Affymetrix NetAffx™ provides array design and annotation information for its GeneChip™ array results. You can sign up for and use the NetAffx™ Analysis Center through Affymetrix’s website at http://www.affymetrix.com. SVS is able to communicate with NetAffx™ through a web service interface allowing you to download and update genetic marker map information mappable to Affymetrix data.

   Begin by clicking on the Download from Affymetrix NetAffx button in the Manage Marker Maps window. You will be prompted for your Affymetrix NetAffx login information.

   After entering your NetAffx login information, the Download Annotations window will appear listing the latest annotation files provided by Affymetrix.

   Note

   There are actually two annotation files for the 500K array – 250K_Nsp and 250K_Sty. Both need to be downloaded simultaneously for the program to properly merge them. To download both annotation files simultaneously, highlight the first annotation file and then Ctrl+click to highlight the second. Click Download.

   Data that is available through Affymetrix NetAffx™ is also available on the Golden Helix server, eliminating the need to go to more than one location to download maps for different arrays. To do this click on the Download from Golden Helix button in the Manage Marker Maps window.

   These files are quite large and may take a few minutes to download depending on the speed of your Internet connection. Once finished, you will be prompted to select the fields you want imported, in addition to the six defaults.

   See Download Affymetrix Annotation Files

3. The Golden Helix data repository contains marker maps for both Affymetrix and

   Illumina arrays as *.dsm files, ready to apply to a spreadsheet once downloaded. The annotation files in through the Affymetrix NetAffx™ site are only the latest version. If an older version or human genome build is required then these maps can be obtained from Golden Helix.

   Begin by clicking on the Download from Golden Helix button in the Manage Marker Maps window. Select one or more marker maps files to download. Once downloaded, the files will be saved to the Marker Maps folder and will be visible in the Marker Map file list in the Manage Marker Maps window.

   See Download from Golden Helix for more information.

4. Additional annotation data can be added to any marker map through a utility

   function available in the Manage Marker Maps window. For example, gene names from a gene annotation track, or sense/nonsense classifications from a SIFT track can be added to a marker map.

   To add annotation data to a marker map, click on the Utilities button in the Manage Marker Maps window and select Add Annotation Data to Marker Map. Choose the marker map to add the data to and the annotation track that contains the data you want to add. Clicking Next > will bring up a new dialog that lists fields from the annotation track. Select the field, the name for the field (if other than the default name) and the overlap conflict resolution. Click Next >. The new marker map will be created and saved in the marker maps folder.

   See Add Annotation Data to Marker Map for more information.

5. Next you will need to apply the marker map file you converted to your

   spreadsheet containing genetic data. Open your spreadsheet containing genetic information and go to File > Apply Genetic Marker Map. Select the map file you just converted.

   

   Figure 7. Marker mapped spreadsheet display map and annotation information about each marker

   Note

   SVS 7 allows you to apply a marker map to a spreadsheet with marker names as either column headers or row labels, such as an outputted p-value spreadsheet. You will need to indicate this at the bottom of the Apply Genetic Marker Map window under Marker Names Are.

6. Once the genetic marker map is applied, the Map button in the upper left of

   the spreadsheet will turn green. You can view each marker’s associated map information by clicking this button as in Figure 7.

   Note

   Genotype data is a special data type. You can still map other genetic data types (e.g. CNV, LogRs) as long as the marker name in your data set maps to a name in the marker map spreadsheet.