Step 2. Import and Apply Genetic Marker Map

The Runs of Homozygosity feature can only be run from a genotype spreadsheet that has a genetic marker map applied to it. Among other things, genetic marker maps are used to reorder the SNPs in a spreadsheet according to chromosome and physical position. This makes sense as ROHs involve homozygous SNPs sequentially ordered across the genome. Trying to detect them on an improperly ordered spreadsheet would be erroneous.

To apply a genetic marker map to your genotype spreadsheet, you first need to import a genetic marker map containing, at minimum, the chromosome and physical position for each SNP in your data set. Because this tutorial focuses on analyzing Affymetrix 500K data, you will need to import an Affymetrix 500K marker map.

The latest Affymetrix marker maps can be downloaded using the Affymetrix NetAffx service in HelixTree. To access this feature, from the main Project Navigator window, select >File >Import Data >Download Affymetrix Marker Map. You will be prompted for your Affymetrix NetAffx login information, which can be freely obtained by registering on Affymetrix’s website:

https://www.affymetrix.com/analysis/netaffx/index.affx

After entering your NetAffx login information, the Download Annotations window (Figure 1) will appear listing various Affymetrix marker maps (annotation files).

IMPORTANT: There are actually two annotation files for each of the 500K, 5.0, and 6.0 files (500K = NSP + STY, SNP 5.0 and 6.0 = SNP + CN probes). For each file set, both corresponding annotation files need to be downloaded simultaneously for HelixTree to properly merge them. To do this, highlight both annotation files as seen in Figure 1. Make sure the box Import into project when downloaded is checked, and click Download. If you downloaded the annotation files previously, they would show up as a single merged file in the lower section of the window. If this is the case, you can just highlight that file and click Load Into Project.

Once the marker map has loaded it will show up as a node in the Project Navigator window.

To apply the loaded genetic marker map, Open the genotype spreadsheet imported in Step 1 and select >File >Apply Gene Marker Map. A marker map chooser window will appear with the imported marker map highlighted in white. Select the marker map and click OK.

The result will be a new marker mapped spreadsheet. In the Project Navigator window, the marker mapped spreadsheet will appear as a sub-node under the genotype spreadsheet.