Family-Based Association

Please note, LAB is only available in Progeny 10 and older versions of Progeny, which are EOL.

To create a family-based association export

1. On the main window navigation bar, click the Analysis button to open the Analysis module and select the folder in which to the association export will be saved.
2. On the window toolbar, click the Family Assoc button, the Specify Family-Based Association Settings dialog box opens.

Specify Family-Based Association Settings dialog box

Settings

1. Name – the name or description of the export.
2. Required Fields
   • Unique ID – click the field button to the right to open the Select Field dialog box and select the field that represents the Unique ID for everyone that is to be included in the association export.
   • Affection Status – click the field button to the right to open the Select Field dialog box and select the field that represents the Affected Status for everyone that is to be included in the association export.
3. Select the fields that are to be included in the association export by doing the following:
   • In the folders pane of the dialog box (middle left), select the folder that contains the individual data fields that are to be included in the association export.
4. In the Fields pane (middle right) pane of the dialog, select the fields (CTRL-click to select multiple fields) that are to be included.
5. Drag any fields into the Selected Fields pane at the bottom of the dialog box.

Pedigrees

1. In the Folders pane of the dialog box, select the folder that contains the pedigrees for which the linkage export is being created.
2. In the Pedigrees pane of the dialog, select the pedigree (CTRL-click to select multiple pedigrees) for which the linkage export is being created.
3. Drag the selected pedigrees to the Selected Pedigrees pane of the dialog box.
4. Include Options
   • Include only selected individuals marked “Include in Analysis” – includes only those individuals in a pedigree who have been specifically marked for inclusion in an analysis.
   • Include all selected individuals – includes all individuals in the selected pedigrees.
   • Query within selected Individuals – includes only those individuals in the export linkage who meet specific criteria. Click the … button to open the Specify query dialog box and define a new query or load a saved query format.
5. Pedigree Options
   • Use pedigree IDs—Converts a text-based pedigree name into a numerical ID.
   • Use pedigree names—Use pedigree names as-is.

Markers tab

• To include an entire marker set in the analysis, drag the marker set from the Sets pane to the Selected Markers
• To include all the markers for a specific chromosome in the analysis, drag the chromosome from the Chromosomes pane to the Selected Markers
• To include only specific markers in the analysis, select the marker (CTRL-click to select multiple markers) from the top right pane and drag and drop to the Selected Markers
• Marker Options
  • Include all markers – includes all markers within the Selected Markers pane in the linkage export.
  • Query within selected Markers – includes only those markers within the Selected Markers pane in the linkage export that meet specific criteria. Click the … button to open the Specific query dialog box and define a new query or load a saved query format.
• Include polymorphic markers only – filters the selected markers and export only those markers that have at least one heterozygous genotype.

To run a family-based association export

After you specify the necessary export settings on all three tabs, you must return to the Settings tab, and then click OK on the tab. The Export to Family Association Files dialog box opens.

1. Click Browse to open the Browse for Folder dialog box and browse to and select the folder in which the association export files are to be stored.
2. File Break Options.
   • Break by Marker—Indicate how many markers are to be contained in each linkage file. If you select this option, you must also indicate the number of overlapping markers in each file.
   • Break by Chromosome—Creates a new file for each chromosome that is exported.
3. Click Export. The Export to Association dialog box opens indicating the status of the association export. When the export is complete, click Close to close the dialog box and return to the Analysis module.

Deleting a Family-Based Association Export

You can delete a family-based association export by doing one of the following:

• Right-clicking on the association export in the Analysis module and clicking Delete Export on the context menu that opens.
• Selecting the association export in the Analysis window, and then click the Delete key on your keyboard.

Saving and Loading a Family-Based Association Export Format

To save a family-based association export format

1. Set up the family-based association export format but do not run the format.
2. Click the Save Fmt button on the Specify Family-Based Association Settings dialog box.
3. The Save Format dialog box opens. Enter a Format Name for the association export format.
4. Select the folder in which to save the format and click Save.
5. You can then load this saved format and run it on an as-needed basis.

To load a family-based association export format

You can a retrieve a saved family-based association export format and run it on as-is needed based.

1. Open the Specify Family-Based Association Settings dialog box by clicking the Family Assoc
2. Click the Load Fmt button on the Specify Family-Based Association Settings dialog box.
3. Open the folder that contains the association export format that you are loading, select the format, and then click Load.
4. The Specify Family-Based Association Export Settings dialog box is refreshed with the loaded format. You can modify the format as needed and export the association format.

To Select Individuals in a Pedigree for Inclusion in an Analysis

Open each affected pedigree, and manually select the appropriate individuals. You can select a single individual, or CTRL-click to select multiple individuals, and then right-click on any selected individual, and on the context menu that opens, click Analysis > Include in the analysis.

To View and Rerun a Family-Based Association Export

1. In the Analysis module, select the association export that you want to view. Two tabs open in the bottom pane of the window—Pedigree Map and Allele Map.
2. The Pedigree Map tab displays the mapping of the original Pedigree ID to the Pedigree Name generated for the export file. These values are not editable; however, you can sort the data by clicking on the column heading.
3. The Allele Map tab displays the mapping of the original calls for each Marker to the Allele and Call generated for the export file. These values are not editable; however, you can sort the data by clicking on the column heading.
4. Optionally, to rerun the association export, right-click on the selected export, and on the context menu that opens, click Open Export. The Specify Linkage Settings dialog box opens. You can now modify any of the needed settings and click OK on the Settings tab to rerun the export.