PDF reports of electropherograms and pedigree diagrams of mother, father, and proband are easily exported from both GeneMarker and GeneMarkerHID.
Electropherogram Reports:
After analysis and review of the allele calls for the mother, father, and proband samples, select the Print Report options from the printer icon in the tool bar at the top of the analysis screen. During SOP development, create a print template with the settings of the Standard and Advanced tabs. The screen shot below is an example of a commonly used template that displays electropherograms only (no peak tables), dye channels with amplicons (excludes the size standard channel), includes the project comments and report header, and groups the samples by dye. Grouping by dye is often preferred as mother, father, and proband for each dye are displayed on the same page (Figure 2). Applying sample grouping is also commonly used when the project includes multiple family trios.
After selecting the print template (or specifying other print report options) click OK.
Figure 1: Print Report options
Figure 2: An example of one page of the report created using the print report selections above. If desired, the sorting option in the main analysis screen can be used to change the order the electropherograms are displayed. Electropherogram reports may be saved as .pdf, .png or .jpeg files.
Pedigree Diagram Reports:
After analysis and review of the allele calls for the mother, father, and proband samples, select Applications – Relationship Testing.
- Select the appropriate allele frequency from the Tools drop-down menu.
- Note: while no calculations are required, the allele frequency table provides the names of all of the alleles in the multiplex.
- If the files were amplified from a single multiplex, use the family group tool to group the trios. Select each family from the drop-down menu to review and export the pedigree pdf (Figure 5).
- If the files were amplified from more than one multiplex, use the Merge Project tool in GeneMarker to produce a single .txt file with the complete genotype of each sample (unfortunately, this tool isn't available in GeneMarkerHID). The merge project tool also exports a .txt file with the appropriate format for the allele frequency function in Relationship Testing.
- Select Applications – Relationship Testing
- Select Tools – Allele Frequency – Import the allele frequency .txt
- Select Database – Save to Database – Load from .txt file – import the .txt file of genotypes and use the save icon to save the genotypes to the relationship testing database
Figure 3: Saving genotypes from the Genotype Merge Tool into the Relationship testing database
- Select File – New Pedigree – make the appropriate selections to import the genotypes from the database to draw the pedigree
Figure 4: Build a pedigree from genotypes retrieved from the Relationship Testing Database
Figure 5: The pedigree displays apparent UPD on the appropriate side of the diagram (maternal or paternal). In this example, eight of the loci have both alleles in common with the mother. Right mouse click in the area of the pedigree and export the image as a .pdf, .png or .jpeg.
Note: Pedigrees appear as in Figure 5 whether they are produced by the family group tool or when using the New Pedigree from genotypes in the database.