A default panel can be changed so that the genotyping portion of the analysis uses a different Peak Detection Threshold than the default RFU's, by making the changes to the panel within the Panel Editor.
Go to Tools -> Panel Editor and follow the instructions below:
- Select the panel (labeled A in screenshot below) from list on left side of Panel Editor (once selected, go to File -> Save as New Panel to save the modified panel with a new name to indicate modified peak detection settings or simply modify panel directly without saving as a new panel, if not renaming).
- Double-click on any marker (B) above the electropherogram to open the Edit Marker window.
Set Minimum Heterozygote/Homozygote Intensities and < = Inconclusive <= values to desired RFU’s, such as 100 in example (C).
Note: < = Inconclusive <= values can be set differently than minimum intensities to flag peaks at a certain range. For example, setting the < = Inconclusive <= values to 150, but leaving the minimum intensities set to 100, the software will flag peaks occurring between the ranges of 100-150 RFU's. If you would prefer no flagging and to only call peaks at 100 RFU's or above, then all values can be set to 100 as shown in screenshot (more common).
- Select Apply Homo/Hetero Settings to All Markers (D).
- Click OK (E) to apply settings to panel.
- Click brown disk icon
(F) to save changes to panel.
- Proceed to run genotyping analysis with modified panel settings.
Note: These changes will only apply to the genotyping portion of the analysis, not the chimerism analysis.
For the chimerism analysis run, the chimer panel (labeled A in screenshot below) will have minimum intensity value settings set at 50 RFU's (B) by default for chimerism analysis. It is common to keep this default of 50 RFU's to detect the smallest peaks in any given post-sample, especially in cases where either the donor or recipient DNA is occurring at low concentration. If you wish to have change the Peak Detection Threshold to another RFU's for the chimer panel, similar changes can be made as shown with the above instructions to each chimer panel. This process will need to be done with every new chimerism panel, since a new panel is created with each donor/recipient case. This can be done in the Panel Editor as shown above, but select the Chimer panel (A) to modify.
Alternatively, the chimer panel can be edited in the Run Wizard second window, as shown below. This will need to be modified for each donor/recipient pair/ chimerism analysis (each chimer panel). See instructions below:
- Click the gear icon
(labeled as A in screenshot below) next to "Customize Marker Parameters"
- Set Minimum Heterozygote/Homozygote Intensities and < = Inconclusive <= values to 100 RFUs (B)
- Click OK (C) to apply settings to chimer panel
Result: New Peak Detection Threshold will apply for this chimerism panel. For this example, only peaks at 100 RFU’s or higher will be called in the chimerism analysis.