This Guide walks you through the basics of the Mixture Interpretation Tool. It will explain the different basic features of the Mixture Interpretation Tool. It also explains how to load the sample into the tool. There are additional guides available on how to make calls using the Mixture Interpretation Tool as well as additional features to help you make calls in the tool.
The Mixture Interpretation Tool is used to interpret mixtures for any selected sample. It gives you the information to aide you in making the appropriate calls. It lists all available combinations at each Locus based on your settings. It keeps track of the proportions for each profile, as well as gives you a graphical visualization of the proportions as you choose each combination. The Mixture Interpretation tool can be used for a 2 or 3 contributor mixture. It allows you to set references and apply stutter when appropriate.
To start using the Mixture Interpretation Tool, click on the Begin Mixture Interpretation command.
Shortcut: You can also open the Mixture Interpretation window, by holding down the “alt” button and clicking on any of the Loci or the sample name for the sample you wish to interpret. The Mixture Interpretation window for that select sample at that locus will open. If you are on the sample name, the first locus is displayed. This enables you to skip the select sample step below.
Select the sample you would like to interpret. The pick via mouse option will allow you to select the sample using your mouse. Clicking the ▼arrow will provide a drop down list of all available samples from which you can select the appropriate sample.
Once the sample is selected, the information will fill into the Mixture Interpretation Window. The selected sample and current Locus will be highlighted on the sample table page. If you prefer for the selected sample to not be highlighted uncheck the box next to Highlight in Mixture Interpretation Section.
Note: You can click on the highlighted cell and detailed information about that Locus displays. Click on the detailed information to make it disappear.
For Example in the figure shown, D21S11 is highlighted. By clicking on the highlighted cell, the details for D21S11 for the selected sample appear as shown.
Select number of Contributors: Select the number of contributors using the Contributor selection box in the upper right corner. The default number of contributor is 2. Click on the ▼arrow to change the number.
Apply Reference(s) (optional): Next select any available references as permitted by your individual lab’s mixture interpretation protocol. Click on the Reference button under the Contributor selection box and the References Selection box will appear. Click the ▼arrow in box 1. A drop down list of all your available samples will appear. Click the one you would like to set as Reference 1. Once you select a reference the button next to the reference will change from Apply Reference to Remove Reference. If you would like to remove a reference, click on the Remove Reference button. To set more than one reference, proceed to Box 2, etc. and repeat the steps above to apply reference.
All selected references will be highlighted blue on the sample table. The reference(s) will also be indicated as such, i.e. Ref 1, Ref 2 in the Mixture Interpretation area of the Mixture Interpretation Window. NOTE: Only combinations including the references will be shown in the Mixture information area.
Click on the Auto-call references button to automatically fill in the Reference 1 as Profile 1 and Reference 2 as Profile 2. This feature will allow you to only have to select a call for the unreferenced profile(s). Note: The Auto-call Reference feature is only auto populating the profile with the chosen reference. It is not taking into account any calculations or making any kind of interpretation.
The List Foreign option will list all alleles that are foreign to the reference on the View Call Report. Click on this to enable it, before you click on “Auto-call references” button
Settings: The Peak Height Ratio (PHr), Minimum Peak Height (mPH), Minimum Proportion (mP), Homozygote threshold (HT), and Stutter % are defaulted from the Mixture Interpretation Settings. You can change these values on the arrows next to each box to appropriate value in accordance with your individual lab validated thresholds. The changed value will remain active as long as the Mixture Interpretation Window stays open or you manually change it to another value. The default values set in your Mixture Interpretation Settings will appear when a new Mixture Interpretation Window is opened. The Lock locus option, allows you to lock in the settings for the current locus, allowing settings to be changed without altering the final report.
The Multi PHr button allows you to set a PHr range. The PHR Range (peak height ratio) is for each separate locus. A default range can be set up using the ArmedXpert options window. See instruction in Chapter 2 under the Interpretation Quality Control options section to set up a default range. To activate this feature click the box left of the Multi Phr button to activate this feature.
Note: The default PHr value to the left of the Multi PHr will be used if the feature is not activated or no range is added to the Multi PHr feature.
If defaults have not been added or you want to change a range for a Locus, click on the “Multi PHr” button. The window show below will appear. You can type a Minimum rfu value with an appropriate Phr and/or a Maximum rfu value with an appropriate Phr. Click on the + button to add another range. To delete a range, click on the X next to the appropriate range
The mixture information area will only show combinations that are equal to or greater than the settings and include the reference profiles if applied. The proportions (p) can be displayed as a dilution instead of a percentage. To do this, go to the Mixture Interpretation subsection under the Interpretation section in the ArmedXpert Options Window. Click on the box next to “List proportions as dilutions (1:X)”. This can be turned on and off while in the Mixture Interpretation Window.
The mixture interpretation tool also has a feature to removes alleles that are below the mPH setting. If you click the box next to “Ignore alleles below mPH,” a check mark will appear in the box. Click on it again to remove the check mark and disable the feature. Once checked, no alleles below the prescribed mPH’s will be considered in the mixture combinations and show as grayed out. As shown in the example below, Allele 9.3 has a value of 81, which is below the 100 setting for mPH. Allele 9.3 has been grayed out and all combinations including Allele 9.3 are excluded from the possible mathematical options shown in the mixture interpretation results.
Apply Stutter: The Mixture Interpretation tool also includes features to apply stutter. You can either apply stutter to an individual locus or apply it globally to all loci. To apply stutter to just the individual locus, click on the Apply Stutter button. If you wish to apply stutter to all loci, click on the box next to “Apply Globally.” As shown in Figures 7.15 and 7.16, the RFU amount under locus 12 was refigured from 1580 to 1392 once stutter was considered and the amount is now highlighted in green to indicate stutter was applied. This also changed the calculations in the Mixture Information section. If the Apply Globally option is checked, it will apply stutter to all applicable alleles at each locus.
As shown below, once Stutter has been applied the Apply Stutter button changes to Remove Stutter. In addition, in the Mixture Information portion of the window, a note has been made to indicate that the RFU’s have been recalculated for stutter. To remove Stutter on a specific locus, click the Remove Stutter button. If you want to turn the Apply Globally feature off, click the box left of it and the check mark will be removed. All Stutter applied to all loci will be removed.
