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Chapter 8 Additional Tools
Group Size: Enter the number of groups for the analysis. Standard MS-MLPA analysis would use 2 groups, an
LOH analyses comparing one normal sample to three grades of tumor would use 4 groups.
Control Identifier
Enter the character from the Control Identification section (highlighted green) that describes the control or
reference sample. Example: N = normal or R = reference. Select Case Sensitive if the Control Identifier needs to
be identified by upper or lower case letters.
Control Match Mode
Choose either Whole Words or Include.
Whole Words should be used if the characters entered into the Control Identifier field need to match exactly.
Include should be selected if the characters in the Control Identifier field only need to be identified in the filename,
i.e. not an exact match.
Macromolecules
Tools  Macromolecules
The Macromolecule Tool aids with analysis of macromolecules without an internal lanes size standard.
Depending on the macromolecule size and configuration, migration rates through CE vary greatly. Internal size
standards of the same macromolecule may not be readily available. This tool enables researchers to physically
identify reference peaks known to have the same size and uses the information to calibrate from one capillary to
another. Characteristics of the aligned data (such as relative size, peak height, peak area) can then be exported in
an excel sheet or printed as an allele report.
Procedure
1.
2.
3.
Select File  Import Data from the main analysis window
Select Tools  Macromolecules  Settings
Select Add and enter peak range for one group of
fragments
4. Repeat for a second group of fragments at the opposite
end of the size range
5. Select Ok and verify fragment selection (white boxed)
6. If needed, select Tools  Macromolecules Range to
launch the Peak Range Editor and correct for any
fragments outside of the range
7. Align the results, Tools Macromolecules  Show
Results
8. Analyze data with Project  Run  Select Analysis type
Animal  Next  Next  OK
9. Review data, Export Report Table (.xls or .txt) or Print the
Allele Report
10. If desired, a panel may be made in the Panel Editor to
allow application of local max filter in the Run Wizard
11. Project  Run  Select Panel from the drop down menu
12. Next  Next  OK
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May 2012