SoftGenetics - Software PowerTools for Genetic Analysis


MLPA® Analysis


Multiplex Ligation-dependent Probe Amplification (MLPA) is a rapid, high-throughput technique for detecting copy number changes, with both general and clinical research applications. Kits are commercially available through MRC Holland. GeneMarker® software provides an entire module dedicated to MLPA analysis in house, no internet needed. The MLPA analysis application is linked directly to the program, allowing the user to  process raw data, normalize samples , and perform MLPA analysis all in one program - eliminating unnecessary data transfers.


MLPA analysis with GeneMarker software is both rapid and accurate, allowing complete MLPA , MS-MLPA, or Luminex-MLPA analysis of 96 samples in just minutes. GeneMarker software is compatible with the output from all major genetic analyzers, including: ABI®PRISM, Beckman-Coulter®, and MegaBACE®. Access MLPA panels through GeneMarker software's panel editor, our website, or GeneMarker software's MLPA application has been validated by research hospitals worldwide, is included in EuroGentest validation report, and is an excellent alternative to GeneMapper®, Genotyper™, GeneScan®, SequencePilot® and Coffalyser.Net Software.

Please keep reading to learn more about the benefits of MLPA analysis with GeneMarker software.

Or click here to watch the MLPA analysis webinar.
Click here to read the MLPA application note.


MLPA Normalization Increases the Accuracy and Consistency of Analysis



GeneMarker software gives users two methods of data normalization: Population normalization uses all probes in a sample to normalize the data (recommended for most chemistries) whereas Control Probe Normalization uses only the control probes to normalize (recommended when expecting numerous duplications and deletions). Both methods improve the linearity of the data, allowing more accurate and consistent results.


Automated Quality Control Increases Rigor and Efficiency



The Quality Control Settings are automatically turned on when the MLPA template is selected. The program will alert the user if one or more of the Quality Control Settings are turned off.



This feature is new to GeneMarker software 2.6.0. The program automatically detects important quality control fragments within each sample, and alerts the user if the behavior of any fragment is outside of the norms recommended by MRC Holland. These settings help make quality control easier and more rigorous.


Automated Detection and Repair of Saturated Peaks



Saturation Detection (SD) will detect saturated peaks. The detected peak will be given the Quality Reason, SD, and a red underscore at the corresponding location on the electropherogram. Saturated and Saturated/Repaired peaks are not recommended for any quantitative calculations and will result in a pop-up warning message.


Additional Quality Warnings for Analysts moving to Post-genotyping Applications



If there are flagged alleles present in one or more of the samples, the program will warn the user when attempting to access a Post-genotyping Application before the flags are resolved. This setting can be turned on/off under View Preferences.


Detailed Reports Ensure Results are Communicated Clearly and Effectively




Reports include an informative header, electropherogram, ratio plot, validation box, and report table. They can be customized to display the entire sample, a particular peak, or clusters of peaks. When the Automated Quality Control Settings are used, the final report will denote whether the Quality Control Fragments passed or failed. If the Quality Control Fragments do not pass, a failed message will be shown in red font on the final report. Reports may be printed directly, or electronically saved in .PDF, .PNG, or .JPEG formats.


Highlight Probes of Interest



Highlighting helps draw attention to probes of particular interest. These probes will also be displayed as triangles in the ratio plot. Highlighting may be included in the print reports as well.


Easily Customize your Analysis Settings



GeneMarker allows for easy customization of analysis settings. Or, you can proceed directly to the analysis using the recommended defaults.


Use Templates to Save Settings For Commonly Used Chemistries



Analysis settings can be saved in templates, reducing clicks and increasing the speed of analysis.


Share Panels, Size Standards, and Template Files Over Your Network



The working directories for panels, size standards, and templates may be changed, allowing these files to be easily updated, saved, shared, and distributed over a network. An export directory may be set in order to save all reports to a common location.


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SoftGenetics - Software PowerTools for Genetic Analysis

SoftGenetics - Software PowerTools for Genetic Analysis


















SoftGenetics - Software PowerTools for Genetic Analysis





SoftGenetics - Software PowerTools for Genetic Analysis

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