GeneMarker Genotyping Software: User-Friendly, Linked Navigation with Tools to Simplify Data Analysis and Provide Audit Trail

The basic operation of GeneMarker software automatically corrects for most instrument and chemistry errors, such as saturated peaks, noisy data, wavelength bleed-through, instrument spikes, and stutter peaks. GeneMarker’s automated Run Wizard is designed to make repetitive analysis quick and accurate. The program is compatible with ABI®PRISM, Beckman-Coulter®CEQ, MegaBACE® genetic analyzers and most slab gel systems, such as LiCOR®, when used in combination with JelMarker® software. Additional tools in GeneMarker software include User Management, providing control of access rights, audit trail, electronic signature and a Project Comparison tool to assist with validation studies and ensure consistent analysis for long term projects.

Nearly every function of GeneMarker has been automated so that once the template is selected from the menu, or created by the user, the software automatically performs the analysis, providing a myriad of display and reporting options. Once the analysis has been completed and confirmed the software saves all of the analysis parameters, raw data and results for easy archiving and call back at a future date. An Introductory GeneMarker webinar provides an overview of GeneMarker software.

GeneMarker's wizard simplifies parameter setting by "walking" the user through 3 simple steps. Templates can either be selected from several embedded templates or the user can create and save additional templates; detection settings are presented in one dialogue box that creates required flexibility in a simple to use format. Panel management and creation requires only a few mouse clicks! Once set the parameters can be saved and called back for future analysis.

User Management for Audit Trail, Electronic Signature/Verification of Analyst and Control of User Access Rights in GeneMarker Genotyping Software

User management provides control of user access rights, automatically generates an audit trail of all edits to genotyping projects and is used to record the Organization and Operator fields in the clinical research print reports (MLPA®, Trisomy, LOH, MSI

Date/Time
Records the computer's date and time for the activity.
User
Identifies the username of the person that performed the activity.
Events
Records the user manager activity that was performed.
Comments
Gives additional information for the event that was performed. For example, if a user is added, then the username of the person that was added is recorded under Comments.

Example of Clinical Research Report Customization with Institution and Analyst Identification
supplied from the User Management Tool in GeneMarker.

Project Comparison Tool for Instrument or Analysis Parameter Validation

The Project Comparison is a review tool that provides a fast, side by side comparison of two replicate projects. Uses include establishing and comparing analysis parameters, validation studies to develop laboratory standard operating procedures, ensuring consistent calls of edited alleles (especially beneficial for long term projects to confirm that edits/comments are consistently applied).

The Two projects are compared using some or all of the options in the Project comparison settings box. If there are no difference in the same sample in the two projects the table is not highlighted. Any peak with a difference in the selected parameter(s) will have a highlighted cell. Double click on the cell to display that section of the electropherogram with details provided in the table below the electropherograms.

Project Comparison Tool

• Establishing Analysis Parameters
• Validation Studies
• Ensuring Consistent Calls for Edited Alleles
  Tools —> Project Comparison

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GeneMarker Applications:
MLPA® (Multiplex Ligation‐dependent Probe Amplification)
MS‐MLPA®
Trisomy Analysis
Macromolecule Analysis Tool
ARMs & Comparative Analysis (Cystic Fibrosis Analysis)
MSI (Microsatellite Instability) Analysis
Merge Project
Kinship Analysis of Wild Populations and data base
AFLP
t‐RFLP
Microsatellite (SSR, STR, VNTR)
MLVA
SBE/ SnapShot®
Cluster Analysis
TILLING® & EcoTilling with slabgel or capillary data
SNPWave®/SNPlex®
Haplotype Analysis
Loss of Heterozygosity Analysis (LOH)