Genemapper 4.1 User Manual

Genemapper 4.1 User Manual

When you select your country, you agree that we can place these functional cookies on your device. Your commerce experience may be limited. Please update your browser to Internet Explorer 11 or above. After that, you will need to contact Customer Service to unlock your account. Please try again or contact Customer Service. Please request another reset link. Please try again or contact Customer Service. A verified email address is required to access the full functionality of your Promega.com account. Please try again or contact Customer Service. Please try again or contact Customer Service. Please try again or contact Customer Service. Please check your network settings and try again. Please try again or contact Customer Service. Before setting up your initial connection to the desktop, and each subsequent time you access it for data analysis, you must schedule a session on our Online Calendar at. Sessions are limited to 4 hours per customer per day.To schedule a session, go to the online calendar at.All times are CST. You can choose up to four hours a day. Select the plus sign.Login again using your IGB account username and password.The Genemapper software will open. At the end of your session, first exit out of the GeneMapper software and then log off of the Genemapper computer. Then, log out of. Please note that if you simply close the remote window you will not be logged off and others will be prevented from accessing the computer.Upload your data to U of IL Box and then download to a folder in Remote Desktop for analyzing. Here is a link to U of IL Box. Another alternative is to use WinSCP, which is installed on Genemapper.We have unfortunately had instances in the past when the Remote became corrupted and all data was lost. Please do not use the Remote Desktop as an archive for your files. Biosystems. DNA fragments relative to their length to the allele designation of the STR loci.

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Optionally, the corresponding fragment length of peaks in base pairs or peakThe following documentation shows the analysis of PCR products of theFor general introductions of the software, please read the GeneMapper IDMore info about Human Identification products (HID) from Applied Biosystems:Validity for HID. The Biotype STR-Kits require a calibration with an allelic ladder. Therefore, theThis Biotype Template Files are valid with GeneMapper IDOrdering InformationB. Panels and BinSets. 12. C. Analysis Methods. 14. D. Plot Settings. 22. E. Table Settings. 24GeneMapper ID Template Files. March 2010Panels and BinSets are imported by the Panel Manager. Other template filesGeneMapper ID Template Files. March 2010Recommendation: For Biotype’s Panels and BinSets install a “Biotype folder”. Content. Select the folder Panel Manager, mark the designated panel version andSelect the corresponding Panel from the Panel Manager, mark the equivalent. BinSet version and import (see Figure 1). Fig. 1 Import of Panels and BinSetsGeneMapper ID Template Files. March 2010Use GeneMapper ID Manager to import Analysis Methods, Table Settings. ID software. Table Settings, Plot Settings or Size Standards should be saved as new folders. Select the designated tab and click the button Import. Imported Analysis Methods, Table Settings, Plot Settings or Size. Standards could be redefined and saved by the user. New Analysis Methods, Table Settings, Plot Settings or Size StandardsAdvanced version. GeneMapper ID Template Files. March 2010Workings with the GeneMapper ID Software are done with related analysisThe allelic ladder of the used test kit should beFor calibration the measured allele sizes are transferred automatically to theIn general, calibration bases on oneIf more runs will be used, calibration isThe correct assignment ofIf not, DNA samples should be further runs withCalibration using Multi-Capillary Analysers.

To ensure a reliable allelic assignment on multi-capillary analysers, a numberThe room temperature might influence the running performance of PCRPlease pay attention to keep conditionsSystem Parameters. Different analysis instruments, DNA size standards or polymers may result inThus, DNA samples and allelic ladders from oneGeneMapper ID Template Files. March 2010The table sheetAnalysis Method, Panel, Size Standard, Matrix as well as the quality. Table 1. Process quality values (PQV). DefinitionFor more information, please check the chapter Process Quality Values of the. GeneMapper ID Software User Guide.Optionally, data of the control DNA might serve as positive control, dataGeneMapper ID Template Files. March 2010The analysis method is already prepared for evaluation of data fromImportant Annotation. New analysis methods refer to the last BinSets used of the GeneMapper ID. Fig. 2 Analysis Method, tab Allele, check here Adjustment of the BinSet. DNA Size Standard 550 (ROX)Fig. 3 Start Analysis. Annotation. Use the function Fill Down in order to analyse all samples with the same. March 2010EditScaling of the Analysis RangeTo return toFig. 4 Scaling of the Analysis Range in Sample Plot. March 2010BinSets. Analysis MethodTable for 2 Alleles. Table for 10 Alleles. Panels and BinSets always need to be executed whereas the use of additional. Template Files is facultative. March 2010Software. Thus, the red panels (DNA Size Standard) of all samples areSize Standard 550 (ROX) that should be 50, 60, 70, 80, 90, 100, 120, 140,If sizes differ, further analysis shouldIf necessary, create a new sizeAdjustment of the basic templateIf for example only 400 bp are necessary for analysis ofFig. 5 Electropherogram of the DNA Size Standard 550 (ROX), Lengths of Fragments in bp. Definition of a New Size Standard. To define a new size standard, please perform the following steps.

Select the tab Size StandardsSee also horizontalBTY, BTR, and BT0 (matrix BT5) the DNA Size Standard 550 (BTO) in orange. March 2010Panels. The following features of the test kit’s markers (STR-Loci) are depicted:Fig. 6 Structure of a Panel. March 2010The following features of the allelic designation are depicted:Fig. 7 Structure of a BinSet. March 2010HID analysis method with 20% Filter for samples of one DNA. HID analysis method with 20% Filter for samples of one DNA. Sensitive HID analysis method for stains and DNA mixtures. Sensitive HID analysis method for stains and DNA mixturesPeaks will be designated with theProblems with importing analysis methods. To solve import problems, please create own analysis methods in your. GeneMapper ID software according to Applied Biosystems instructions and fillGeneMapper ID Template Files. March 2010GeneMapper ID Template Files. March 2010Cut-off Value. Cut-off Value 0.2 corresponds to 20% filter in comparison to the highest peakMethod limitationGeneMapper ID Template Files. March 2010Peak Window Size can be minimized to 11 pts. For improved peakOnly the setting for Peak Window Size is different to defaults from Applied. Biosystems for HID analysis. March 2010All settings here are defaults from Applied Biosystems for HID analysis. March 2010Fig. 14 Tab Allele for adjustment of the filter values, pre-selection: No Cut-Off filter. Changing the Filter Value in the Allele tab. To change the lower thresholds please perform the following steps:MinusA, Minus Stutter, Plus Stutter (see figure 14)GeneMapper ID Template Files. March 2010Changing the Filter Value in the Peak Detector tabCommon values are 50-200. RFU and should be determined individually be the laboratory. Recommendation: The minimal peak height should be three times higherGeneMapper ID Template Files. March 2010Display of two colour panels (B, R). Display of three colour panels (B, G, R). Display of four colour panels (B, G, Y, R).

Display of four colour panels (B, G, Y, O). Display of five colour panels (B, G, Y, R, O). DescriptionFig. 16 Plot Window with allelic ladder and DNA Sample. March 2010To change peak designation, please perform the following steps:Height, Size (see Figure 17)Fig. 17 Plot Setting, Tab Labels for Designation of the PeaksFig. 18 Plot Setting, Tab Sizing Table for Table Display. March 2010Table for 2 Alleles. For samples with one DNA. For samples with DNA Mixtures. Table for 2 AllelesFig. 19 Output File after Execution of Table for 2 AllelesPeak quality assessment via different signals. Signal. Pass. Check. Low Quality. TableGeneMapper ID Template Files. March 2010DefinitionControl DNAFor more information, please check the chapter Process Quality Values of the. GeneMapper ID Software User Guide. March 2010Fig. 20 Output File after Execution of Table for 10 Alleles. Table ExportFor general instructions for table export, please read the chapter Exporting. Table Data from GeneMapper ID Software User Guide. March 2010General Procedure for AnalysisCheck Size StandardFig. 21 Checking Size Calling. March 2010Fig. 22 Checking Allelic Ladder. Controls. In order to check allele designations please compare the alleles of the allelicWe recommend the quality value. March 2010Fig. 23 Checking Control DNA. Positive Control. We recommend the following quality value. Negative Control. The negative control contains no DNA and is a helpful information forGeneMapper ID Template Files. March 2010Fig. 24 Changing the Allele Designation. Off-Ladder Allele. These labels have to be checked manually and may be deleted or redefined byDelete AlleleOL -icon below the peak (icon gets bold). Open pull-down menu by clickingRename Allele. Inside the pull-down menu, known alleles of the marker can be chosen fromGeneMapper ID Template Files. March 2010In order to modify,Important: VersionAnnotation. New categories can be created in the same way e.g.

for newly found pointBiotype assumes no liability for changing of Panels and BinSets. The actualSmall, Medium, Large (to scale the plot size per page). March 2010General Help in softwareObservation. Possible Cause. Comments. Error message during savingCountry setting. Setting from the PC has to be edit to. English (United States). Error message during importPath on your computer. AppliedBiosystems\GeneMapperFirst, delete all Panels in the PanelPanels and BinSets are notCompatible versions of Panels and. BinSets have to be saved within oneError message during importGeneMapper ID v3.1 does notExplorer and change the penta repeatThen, import the new panel data again. Alternatively, install at least version 3.2Error message during importTable Setting, Size Standard). GeneMapper Software is not. GeneMapper ID Software. Install GeneMapper ID Software. Essor message duringError Message in the info view. An invalid BinSet is preselected in. Analysis Method. Select the actual BinSet.Data from different analysers like. ABI 310 and ABI 3130 have beenData from different analysers alwaysAn additional signal can beStandard (in bp) of the allelic ladder. Always use the DNA Size Standard. One peak of the allelic ladder isThe allelic ladder has to be load withGeneMapper ID Software. One peak of the allelic ladder is notFirst compare the length of theGeneMapper ID Template Files. March 2010Possible Cause. Single marker is not identified. Various causes. Open the “project” folder, mark theError Message in the tab Info orDNA Size Standard 550 (ROXClick onto the red icon Size Match. Editor in the upper toolbar or the. GeneMapper ID Software. CheckDNA Size Standard 550 for. Too high intensities at theReduce the injection time up toPCR amplification product forDNA for PCR. Bubbles in the capillary lead toRepeat electrophoresis to confirmDifferences in the capillaries’For reliable allelic assignment onPoint alleles, i.e. alleles with atThe point alleles were notID Software.

Check the settings of the analysisSize value to 11 pts. Homocygote alleles are notPreferences of the. Adjustment can be changed via. Analysis and the setting. Duplicate homozygous allelesTrademarks. Applied Biosystems are trademarks of Life Technologies. March 2010. For Research Use Only. Not for use in diagnostic procedures. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document. Notice to Purchaser: License Disclaimer. Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly, or by estoppel. GeneMapper Software has not undergone specific developmental validation for human identification applications. Human identification laboratories analyzing single-source or parentage samples which choose to use GeneMapper Software for data analysis should perform their own developmental validation studies. AFLP is a registered trademark of Keygene N.V. AppleScript and Macintosh are registered trademarks of Apple Computer, Inc. This product includes software developed by the Apache Software Foundation ( Copyright The Apache Software Foundation. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., Microsoft Windows NT and Microsoft Excel are registered trademarks of Microsoft Corporation. Oracle is a registered trademark of Oracle Corporation. All other trademarks are the sole property of their respective owners.

Applera Corporation is committed to providing the world s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses.This guide is intended for trained laboratory personnel. Applied Biosystems is not liable for damage or injury that results from use of this guide by unauthorized or untrained parties. This guide uses the following conventions: Bold indicates user action. For example: Type 0, then press Enter for each of the remaining fields. Italic text indicates new or important words and is also used for emphasis. For example: Before analyzing, always prepare fresh matrix. A right arrow ( ) separates successive commands you select from a drop-down or shortcut menu. For example: Select File Open Spot Set. Right-click the sample row, then select View Filter View All Runs. Two user attention words appear in Applied Biosystems user documentation. Each word implies a particular level of observation or action as described below: Note: Provides information that may be of interest or help but is not critical to the use of the product. IMPORTANT! Provides information that is necessary for proper operation, use, or best practices for the GeneMapper Software.Contacting Applied Biosystems How to Obtain Services and Support Send Us Your Comments For the latest services and support information for all locations, go to then click the link for Support. At the Services and Support page, you can: Search through frequently asked questions (FAQs) Submit a question directly to Technical Support Order Applied Biosystems user documents, MSDSs, certificates of analysis, and other related documents Download PDF documents Obtain information about customer training Download software updates and patches In addition, the Services and Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities.

Applied Biosystems welcomes your comments and suggestions for improving user documents.Table 1 Troubleshooting Checklist Information for Technical Support Briefly summarize the problem: Have you been able to repeat the problem. The minimum requirements may not provide optimal performance. Applied Biosystems does not guarantee support for a GeneMapper Software installation in this environment. Microprocessor Compatibility Hard Drive Partitioning GeneMapper Software is not compatible with the following processors: Dual-processors Intel Xeon processors For optimal performance of the GeneMapper Software, partition the hard drives on your computer. In addition to serving as a common data repository, the database provides user authentication, robust and scalable data management, and flexible archive capabilities via the utilities provided with the GeneMapper Software. Applied Biosystems does not support access to the Oracle database through any means other than the GeneMapper Software. User Access The Oracle database version included with the GeneMapper Software v.3.7 is an embedded license database. This license allows access to the database for up to five named users at any given time. If you want to accommodate more than five named users, you can purchase either additional GeneMapper Software licenses, or additional Oracle-named user privileges and thereby, honor Applied Biosystems agreement with the Oracle corporation. Note: When installing the GeneMapper Software, log into the computer as the administrator and into the local domain. IMPORTANT! Do not log on to the network. The first time that you log into the software, use the default user name and change the password. Do not misplace the password for the default user account. If the password is lost before additional user accounts are created, then the GeneMapper Software will be inaccessible and all data it contains unrecoverable.

The password for the default user account is pre-expired and must be changed on first login. 3. Click OK to display the Change Password dialog box. 4. Type a new password, retype the new password to confirm it, then click OK. 5. Two license agreements are displayed during the first login. Click Accept for each.If you are the Administrator, use: User Name: Administrator Password: Administrator If your password is pre-expired, you are prompted to create a password when you click OK. 3. Enter your password. IMPORTANT! Applied Biosystems recommends changing the password for the Administrator user account after installing the software. 4. Click OK. Note: If you unsuccessfully attempt to log in to the software more times than allowed by your password policy, your account becomes suspended. To activate a suspended user account, either wait the time specified by the policy associated with the account, or ask your administrator to reactivate (see Access Control on page 2-3 for more information). The window displays the new database host and its user names list. If the GeneMapper Software cannot connect to the database host you entered, the error message: You have entered an invalid host is displayed. Click OK to exit, then reenter the database host information. b. Select the appropriate machine type. c. Click OK. IMPORTANT! If at any point the network connection is interrupted or lost, the GeneMapper Software will become unusable. When you log out of the GeneMapper Software with a GeneMapper project that has unsaved changes, you are prompted to save or discard the changes you made since the last time you updated the project. If you close the GeneMapper Software using the File Logout command, the login window reopens after you select either Yes or No. GeneMapper Software closes completely if you use either the Exit command or the Close button. To open the Panel Manager, click (Panel Manager) in the GeneMapper window toolbar (or select Tools Panel Manager).

Menu bar Toolbar Navigation pane Reference pane Figure 1-4 Panel Manager Panel Manager Toolbar The active buttons on the toolbar vary according to which items (kits, panels, bin sets, markers, bins, or reference data) are selected and viewed. The table that you use to access the cluster plot affects which electropherogram plot is accessible from the Cluster Plot Manager. The cluster plot displays for each marker: Cluster Plots: Scatter plot of the homozygous, heterozygous, and undetermined genotype calls for selected samples and controls SNP Table: Information, results, and confidence values for each SNP Cluster Plot Genotypes Table: Information, results, and quality values for samples Opening the Cluster Plot Manager Click (Display Cluster Plots) to open the Cluster Plot Manager. The peak height for: Allele 1 is plotted along the x-axis Allele 2 is plotted along the y-axis The following symbols indicate the genotype calls for the samples and genotype clusters at different locations in the cartesian cluster plot. Column (Analysis Status) Description Analyzed ( ) Requires reanalysis ( ) Unanalyzed ( ) SNP Name of the SNP tested in the SNPlex assay. Comes from the SNP set used to analyze the samples Marker Run Name Panel Name Dye Allow Autocall Name of the marker from the panel file used to analyze the samples Name of the run from the.fsa file Name of the panel file used to analyze the samples Color of the dye on the ZipChute probe used to detect the SNP Check box for displaying samples in the cluster plot: Select for the software to make the calls based on the clustering algorithm. Deselect to make the calls manually. Note: Depending on the settings that you use, not all columns will be visible. Cluster Plot Genotypes Table The Cluster Plot Genotypes table, located in the lower left of the Cluster Plot Manager, shows information, results, and quality values for the samples after selecting a SNP in the SNP table.

Light gray bar between the SNP table and genotypes table to adjust the size of tables. To adjust a pane: 1. Position the cursor over a sizing bar until the cursor changes to sizing arrows. 2. Drag the sizing arrows to adjust the size of the panes. To restore the default view, click the sizing bar. To display or hide the cluster plot using the dark gray bar to the left of the cluster plot, click the: Upper black triangle to display the cluster plot only. Lower black triangle to hide the cluster plot. Adjusting the Cluster Plot Graph Settings 1. Right-click the cluster plot, then select Graph Settings. 2. Select the type of cluster plot to view: Cartesian or Polar. 3. Set the scale for the x-axis and the y-axis. Select Auto Scale for the software to scale each plot to the maximum x and y values obtained for the marker. Deselect Auto Scale and enter Minimum and Maximum values to view for all plots. 4. Click OK to activate the cluster plot settings. Zooming In and Out of the Cluster Plot (Cartesian Plot Only) To zoom in: Select (Zoom In) in the toolbar, click the plot, then draw a box around the samples to view more closely. To zoom out: Select (Zoom Out) in the toolbar, then click the plot until you obtain the desired view. A user s access to functions is not controlled by membership in user groups. Instead, each function is enabled or disabled in an object called a User Profile. Each user is assigned a single user profile, allowing administrators to control data and function access independently. And, only one administrator is allowed to modify Access Control data at one time. Do not misplace the administrator password. If the administrator password is lost, access control must be reset, resulting in the loss of all users and profiles. Type Selection In the left Tree pane, Users or Applications are types. When you select a type, the List of Users pane displays a list of identifiers of the type selected.

Note: If you select EULA (End User License Agreement), the license agreement is displayed the next time the user is authenticated. Properties Panes Access control identifiers have an additional drop-list labeled, Control Security Group. This defines the security group for control of access to the corresponding access control data itself within the Administrative Tool. The identifiers under access control are: User Profile When a reserved (undeletable) identifier is selectable, a label in the Properties pane indicates this (see the specific Property panes below). Clicking the column header again sorts in reverse alphabetic order. Ascending order Click header Descending order Figure 2-1 Sorting rows in the List pane The column width can be widened or shortened. When widening or shortening the column width, no sorting occurs. Table 2-1 Description of Toolbar Commands Icon Description Save commits changes in the Admin Tool to data store and is accessible from the menu bar, keyboard shortcut, or toolbar. Reload refreshes the Admin Tool with the content of the data store and is accessible from the menu bar, keyboard shortcut, or toolbar. You can exit by the upper-right-corner button or by selecting Files Exit. If you have updated memory but have not yet committed changes to data store, a dialog box prompts you to save the changes. You can click Yes, No, or Cancel. Duplicates the selected indentifier. Duplicate is accessible from the menu bar and toolbar. Locates the name specified in the text field in the navigation pane. Prints all or some identifiers in various formats selected from the dialog box shown below. Menu Bar Commands Each command has a corresponding menu item. Each menu item has a unique mnemonic. The mnemonics are an underlined letter or number when viewing menu items (for example, View, on the toolbar). Profiles allow the administrator to grant or deny a user the right to access functions.

When one user is selected in the navigation pane, the user profile is displayed in the User Properties page and the User Details page. Note: When a user is deleted, the user name is not displayed although it is permanently stored in the database; it cannot be used again. Note: In the User Details page, the administrator can change the status of a user to Inactive to block access by the user. Execute: Give access to the function to any user assigned to this Profile. OIR: Overrides inherited rights. Any lower level in the hierarchy inherits the access rights of the node above it. To override the inherited defaults, select OIR. This allow the administrator to grant or deny the groups ability to execute a specific function on a lower level of the hierarchy tree. 4. Click Next. The Summary page displays the properties and associations of the new profile name. 5. Click Finish to complete the creation of a new User Profile Name. IMPORTANT! Upon installation of the GeneMapper Software, the auditing feature is OFF by default. Consequently, changes to projects, analysis methods, and panels are not recorded until the feature is activated. There are three basic categories of data changes: Project changes Analysis methods changes Panels changes An audit is generated when data are changed in a project, analysis method, or a panel. The events within them that generate an audit. Audited Object An audit record is generated when you. Projects Create, delete, or rename a project Add or delete a run Add or delete a sample Overwrite a GQ value Add, delete, or modify an allele Analysis Methods Add an analysis method Change any analysis parameter values Delete an analysis method Panels Add, delete, or rename a panel Add, delete, modify a marker Add or delete a bin set Add, delete, or modify a bin Add, delete, or rename a chemistry kit Note: Deleting a kit is recorded as one audit record.

When you delete a kit, all panels, markers, and bin sets associated with that kit are deleted as well, but they do not generate any individual audit records. The old and new values, if applicable. A text box where you enter the reason for the change, click OK to save changes to the attribute and the audit data. Note: When auditing is ON, the software always generates audit records. Example 1: Modify Bin Refer to Table 2-2, Text Box Description: Modify Bin, for descriptions of the text boxes in the Reason(s) for Change dialog box. Audit Maps are used to control how auditing is performed on a given data type. With the Audit Map Configuration Tool: You can set the audit states of an audit attribute to On, Off, or Silent. All changes to audit maps are saved automatically. There is no SAVE command. The Audit Map Configuration tool checks if an application is known by the Security component. If Security does not know about the application, the application does not start. Note: Any changes you make to an audit map do not take effect until you restart the GeneMapper Software. To access the Audit Map Configuration tool: 1. In the GeneMapper window, select Tools Audit Manager Setting. 2. In the System Authentication dialog box, type your login name and password, then click OK to display the Audit Map Configuration window. Change the audit state of an attribute Select a different audit state in a cell under the State column in the Attributes page. Audit states are: On, Off, or Silent. Sort a row Click a column header. Note: Disabled Audit Maps (Enabled column) display their attribute list in italics. Table 2-4 Audit Map Configuration Tool Commands Menu Command Function File Visual Print Displays the Print dialog box. Visual Print Preview Exit Displays the Print Preview dialog box. Exits the Audit Map Configuration application. Auditing On Select auditing to be turned on for the Audit Map Configuration.