GeneMapper ID-X Software Version 1.2

Transcription

1 GeneMapper ID-X Software Version 1.2 USER BULLETIN DECEMBER 2010 SUBJECT: Verification Experiments and Installation Procedures Purpose of this user bulletin In this user bulletin This user bulletin: Describes the results of experiments performed by Life Technologies to verify the following: The GeneMapper ID-X Software Version 1.2 performs as designed to analyze data generated on legacy human identification capillary electrophoresis platforms such as the ABI PRISM 310, 3100, 3100-Avant, 3130, and 3130xl Genetic Analyzers, and the 3730 DNA Analyzer. The new features added do not adversely affect the software functionality carried over from GeneMapper ID-X Software Version Provides instructions for installing GeneMapper ID-X Software Version 1.2. This user bulletin covers: About GeneMapper ID-X Software Version Verification Software verification testing and results Sizing and genotyping concordance Mixture analysis Results Conclusions Installing GeneMapper ID-X Software Version General installation instructions About co-installation with Data Collection Software Perform a fresh GeneMapper ID-X Software Version 1.2 installation Upgrade from a previous version Troubleshooting Obtaining support

2 About GeneMapper ID-X Software Version 1.2 About GeneMapper ID-X Software Version 1.2 GeneMapper ID-X Software Version 1.2 contains the same functionality as GeneMapper ID-X Software Version 1.1.1, with additional capability to analyze.hid sample files generated on the 3500 and 3500xL Genetic Analyzers. Features incorporated from v1.1.1 software include: An option to separate each sample plot and table on individual pages when printing multiple samples at a time An option to enable/disable spike detection for allelic ladder samples Enhancements to printing speed to decrease total print time and increase print speed per page The full list of features incorporated from version are described in more detail in the GeneMapper ID-X Software Version User Bulletin (PN ), which is available to view or download at: applied_markets_support/documents/generaldocuments/cms_ pdf New features in version 1.2 software include: The ability to analyze.hid sample files generated on the 3500 and 3500xL Genetic Analyzers and view additional sample file information The ability to enable/disable the normalization of sample peaks when the normalization feature is enabled in 3500 and 3500xL Data Collection Software Compatibility with Windows Vista in addition to Windows XP and Windows 2000 Professional Operating Systems Updated database to the newest Oracle 11G database Verification Software verification testing and results The tests performed in this validation include the following: Concordance testing comparing a historical data set collected from legacy Genetic Analyzer instruments using a variety of AmpFlSTR kits analyzed using GeneMapper ID-X Software versions 1.1 and 1.2 (compare data in Genotypes and Sizing tables). Concordance testing comparing mixture analysis results generated from a historical mixture data set on the 3130xl Genetic Analyzer, using existing AmpFlSTR kits and analyzed using GeneMapper ID-X Software version 1.1 and 1.2. Verification of features carried over into GeneMapper ID-X Software Version 1.2 from GeneMapper ID-X Software version including: Adjustment of profile-comparison match-filtering to correct an issue where some matches were not properly displayed Update to correct marker name sorting in the profile comparison display Changes to the CODIS export file format to remove the registered trademark which could not be translated by Chinese operating systems Changes to the CODIS export file format to display September in 3 character format (SEP) The option to turn allelic ladder spike detection on or off 2 GeneMapper ID-X Software Version 1.2 User Bulletin

3 Verification Update to the local southern sizing algorithm to address a rarely observed issue with GeneScan 600 LIZ Size Standard, in which size standard fragments form a perfect line resulting in incorrect plot display and abnormal peak morphology Address an issue where modifications to the size standard or analysis method do not get exported when the project is exported (if the project is not re-analyzed) The test cases performed in this verification study and the passing criteria are summarized in Table 2 on page 5. A summary of the verification study tests and results is shown in Table 3 on page 7. Sizing and genotyping concordance A total of 2204.fsa sample files were used in the concordance test. The sources and types of samples are listed in Table 1 on page 4. GeneMapper ID-X Software Version 1.2 User Bulletin 3

4 4 GeneMapper ID-X Software Version 1.2 User Bulletin:Verification Experiments and Installation Procedures Table 1 Number of sample files by type used in concordance testing. The capillary electrophoresis instrument, data collection software version, and AmpFlSTR kit used to generate data are noted. Instrument/ Data Collection Software ABI PRISM 310 Genetic Analyzer DC Software v3.0/ Genetic Analyzer DC Software v1.1/ Avant Genetic Analyzer DC Software v xl Genetic Analyzer DC Software v Genetic Analyzer; DC Software v3.0 AmpFlSTR Kit Single Source Sensitivity Mixture Low Quality DNA LOR OMR Spike Good Ladder Low Quality Ladder Positive Negative Total COfiler Profiler Plus Identifiler SGM Plus SEfiler Yfiler MiniFiler COfiler Profiler Plus Identifiler SGM Plus SEfiler COfiler Profiler Plus Identifiler Profiler Plus Identifiler SGM Plus SEfiler Yfiler MiniFiler Sinofiler Identifiler Total Verification Experiments and Installation Procedures Verification

5 Verification The data listed in Table 1 were analyzed using both GeneMapper ID-X Software versions 1.1 and 1.2. The Genotypes and Sizing tables were exported and compared using Beyond Compare Software version to determine whether any differences in data output resulted. The peak heights, peak areas, data points, sizes, allele names, and all the PQV scores were compared between the two software versions. Mixture analysis A historical mixture sample data set was used to validate the concordance of the mixture analysis results between the GeneMapper ID-X Software versions 1.1 and 1.2. The data set included 2-contributor mixtures made from 8 pairs of genomic DNA samples prepared in 11 mixture ratios: 1:0, 1:1, 1:2, 1:3, 1:5, 1:9, 9:1, 5:1, 3:1, 2:1, and 0:1. The mixture samples were amplified with the AmpFlSTR Identifiler (1 ng and ng), Profiler Plus, COfiler, and SGM Plus PCR Amplification kits. The samples were analyzed on two 3130xl instruments. 476 sample files were used to test Mixture Interpretation Threshold (MIT) pruning and sample segregation; 287 sample files were used to compare pattern extraction; 31 sample files were used to test Random Match Probability (RMP), Combined Probability of Inclusion/Exclusion (CPI/ CPE), and Likelihood Ratio (LR) calculations; 24 sample files were used for known matching; 4 pairs of sample files were used to test multiple kit merging. Table 2 Verification test cases The following mixture analysis log files or exported files in.txt format were generated on both versions of the software with the exact same population databases, MIT and PHR thresholds, theta values, LR hypotheses, and conclusive options: SampleClassification_Log for MIT pruning and sample segregation. MixtureSamples and MixtureSamples (analysis log) for pattern extraction, PHR, residual, Mx and Avg Mx calculation, as well as UI flags and values. MixtureSampleStatsCalc_Log for RMP, CPI, and known matching calculations. Individual MAData export files for RMP, CPI, LR, and multiple kit merging calculations. These text files were compared using the Beyond Compare Software v The comparison tool lined up the text files from the two software versions, and compared the file contents for concordance. Tested Cases Test Description Passing Criteria CODIS export removal of registered trademark CODIS export date format Profile Comparison Match Display Profile Comparison Marker Order Display Perform analysis of 10 single-source samples. After genotyping analysis, export the CODIS tables. Perform analysis of 10 single-source samples from projects created in September After genotyping analysis, export the CODIS tables. Using a project displaying the issue, set the percent match threshold to 90%, 80%, and 70%. Check the accuracy of the profile match filtering. Select one mixture sample set each from Identifiler, Profiler Plus, SGM Plus, and COfiler kit data with mixture ratios of 0:1, 1:1, 1:3, 1:5, 1:9, and 1:0. Set the percent-match threshold to 90%, 80%, and 70%. Check the accuracy of the matching entry filtering. Using test data above, verify matching entries displayed in the same marker order. Verify the registered trademark is removed in CODIS export file. Verify September date is displayed as SEP. Verify all matches correctly displayed at each match threshold. Verify all matches correctly displayed with marker order sorted by dye color and size. GeneMapper ID-X Software Version 1.2 User Bulletin 5

6 Verification Tested Cases Test Description Passing Criteria Modified Size Standard/ Analysis Method Export Size Calling Issue Y-scale Display Print Individual Sample Followed by Page Break Disable Spike Detection for Allelic Ladders Select 3 single-source samples from a previously analyzed project. Modify the size standard by adding or deleting one or more peaks and click OK to save. Without re-analyzing the data, export the project and delete the project from GeneMapper Manager. Reimport the project, open it, verify that the changed size standard settings are persisted. Select 3 single-source samples from a previously analyzed project. Modify the Analysis Method by changing any of the parameters and save. Without reanalyzing the data, export the project and delete the project from GeneMapper Manager. Re-import the project, open it and verify that the changed Analysis Method settings are persisted. Using a project displaying the issue, verify the issue is corrected. Select 5 single-source samples from previously analyzed projects, including data generated on the 3730 with GS600, 31xx with GS500LIZ and 31xx with GS500ROX. Re-analyze the data to verify no changes happened due to this update. Perform analysis of 10 single-source samples. After genotyping analysis, zoom in on the y-scale of each sample to view the y-scale values. Print the electropherograms. Perform analysis of 10 single-source samples. After genotyping analysis, print the profiles and genotype tables with the page break. Perform analysis of 10 single-source samples and 10 allelic ladders containing spikes. Genotype the data with the spike detection for allelic ladder enabled and disabled. Compare the allele calls, sizing, and PQV results. Verify that size standard changes are persisted and can be exported with the project. Verify that analysis method changes are persisted and can be exported with the project. Verify that the issue is corrected for a sample that was previously affected. Verify that all remaining data were correct and unaffected by the update. Verify that the Y-scale is printed according to the plot settings. Verify the page break is inserted properly. Verify that spikes are not detected in allelic ladders when the spike detection option is disabled. Verify that spikes are detected in allelic ladders when the spike detection option is enabled. Verify that spikes are detected in samples when the Allelic Ladder spike detection option is enabled and disabled. 6 GeneMapper ID-X Software Version 1.2 User Bulletin

7 Verification Table 3 Summary of verification testing results Testing Categories Subcategories Expected Outcome Result Concordance with GMID-X v1.1 Genotyping Allele calls 100% concordant, with ladder spike detection on. Peak Detection Size, height, area, and data point 100% concordant. Pass PQVs With the ladder spike detection on, all the PQV scores, including SQ values, shall be 100% concordant. With the ladder spike detection off, the relevant PQV scores are expected to have discrepancies. Pass Pass Mixture Analysis All the mixture analysis calculations and flags shall be 100% concordant using the same analysis method and thresholds. Pass Verification of patch updates Profile Comparison Incorrect Result The % match filter shall generate correct result all matching entries shall be displayed when the match threshold is adjusted. Pass Profile Comparison Sorting of Marker The markers shall be sorted consistently across the samples in the Profile Comparison view, first by dye then by the size order. Pass CODIS Export - Date Format Issue For CODIS export, all months shall be three letters. The September shall show up as SEP. Pass CODIS Export - Registered Mark Issue In the CODIS export, the registered trademark in the software name shall be removed. Pass Start a New Page to Print for each Sample With the option to insert a page break after each individual sample plot, the printout will show that each sample is printed starting on a new page, even though one sample may overflow to multiple pages. Pass Results All metrics were met as described above and only one result of note was identified. In one specific case, a labeling difference was found between the two software versions in the size plot and table. This instance involved one AmpFlSTR Sinofiler kit allelic ladder sample which was deemed to be low-quality due to poor resolution (broad peaks). Due to a broad peak, the 19.3 and 20 alleles in the D12 marker were labeled as a single 19.3 allele and, in GeneMapper ID-X Software version 1.1, shifted every subsequent peak to the right. This resulted in labeling the first peak (allele 7) in D18 as the last peak (allele 27) in D12. The OVL warning was properly triggered and the Genotype Quality flag for the D12 marker was red, indicating that the ladder failed. GeneMapper ID-X Software Version 1.2 User Bulletin 7

8 Verification Two issues were observed: 1. In both v1.1 and v1.2 software, labeling of the first D18 peak in the sample plot was not consistent with the allele name in the size table. 2. Labeling of the first D18 peak in the sample plot was different between v1.1 and v1.2 software. In v1.1 software: The allele designation was 7 in the sizing table The allele designation was 27 in the sample plot When the peak in the sample plot was highlighted, the D18 row in the sizing table was selected In v1.2 software: The allele designation was 27 in the sizing table The allele designation in the sample plot was 7 When the peak in the sample plot was highlighted, the D12 row in the sizing table was selected In all cases, the contents of the genotypes table from v1.1 and v1.2 match each other. This issue was not observed with any allelic ladders that passed all quality metrics. Conclusions The GeneMapper ID-X Software Version 1.2 can be used to process.fsa files generated on legacy capillary electrophoresis instruments and with existing AmpFlSTR kits. The same results for sizing, genotyping, and mixture analysis were obtained using GeneMapper ID-X Software versions 1.1 and 1.2. All updates to GeneMapper ID-X Software Version 1.2 were successfully and correctly implemented without deleterious effects on other software functionality. A difference in handling overlapping marker data was observed between the two software versions in one instance of a low-quality Sinofiler kit allelic ladder. Based on the nature of the modifications addressed in this update, and the testing that we performed, it is recommended that users evaluate this software as appropriate for their laboratory workflow to demonstrate concordance to previously validated GeneMapper ID-X Software versions. Laboratories should determine the appropriate level of testing required based on their internal software validation guidelines and those of the appropriate governing agencies. 8 GeneMapper ID-X Software Version 1.2 User Bulletin

9 Installing GeneMapper ID-X Software Version 1.2 Installing GeneMapper ID-X Software Version 1.2 General installation instructions About coinstallation with Data Collection Software Perform a fresh GeneMapper ID-X Software Version 1.2 installation Before installing the GeneMapper ID-X Software Version 1.2, review the GeneMapper ID-X Software Version 1.2 Installation Guide and any supplemental documentation. General guidance to ensure successful GeneMapper ID-X Software Version 1.2 installation or upgrade from previous GeneMapper ID-X Software versions includes: Computer with 1 GB or higher memory is highly recommended Computer virtual memory should be set at Custom Size ( MB) before software installation or upgrade User must log in to the local computer and have Administrator privileges when installing, un-installing, or upgrading the GeneMapper ID-X Software Version 1.2 When un-installing the GeneMapper ID-X Software, the user should log in using the same user name as the one used when installing the software to ensure clean un-installation. User must follow the un-installation message prompts during uninstallation process. When performing an upgrade on a stand-alone computer, use the Add/Remove Program feature in Microsoft Windows to un-install the previous version of GeneMapper ID-X Software Computers with both GeneMapper ID-X Software Version 1.2 and Data Collection Software installed (referred to as a co-installation ) should not be used as the host computer for other clients. Such host computers can only connect to one client computer. When GeneMapper ID-X Software Version 1.2 is not co-installed with Data Collection Software, remote autoanalysis is supported for the 31xx platform, but not for the 3500/3500xL and 310 platforms. Use the GeneMapper ID-X v1.2 Full or Client installation CD for fresh installations or installations to computers installed with GeneMapper ID Software v3.2. A detailed description of different fresh installation scenarios and steps performed by the user is summarized in Table 4 on pages 10 and 11. GeneMapper ID-X Software Version 1.2 User Bulletin 9

10 10 GeneMapper ID-X Software Version 1.2 User Bulletin:Verification Experiments and Installation Procedures Table 4 Fresh installation scenarios and steps Installation Type GeneMapper ID-X Software Version 1.2 Full installation GeneMapper ID-X Software Version 1.2 Full fresh installation GeneMapper ID-X Software Version 1.2 Full installation to a computer installed with GeneMapper ID Software v3.2 Scenario Choose CD Steps Stand Alone Computer without any version of GeneMapper ID-X Software or Data Collection Software installed Co-Install to a computer with Data Collection Software installed # Stand Alone Computer with GeneMapper ID Software v3.2 Co-Install to a computer with GeneMapper ID Software v3.2 and Data Collection Software installed # GeneMapper ID-X v1.2 Full PN Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. Installation takes about 1 hour to complete. 3. Enter the Registration Code to launch the software. 1. Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. The software detects the GeneMapper ID Software v3.x. 3. Export the data objects (projects, analysis methods, etc.) 4. Uninstall the GeneMapper ID Software v3.2 (Remove Program). 5. Restart the computer, then log on to the local computer to an account with Administrator privileges. 6. Install the GeneMapper ID-X Software v1.2 Full. 7. Enter the Registration Code to launch the software. Verification Experiments and Installation Procedures Installing GeneMapper ID-X Software Version 1.2

11 GeneMapper ID-X Software Version 1.2 User Bulletin:Verification Experiments and Installation Procedures 11 Installation Type GeneMapper ID-X Software Version 1.2 Client installation Fresh client installation Fresh installation to a computer with GeneMapper ID Software v3.2 Scenario Choose CD Steps Stand Alone Computer without any version of GeneMapper ID-X Software installed Co-Install to a computer with Data Collection Software installed # Stand Alone Computer with GMID v3.2 installed Co-Install to a computer with GeneMapper ID Software v3.2 and Data Collection Software installed GeneMapper ID-X v1.2 Client PN Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. Installation takes about 15 minutes to complete. 3. Enter the Registration Code to launch the software. 1. Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. The software detects the GeneMapper ID Software v3.x. The installation stops because GeneMapper ID-X v1.2 Client version does not have an export utility. 3. Insert a GeneMapper ID-X v1.2 full version CD to export the data objects (projects, analysis methods, etc.). 4. Uninstall the GeneMapper ID Software v3.2 (Remove Program). 5. Restart the computer, then log on to the local computer to an account with Administrator privileges. 6. Install the GeneMapper ID-X Software v1.2 Client. 7. Enter the registration code to launch the software. In order to use the Client version, a GeneMapper ID-X Software Version 1.2 Full version must be installed on another computer first. If GeneMapper ID Software v3.1 is installed on the computer, uninstall v3.1 or upgrade to GeneMapper ID v3.2 before installing GeneMapper ID-X Software Version 1.2. # GeneMapper ID-X Software Version 1.2 can be co-installed with legacy Data Collection Software v2.0 and 3.0, 3500 Data Collection Software on Windows XP OS, or on 3500 Data Collection Software on Windows Vista OS. However, co-installation with 3500 Data Collection Software is not recommended. Verification Experiments and Installation Procedures Installing GeneMapper ID-X Software Version 1.2

12 Installing GeneMapper ID-X Software Version 1.2 Upgrade from a previous version GeneMapper ID-X Software versions 1.0, 1.0.1, 1.1, and can be upgraded to GeneMapper ID-X Software Version 1.2 by using the GeneMapper ID-X Software Version 1.2 Full Upgrade or Client Upgrade CD. Table 5 Upgrade scenarios and steps 1. Before upgrading the software, back up all GeneMapper ID-X Software project data and results, close all instances of previous versions of GeneMapper ID-X Software (on both Client and Full computers), and close all other software programs and open windows. 2. During the installation of GeneMapper ID-X Software Version 1.2 (in both fresh installation and software upgrade cases): a. Install the GeneMapper ID-X Software Version 1.2 on the Full version first and then on all Client versions which will connect to the Full version database. b. Allow the CD to Autostart, or double-click the Setup.exe file to launch the installer. 3. After the software upgrade, enter the registration code obtained with the previous software version to launch the software. The data analyzed from previous GeneMapper ID-X Software versions can be imported and viewed in GeneMapper ID-X Software Version 1.2. A detailed description of different upgrade scenarios and steps performed by the user is summarized in Table 5. Installation Type Scenario Choose CD Steps Upgrade to GeneMapper ID-X Software Version 1.2 Full Upgrade GeneMapper ID-X Software v1.0, 1.0.1, or 1.1 Full installed on a stand-alone computer GeneMapper ID-X v1.2 Full Upgrade PN Log on to the local computer to an account with Administrator privileges. 2. Export the data objects (projects, analysis methods, etc.) 3. Uninstall the previous version of GeneMapper ID-X Software (Remove Program). 4. Restart the computer, then log on to the local computer to an account with Administrator privileges. 5. Insert the CD. 6. Install the GeneMapper ID-X Software v1.2 Full Upgrade. 7. Enter the Registration Code from the previous version to launch the software. Upgrade GeneMapper ID-X Software v1.0, 1.0.1, or 1.1 co-installed with Data Collection Software 1. Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. 3. Enter the Registration Code from the previous version to launch the software. 12 GeneMapper ID-X Software Version 1.2 User Bulletin

13 Installing GeneMapper ID-X Software Version 1.2 Installation Type Scenario Choose CD Steps Upgrade to GeneMapper ID-X Software Version 1.2 Client Upgrade GeneMapper ID-X Software v1.0, 1.0.1, or 1.1 Client installed on a stand-alone computer Upgrade GeneMapper ID-X Software v1.0, 1.0.1, or 1.1 Client co-installed with Data Collection Software GeneMapper ID-X v1.2 Client Upgrade PN Log on to the local computer to an account with Administrator privileges. 2. Insert the CD and follow the instructions. The software detects the previous version of GeneMapper ID-X Software. 3. Enter the Registration Code from the previous version to launch the software. In order to use the Client version, a GeneMapper ID-X Software Version 1.2 Full version must be installed on another computer first. Please note: Upgrade all instances of previous versions of the GeneMapper ID-X Software, including both GeneMapper ID-X Software Client and Full versions before launching the GeneMapper ID-X Software Version 1.2. Depending on your computer configuration, you may be able to directly upgrade the previous version of GeneMapper ID-X Software to version 1.2, or you may need to completely uninstall the previous version before installing version 1.2. For Full installations of v1.2, you must manually uninstall any previous versions. For Client versions of v1.2, the installer software automatically performs the upgrade when you insert the version 1.2 CD. If the GeneMapper ID-X Software is installed on a computer platform that has not been validated by Applied Biosystems/Life Technologies, you may experience difficulties during the software upgrade. Please review the list of recommended software operating systems before beginning installation, and report any issues encountered during installation to your local Human Identification support specialist. Troubleshooting Setup.exe errors during software installation If you see the following error message, or any setup.exe error, when you install the software, the virtual memory settings of your Windows operating system are insufficient and need to be adjusted as follows: 1. Close the error message window and let the installation finish, then uninstall the software using Add/Remove programs. 2. After uninstallation, adjust the virtual memory settings: a. Right-click My Computer, then select Properties. b. In the System Properties dialog, select the Advanced tab, then select Performance Settings. GeneMapper ID-X Software Version 1.2 User Bulletin 13

14 Installing GeneMapper ID-X Software Version 1.2 c. In the Performance Options dialog, select the Advanced tab, then select Virtual memory Change. d. Select the drive that contains the Windows operating systems (usually the C: drive), then select Custom size. Enter 2046 MB for Initial size and 4092 for Maximum size. Note: For some systems, any values larger than 500 MB may be sufficient. e. Click Set, click OK, then click Apply. 3. Restart the computer, then return to the Virtual Memory dialog and confirm that the Paging File Size is set for the drive that contains the Windows operating system (usually the C: drive). 4. Install the GeneMapper ID-X Software Version 1.2. Note: If you receive an error at this stage indicating that Oracle is found on the system, delete the X:\AppliedBiosystems\OracleGMIDX folder, restart the system, then attempt another install. In more severe cases, you may need to run the RemoveOracle.exe program found on the installation CD in the Tools folder. 14 GeneMapper ID-X Software Version 1.2 User Bulletin

15 Installing GeneMapper ID-X Software Version 1.2 Obtaining support For HID support: In the United States and Canada send an to or call option 1. Outside the United States and Canada contact your local support office. For the latest services and support information for all locations, go to: At the Applied Biosystems web site, you can: Access worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities. Search through frequently asked questions (FAQs). Submit a question directly to Technical Support. Order Applied Biosystems user documents, SDSs, certificates of analysis, and other related documents. Download PDF documents. Obtain information about customer training. Download software updates and patches. GeneMapper ID-X Software Version 1.2 User Bulletin 15

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