User Bulletin GeneMapper ID-X Software Version 1.1.1 Update October 2009 SUBJECT: GeneMapper ID-X Software Version 1.1.1 Verification In this user bulletin Overview This user bulletin covers: Overview...................................................... 1 Software verification goals........................................ 2 Software verification testing and results.............................. 2 Print performance test results...................................... 4 Issue updates................................................... 5 New features................................................... 8 Conclusions................................................... 10 Upgrade installation instructions................................... 10 Recommendations.............................................. 10 GeneMapper ID-X Software version 1.1.1 contains the same functionality as GeneMapper ID-X Software version 1.1. Version 1.1.1 incorporates two new features and addresses eight known issues. Current software functionality is not affected. New features 1. An option to separate each sample plot and table on individual pages when printing multiple samples at a time. 2. An option to Enable/Disable spike detection for allelic ladder samples. Updates that address v 1.1 issues: 1. Improvements to the print spooling speed, resulting in faster printing of electropherograms and tables from both GeneMapper ID-X Full and GeneMapper ID-X Client software versions. 2. Removal of the Registered Trademark ( ) character which could not be translated by Chinese operating systems from the CODIS export (.dat) file. 3. Modification of the CODIS export file such that September is displayed in 3 character format as SEP.
4. Resolution of an issue that resulted in occasional incomplete display of matching profiles in the Profile Comparison tool. 5. Resolution of an issue that sometimes resulted in the Profile Comparison tool not displaying the markers for matching profiles by color (B, G, Y, R) and size. 6. Resolution of an issue where, if the project is not re-analyzed, modifications to the size standard or analysis method are not exported when the project is exported. 7. Resolution of a rare issue observed with GeneScan 600 when size standard fragments form a perfect line that results in incorrect size calling and abnormal peak morphology. 8. Resolution of an issue that results in the Y scale being always set to Scale to Maximum Y in the printed plot or print preview for the first time after a plot setting is applied, regardless of the plot settings specified. Software verification goals The goals of the Applied Biosystems software verification were to: Confirm that the updates successfully address the known issues Confirm that the new functionality performs as designed Confirm that the modifications do not adversely affect the existing functionality within the software Demonstrate an improvement to the printing speed Software verification testing and results Table 1 summarizes the software verification tests performed, criteria for passing the tests, and test results. Table 1 Tests and Results Tested Cases Description ing Criteria Results CODIS export removal of registered trademark Perform analysis of 10 singlesource samples. After genotyping analysis, export the CODIS tables. Verify registered trademark is removed in CODIS export file. CODIS export date format Perform analysis of 10 singlesource samples from projects created in September, 2008. After genotyping analysis, export the CODIS tables. Verify September date is displayed as SEP. 2 GeneMapper ID-X Software Version 1.1.1 Verification
Tested Cases Description ing Criteria Results Profile Comparison match display Using a project displaying the issue, set the percent match threshold to 90%, 80%, and 70%. Check the accuracy of the matching entry 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. Verify all matches correctly displayed at each match threshold. Profile Comparison marker order display Using test data above, verify matching entries displayed in the same marker order. Verify all matches correctly displayed with marker order sorted by dye color and size. Modified Size Standard/Analysis Method export 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 reanalyzing the data, export the project and delete the project from GeneMapper Manager. Re-import the project and open it. Select 3 single-source samples from a previously analyzed project. Modify the Analysis Method by changing any of the parameters and save. Without re-analyzing the data, export the project and delete the project from GeneMapper Manager. Re-import the project and open it. Verify size standard changes are persisted and can be exported with the project. Verify analysis method changes are persisted and can be exported with the project. Size calling issue Select 5 single-source samples from previously analyzed projects, including data generated on the 3730 with GeneScan 600, 31xx with GeneScan 500 LIZ and 31xx with GeneScan 500 ROX. Re-analyze the data. Verify size-calling is correct for a sample that was previously affected by the issue. Verify data unaffected by the issue are unchanged after the modification. Y-scale display Perform analysis of 10 singlesource samples. After genotyping analysis, Zoom in the y-scale of each sample to different values. Print the electropherograms. Verify Y-scale is printed according to the plot settings. Print individual sample followed by page break Perform analysis of 10 singlesource samples. After genotyping analysis, print the profiles and genotype tables with the page break. Verify page break is inserted properly. GeneMapper ID-X Software Version 1.1.1 Verification 3
Tested Cases Description ing Criteria Results Disable spike detection for allelic ladders Perform analysis of 10 singlesource samples and 10 allelic ladders containing spikes. Genotype the data with the spike detection for allelic ladder enabled and disabled. Compare the results of allele calls, sizing, and PQV. 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 regardless of whether the allelic ladder spike detection is enabled or disabled. Print performance test results Print Performance tests were benchmarked against the GeneMapper ID-X v1.1 released version, based on the following tests: 96 samples with Traditional Genotype Plot Setting printed on letter size paper (Portrait orientation) Computer Configuration: GeneMapper ID-X Full (Dell 755 desktop, Windows XP SP2, 3 GHz, 1GB RAM) GeneMapper ID-X Client (Dell DX 280 desktop, Windows XP SP2, 2.8 GHz, 512 MB RAM) Printer: HP Color LaserJet 3800, 160 MB Total RAM (System 128MB, Imaging 32 MB) Table 2 shows the improvements observed: Table 2 Improvements in printing speed and in print-speed consistency between GeneMapper ID-X v1.1 software and GeneMapper ID-X v1.1.1 software Factor Spooling time Print time Description Time from clicking Print until Progress bar shows 100% Time from clicking Print until last page printed Difference (GM ID-X v1.1.1 vs. v1.1) 5- to 9-fold faster Full install: 31% faster Client install: 184% faster 4 GeneMapper ID-X Software Version 1.1.1 Verification
Factor Full/client print speed consistency Print time per page Display Print Preview Description For Full and Client installations Time from clicking Print until page printed Time from clicking Print Preview until first page of preview displayed. Difference (GM ID-X v1.1.1 vs. v1.1) Full install v1.1.1: 17.5 min. v1.1: 25 min. Client install v1.1.1: 19 min. v1.1: 54 min. v1.1.1: Full install: 5-7 sec Client install: 5-7 sec v1.1 Full install: 7 sec Client install: 22 sec Interval decreased to 1 sec Applied Biosystems also tested different plot settings with different numbers of pages per print job. In both GeneMapper ID-X v1.1.1 Full and Client formats, the time to print one page is about 6-9 seconds. These results demonstrate that printing speed with GeneMapper ID-X v1.1.1 is faster and more consistent than with GeneMapper ID-X v1.1. Based on the internal and external testing conducted at Applied Biosystems and five external customer sites, we found that printing speed is directly related to printer memory. The bigger the printer memory, the faster the overall printing speed. Furthermore, printing speed may also vary based on the differences in computer configurations, printer settings, the network speed, etc. When printing from a local printer that is directly connected to a GeneMapper ID-X Software host computer, the printing speed may be slower than when printing from a network printer. Issue updates CODIS export file Removed the registered trademark character to enable operating system translation to Chinese (See Figure 1 on page 6) Reduced the display format for September to 3 characters (SEP) to align with other month formats (See Figure 1 on page 6) GeneMapper ID-X Software Version 1.1.1 Verification 5
Registered trademark removed from GeneMapper ID-X Revised date format for September Figure 1 Updated CODIS export file Profile Comparison tool When the comparison tool was run with incremental increases of the match threshold from 60 to 100%, all comparisons were correctly reported at the 60% threshold. In some instances, as the threshold was increased to 70% and 80%, GMIDX v1.1 no longer reported comparisons that were clearly above the 70% and 80% thresholds based on the results at 60%. The correct comparisons were reported again at the 90% threshold. In GMIDX v1.1.1, correct comparisons were displayed at the 50%, 60%, 70%, 80%, 90% and 100% match thresholds. In GMIDX v1.1.1, the marker display order in the match window is always by size within kit dye order, for example blue, green, yellow, red for Identifiler kit data results. Figure 2 shows the data display with the match threshold set to 80%. Figure 2 Match threshold = 80% Size calling algorithm The size calling algorithm was updated to address an issue that occurs in the rare instance that 3 data points form a perfect line when data point is plotted vs. base pair size. This scenario has been observed with GeneScan 600 LIZ size standard but not with GeneScan 500 LIZ or GeneScan 500 ROX, probably 6 GeneMapper ID-X Software Version 1.1.1 Verification
because of the higher density of size standard peaks in the GeneScan 600 LIZ size standard. Reinjection of the samples did not reproduce the issue. Peaks affected by this occurrence demonstrate a characteristic morphology as shown in Figure 3. Figure 3 Affected peak before update This effect resulted from a rounding error in the sizing algorithm. Following the update, the original data displayed normal peak morphology and correct sizing as shown in Figure 4. Figure 4 Correct peak after update After the correction, concordant results were obtained for those samples that had not been affected by the error. GeneMapper ID-X Software Version 1.1.1 Verification 7
New features Page break option for printing This feature adds an option to insert a page break after each individual sample plot and table print. The selection can be made in Page Setup under the Format tab, as shown in Figure 5. GeneMapper ID-X v1.1 GeneMapper ID-X v1.1.1 Figure 5 Page break feature added to Page Setup tab The page break was inserted correctly between samples when printing following selection of Individual Plot and Table by Sample in GeneMapper ID-X v1.1.1. Option to enable and disable spike detection for allelic ladder samples This feature provides an option in the Analysis Method Editor to disable spike detection for allelic ladder samples. This selection can be made in Allelic Detection under the Peak Quality tab, as shown in Figure 6 on page 9. It does not alter the spike detection algorithm and has no impact on detecting spikes for other sample types. 8 GeneMapper ID-X Software Version 1.1.1 Verification
Figure 6 Spike detection enable/disable feature added to Peak Quality tab This feature addresses rare occasions where allelic ladder peaks are labeled as spikes preventing use of the allelic ladder for genotyping. Figures 7 and 8 show the allelic ladder peaks with the spike detection option enabled and disabled, respectively. Figure 7 Spike detection enabled Figure 8 Spike detection disabled GeneMapper ID-X Software Version 1.1.1 Verification 9
Conclusions The internal software verification test results demonstrated that the GeneMapper ID-X v1.1.1 successfully addressed the known issues and added new features without affecting the existing functionality of the software. Upgrade installation instructions IMPORTANT! Upgrade GeneMapper ID-X v1.1.1 on the Full version computer first. Then upgrade all Client versions that will connect to the Full version database. 1. Before upgrading to GeneMapper ID-X v1.1.1: a. Back up GeneMapper ID-X Software project data and results. b. Close all instances of the GeneMapper ID-X v1.1 application (on computers with either Client or Full installations). 2. Upgrade to GeneMapper ID-X v1.1.1: a. Double-click Setup.exe to launch the upgrade. b. Follow the instructions provided. 3. After upgrading all GeneMapper ID-X v1.1 instances, restart the computer, then launch the GeneMapper ID-X v1.1.1 software. Note: You must update all instances of GeneMapper ID-X v1.1 software including GeneMapper ID-X Client and Full versions before launching before launching GeneMapper ID-X v 1.1.1. The GeneMapper ID-X v1.1.1 software update can only upgrade GeneMapper ID-X v1.1 software. It cannot be directly applied to the GeneMapper ID-X v1.0 or v1.0.1 software versions. If GeneMapper ID-X software is installed on a computer platform that is not supported by Applied Biosystems, users may experience difficulties during software upgrade. Please report any issues encountered during the upgrade to your local Human Identification support specialist. Recommendations To achieve fast printing speeds, Applied Biosystems highly recommends using a printer that has at least 128MB memory. Match the paper size setting on both the printer and the software. If a printer has a Mopier Mode option, enable the Mopier Mode to handle multiple collated copies. Based on the nature of the modifications addressed in this update, and the testing performed at Applied Biosystems, it is recommended that laboratories conduct a performance verification to demonstrate concordance with 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. 10 GeneMapper ID-X Software Version 1.1.1 Verification
GeneMapper ID-X Software Version 1.1.1 Verification 11
For Research, Forensic, or Paternity Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in this document is subject to change without notice. APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. Notice to Purchaser: 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 Applied Biosystems, either expressly, or by estoppel. GeneMapper ID-X Software has undergone a verification process defined by Applied Biosystems. However, human identification laboratories analyzing forensic, paternity, databasing, and single-source samples that choose to use GeneMapper ID-X Software for data analysis should perform their own appropriate validation studies. TRADEMARKS: The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. Copyright 2009, Life Technologies Corporation. All rights reserved. Part Number 4444446 Rev. A 10/2009 Stock Number 112UB27-01 Headquarters 850 Lincoln Centre Drive Foster City, CA 94404 USA Phone 650.638.5800 Toll Free 800.345.5224 www.appliedbiosystems.com International Sales For our office locations please call the division headquarters or refer to our Web site at www.appliedbiosystems.com/about/offices.cfm