GeneMapper ID Software User Bulletin (PN 4352543, Rev. A)
Contents
1. Installation Procedures and New Features for GeneMapper ID Software v3 2 35 GeneMapper ID Software Create the To create the HID Classic analysis method HID Classic Analysis Method 1 Select Tools gt GeneMapper Manager to open the GeneMapper Manager 2 Select the Analysis Methods tab then click New to open the New Analysis Method dialog box New Analysis Method x Select analysis type e Bo C SNaPshot Microsatellite OK Cancel 3 Select HID then click OK to open the Analysis Method Editor 4 Select the analysis method settings shown in Table 3a on page 31 through Table 3e on page 35 IMPORTANT You must select your settings on all the tabs before you click OK to save the analysis method and return to GeneMapper Manager What Next After creating analysis methods for the Yfiler kit continue with data analysis as follows 1 Import sample files 2 Select analysis parameters 3 Analyze the project For More For more information refer to the following documents Information GeneMapper ID Software Version 3 1 Human Identification Analysis User Guide PN 4338775 GeneMapper ID Software Version 3 1 Human Identification Analysis Tutorial PN 4335523 AmpFtSTR Yfiler PCR Amplification Kit Users Manual PN 4358101 36 User Bulletin Creating a Table Setting and Uploading Exported Haplotype s Creating a Table Setting and Uploading Exporte2. Unlabeled peak assignments Installation Procedures and New Features for GeneMapper ID Software v3 2 23 GeneMapper ID Software Labels Retained in Base Pair and Data Point Views 24 The X axis can be displayed in either base pairs or data points In GeneMapper D Software v3 1 when switching from the align by base pair to the align by data point views for the X axis the labels associated with the peaks were not retained in both views In GeneMapper D Software v3 2 the labels are automatically retained in both views as shown below Fle Edt View Tools Alleles Hep Passing Cocina fo xij NT NE EST a n z I aid vr TEST CETT ES araple Nerve Poa Q0 sq x wile vt C r B_DYSAFE B E DYSIN i w6 o X9 o 14050160 170 too 190 00 0 200 200 240 250 NO T0 23 023 000 ao xe 2000 1000 D m m m g PI m CDSE E J EDs 1 o Te 4 o r M0 19 mo Mo 22 mo oa 29 00 18 000 29 039 o 35 200 1000 e he r 5 z Lr e 7 uu JAEJNEJNEJNEUSE JGAE IEEE 2 mox m 2000 D ta Ej 3 mey jl ED JE NEC NEC NEC UNE DA DA so w se DAE NE 2E UE E DNE INANE NN RN NN 2000 D m m Ds E Figure 4 Align by base pair Fle Edt View Pret Setting AmpFLSTR Gerctyo ng Tools Alleles Heb sees f A BT MB f wd Ia Bi ale Eu W Surple Nurse Pund Qo sq n mac n a E so m m
3. TRADEMARKS ABI Prism AmpFZSTR Applied Biosystems COfiler GeneMapper GeneScan Genotyper Identifiler LIZ Profiler Profiler Plus and SGM Plus are registered trademarks and AB Design AmpFZSTR Blue AmpF STR Green Applera iScience Design Quantifiler ROX SEfiler and Yfiler are trademarks of Applera Corporation or its subsidiaries in the U S and or certain other countries Acrobat is a registered trademark of Adobe Systems Incorporated GeneAmp is a registered trademark of Roche Molecular Systems Inc Macintosh is a registered trademark of Apple Computer Inc Oracle is a registered trademark of Oracle Corporation Pentium is a registered trademark of Intel Corporation Windows and Windows NT are registered trademarks of Microsoft Corporation All other trademarks are the sole property of their respective owners This product includes software developed by the Apache Software Foundation http www apache org Copyright 1999 2000 The Apache Software Foundation All rights reserved This product includes software developed by the ExoLab Project http www exolab org Copyright 2000 Intalio Inc All rights reserved Science iScience To better understand the complex interaction of biological systems life scientists are developing revolutionary approaches to discovery that unite technology informatics and traditional laboratory research In partnership with our customers Applied Biosystems p
4. Eie Edt Yew Insert Format Tools Data Window Heb Adobe PDF 62 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 183 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 B4 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 85 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 85 3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfile vi CE G5 HID GS500 09 87 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 0 9 88 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 89 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 90 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 91 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 92 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 93 3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 94 3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 95 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfil
5. F Genetic Analyzer e GS STR Pop4 1 ml G5v2 ABI Prism 3100 v1 1 Microsoft Windows NT9 e GS36 Pop4 F Genetic Analyzer e GS 36vb Pop4 G5 v2 0 Microsoft Windows 2000 i 44 User Bulletin Category 1 Peak Detection and Genotyping Reproducibility Category 1 Peak Detection and Genotyping Reproducibility The first test category evaluated genotype concordance using single source population DNA samples male male mixture samples and male female mixture samples All samples were amplified with the Yfiler kit Two comparison studies were conducted to verify genotype concordance using DNA samples previously amplified with the Yfiler kit These data were used to compare the genotype results from data analysis with GeneScan Software v3 7 1 and Genotyper Software v3 7 both running on the Windows NT operating system to GeneMapper D Software v3 2 running on the Windows 2000 operating system using the Advanced mode Single Source The first comparison study consisted of Population DNA Samples Eighty 80 samples from the Yfiler kit population study Four 4 positive controls One 1 negative control Six 6 ladders These samples were electrophoresed on the ABI PRISM 3100 Genetic Analyzer and consisted of 1222 alleles from the samples 60 alleles from the controls and 137 alleles from the ladders The samples were examined for reproducibility Mixture Samples The second comparison study consisted of mixtu
6. e a te E bj LII am E so P v so o A m x LII m axo so eo 2000 i RM m Ej 3 L Yavi n jl E E ere 2000 m fa s E 1 zi Figure 5 Align by data point User Bulletin Section 3 New Features and Procedures Yfiler Kit Section 3 New Features and Procedures Yfiler Kit This section covers New Features and Procedures Summary 0 005 23 Allele Calling Parameters for New Marker Repeat Types ae Plus Stutter Filtering and 2 bp Filtering Workaround 2T Creating HID Analysis Methods for the Yfiler Kit 30 Creating a Table Setting and Uploading Exported Haplotype s 37 New Features and Procedures Summary Two features have been added in GeneMapper ID Software v3 2 to facilitate analysis of the AmpFZSTR Yfiler PCR Amplification Kit Allele calling parameters for new marker repeat types Plus stutter filtering Additionally Applied Biosystems has developed several procedures for using GeneMapper ID Software v3 2 with the Yfiler kit Workaround for the DYS19 locus 2 bp filtering Creating HID analysis methods for the Yfiler kit Exporting haplotypes from GeneMapper ID Software v3 2 Table 2 on page 26 provides a brief summary of these new features and procedures For more detailed information see the pages referenced in the table Installation Procedures and New Features for GeneMapper ID Software v3 2 25 GeneMapper ID Software Table 2 New fe
7. the stutter peak if Peak B the true allele meets two criteria Peak B is higher than Peak A by the specified percentage and Peak B is within the specified proximity size in base pairs range relative to Peak A Table 7 below shows the results for observation 3 Table 7 Observation 3 non concordant loci GeneMapper D Genotyper Software v3 7 Software v3 2 Marker Locus Allele 1 Allele 2 Allele 3 Allele 4 Allele 1 Allele 2 DYS439 11 OL 12 13 12 13 DYS456 15 16 OL 17 15 17 Installation Procedures and New Features for GeneMapper ID Software v3 2 As shown in Figure 3 and Figure 4 on page 52 these two loci alleles did not meet these criteria due to A product resulting in the detection of a third peak Peak C The filtering in Genotyper Software v3 7 compared Peak A to Peak C GeneMapper ZD Software v3 2 appropriately filtered the stutter and the shoulder peak using defined bin sets 51 GeneMapper ID Software Genotyper Software v3 7 ES Genotyper 3 7 Plots Yfiler V1 4 GTA GeneMapper D Software v3 2 File Edit View Tools Alleles Help Plot Setting A mpFLSTR Genotyping EH Panes fr Tix gef LF ME do P adi n Sepe None HE RET RR i ES C US IJi EJ sgo sQ 8 xl 200 202 204 206 208 210 212 214 216 218 220 222 224 226 E210 1a fsa 50 Yellow 10 1a Es 1500 1000 500 i 3 x
8. 20 48X IDE CD ROM 10 100 NIC with RWV internal Monitor 800 x 600 pixels size 1024 x 768 or higher pixels size 17 inch monitor 19 inch or larger monitor Operating System Microsoft Windows NT version 4 0 Microsoft Windows 2000 Service Pack 5 or higher Professional Service Pack 4 Microsoft Windows XP Professional Service Pack 1 Ethernet Capability Network card for Oracle Network card for Oracle installation installation e TCP IP must be installed prior to TCP IP must be installed prior to Oracle installation Oracle installation Special Considerations The GeneMapper ID software does not run correctly on dual processor Pentium computers A single processor computer is required 6 User Bulletin Installation Requirements GeneMapper JD Software v3 2 runs on Windows NT Windows 2000 and Windows XP platforms only Conversion utilities are included for analyzing data from Macintosh based sample files For conversion procedures refer to the GeneMapper ID Software Version 3 1 Human Identification Analysis User Guide PN 4338775 The GeneMapper D Software v3 2 automated installer operates only on computers running Microsoft Internet Explorer If you are using another browser you will need to manually launch the installer instructions are provided in step 2 on page 12 Compatibility The GeneMapper JD software uses an Oracle database with Oracle GeneMapper ID Software
9. Genetic Analyzer that uses Data Collection Software v2 0 the Data Collection software must be running If the Data Collection software is not running the GeneMapper JD software does not register with the Data Service software Login When installing GeneMapper ID Software v3 2 you must Requirements Have Administrator privileges on the local computer that is have complete and unrestricted access to the local computer Login to the local computer not a network domain Besure there is no other Oracle client or Oracle server on the computer GeneMapper ID Software v3 2 is not supported on these configurations 8 User Bulletin Installation Requirements PDF File Reader To open the user documentation included on the GeneMapper ID Software v3 2 installation CD use a program that reads PDF files such as the Adobe Acrobat Reader software The GeneMapper ID Software v3 2 installer does not install Acrobat Reader If you do not have a program that reads PDF files you can download Acrobat Reader from either the Adobe or Applied Biosystems websites www adobe com www appliedbiosystems com support software Installation Procedures and New Features for GeneMapper ID Software v3 2 9 GeneMapper ID Software Installation Procedures What Gets The installer on the GeneMapper ID Software v3 2 CD installs Installed GeneMapper JD Software v3 2 Oracle database Panel folder that contains AmpF STR kit panels and
10. Kit Table 3c Analysis method settings Peak Detector tab Tab Settings Peak Detector xi Peak Quality Quality Flags Peak Detection Algorithm Advanced Select Advanced or Range Peak Detect s E Classic here pm Peak Amplitude Thresholds depending on Partial Range Partial Sizes B fo R e the analysis Start Pt 2764 Start Sizes G fo o fo method you are Stop Pt fi 0000 Stop Size 400 j creating See the YEE EEA Y o Notes below Smoothing ai Si Min Peak Half Width b pts Smoothing C None Light Polynomial Degree b C Heavy Peak Window Size 15 pts r Slope Threshold Baseline Window 5 pts Peak Start foo Size Calling Method Peak End oo 2nd Order Least Squares 3rd Order Least Squares Cubic Spline Interpolation Local Southern Method C Global Southern Method Factory Defaults OK Cancel Notes for the Peak Detector tab From the Peak Detection Algorithm drop down list select Advanced if you are creating an HID Advanced analysis method or Classic if you are creating an HID Classic analysis method Installation Procedures and New Features for GeneMapper ID Software v3 2 33 GeneMapper ID Software Table 3d Analysis method settings Peak Quality tab Tab Settings Peak Quality Analysis Method Editor HID E xj General Allele Peak Detector Peak Quality Qualit
11. a Leave the User Name as gmid and leave the Password field blank b From the Database Host drop down list select the local computer that 1s select the name of the computer you are currently working on c Click OK The Enter Password dialog box opens Enter Password Your password has expired You must change your password before you can log into the system User Name gmid Old Password Password Confirm Password Cancel Create your password a Leave the Old Password field blank b In the Password field enter a new user defined password c Confirm the password d Click OK The GeneMapper JD software starts User Bulletin Section 2 Section 2 New Features All AmpF4STR Kits New Features All AmpF STR Kits This section covers New Features Summaty lt jc 000 sik veer x eme s 17 Export Combined Table Format u ss saya eee erm kla awa 18 Changes to the Electropherogram Displays 22 New Features Summary Table 1 below provides a brief summary of the new features included in GeneMapper JD Software v3 2 For more detailed information see the pages referenced in the table Table 1 New features summary Feature See Description Page Export Combined Table format When exporting from the Samples view you can now export 18 samples that do not pass sizing along with samples that pass sizing This feature combin
12. an al ka ATE EREDA ERN 33 Installation Procedures and New Features for GeneMapper ID Software v3 2 41 GeneMapper ID Software Introduction Test Plan Test Categories Evaluation 42 The test plan which Applied Biosystems has defined as verification of the software was designed to evaluate the performance of GeneMapper ID Software v3 2 for the human identification communities Applied Biosystems performed verification of GeneMapper JD Software v3 2 to assess the performance robustness and feature design in four specific categories Peak Detection and Genotyping Reproducibility page 45 Algorithm Testing page 46 Data Handling page 48 Workflow page 48 GeneMapper ID Software v3 2 verification was performed to Confirm and document the functionality of the new software features Assess the functionality of the minor modifications made to the analysis method Our findings demonstrate that GeneMapper ID Software v3 2 with its default settings and panels and bin sets is valid for forensic paternity and databasing analyses GeneMapper JD Software v 3 2 accurately detects genotypes and performs quality checks when performing STR analysis User Bulletin Materials and Methods Materials and Methods This section describes the AmpF STR kit sample types instruments and software used for the GeneMapper D Software v3 2 verification testing Kit The AmpF STR Yfiler PCR Amplificat
13. bins Microsatellite and SNP genotyping example data Electronic PDF versions of the user guide and tutorial Size standard folder that contains various size standards Default plot and table settings Before You Begin Before you begin the installation be sure all requirements are met the Installation See the references listed below Computer Specifications on page 6 Compatibility with Oracle Databases on page 7 Compatibility with 3100 3100 Avant Genetic Analyzers on page 8 Login Requirements on page 8 PDF File Reader on page 9 Installation Time The total time required to install the GeneMapper JD software is approximately 60 minutes This time may vary depending on your system configuration Procedure If necessary remove previous versions of the Flowchart GeneMapper Software page 11 Install or upgrade the GeneMapper D software page 11 Installation Procedures v Register the GeneMapper ID software page 14 v Launch the GeneMapper D software page 14 10 User Bulletin Remove Non Validated GeneMapper Software If Necessary Install the Software Installation Procedures If you have either GeneMapper Software v3 0 or v3 5 on your computer you must remove it before installing the GeneMapper D software To remove GeneMapper software v3 0 or v3 5 l Log in to the local computer as an Administrator 2 Select Start gt Control Pan
14. instruments operating systems and Data Collection software listed in the table below Compatibility is defined as the ability of the GeneMapper ZD software to perform at least one of the following functions A Analyze sample files generated from the instrument B Coexist with the instrument s Data Collection software C Run concurrently with the instrument s Data Collection software D Work with the automation feature that is autoanalysis in the instrument s Data Collection software Data Functions as listed above Instrument PU Collection y Software A B Cc D ABI Prism 377 Macintosh a 2 6 X DNA Sequencer Microsoft Windows NT 3 0 X X X ABI PRISM 310 Macintosh a 2 1 X Genetic Analyzer Microsoft Windows NT9 v3 0 X X X Microsoft Windows 2000 v3 0 x X X ABI Prism 3100 Microsoft Windows NT9 v1 1 X Genetic Analyzer Microsoft Windows 2000 v2 0 X x X X ABI PRISM Microsoft Windows NT9 v1 0 X 3100 Avant Genetic Analyzer Microsoft Windows 2000 v2 0 X X X X a Data generated from a 310 Genetic Analyzer or 377 DNA Sequencer using a Macintosh platform must be converted to a Microsoft Windows based format before they can be used with the GeneMapper D software For information on converting Macintosh sample files refer to the GeneMapper ID Software Version 3 1 Human Identification Analysis User Guid
15. leave the default values c In the Allele Settings section Enter 2 in the Number of Alleles field Deselect the Keep Allele Size check box 2 Table Setting Editor E xj General Samples Genatypes Genotypes Table Settings Column Settings Show Column Fitering Content 1 m Sample File Show All Records Show Al Records r Run Name Show All Records Show Al Records Click OK to save the table settings close the Table Setting Editor and return to the GeneMapper Manager Installation Procedures and New Features for GeneMapper ID Software v3 2 39 GeneMapper ID Software Upload the Upload the exported haplotype s into the Yfiler Haplotype Exported Haplotype s 40 Database To upload the exported haplotype s 1 Ifyou are not already there open the project in GeneMapper ID Software v3 2 2 From the Table Settings drop down list select the table 2 GeneMapper ID v3 2 Sensitivityseries_Yfiler gmid Is Logged In File Edit Analysis View Tools Help setting you created specifically to export haplotype s for searching the Yfiler Haplotype Database B PY tievi B_DYS456 Marker Allele 1 B_DYS36 B DYS456 15 B_DYS390 E B DYS389t B DYS389113 i EE e lil HUE ER Hl Ej B Table Seting Jamoriste_vtier Upload ta E B amp as AmpFLSTR Table ID Ta
16. tables were exported from the Samples view using the Export Combined Table format Eighty 80 samples from the Yfiler kit population study were used The results obtained verified that GeneMapper JD Software v3 2 is 100 functional in its ability to Export projects using the Export Combined Table format Track all samples in an electrophoresis run samples that do not pass sizing as well as samples that pass sizing 54 User Bulletin Printing Labeled Size Standard Peaks Results for Category 4 Workflow The purpose of this test was to verify that the size standard plots could be printed in different display configurations The results obtained verified that GeneMapper JD Software v3 2 is 100 functional in its ability to display and print labels on size standards in different plot configurations For example displaying five labeled size standards separated into five panes using three levels of magnification Results for Category 4 Workflow Displaying Labeled Peak Assignments Retaining Labels All size standards from eighty 80 DNA samples from the Yfiler kit single source population study were examined All peaks were correctly labeled The results obtained verified that GeneMapper JD Software v3 2 is 100 functional in its ability to switch back and forth between the align by base pair and align by data point views for the X axis Results Summary Applied Biosystems verification testing demonstra
17. 9 and page 20 for an example of each format 5 Ifyou selected One line per marker in step 4 select deselect the Include all marker information checkbox as necessary As shown in the pop up text below if you select this option marker information for samples with no sizing data will be included in the Export Combined Table JExport Combined Table r xi Look in fa GeneMapper ID z a ces 2 GeneMapperlD Export txt Export File As Tab delimited text txt m Merge Recent Desktoj One line per marker C One line per sample V Include all marker information Includes marker information for samples with no sizing data 3 ee My Documents imi Tonic My Computer a oe My Network File name Export tier Hapletypes Export Combined Table Files of type fr and Comma delimited Text xt csv Cancel 6 Type in a File name 7 From the Files of type drop down list select the appropriate file type extension 8 Click Export Combined Table Installation Procedures and New Features for GeneMapper ID Software v3 2 21 GeneMapper ID Software Changes to the Electropherogram Displays In GeneMapper JD Software v3 2 two changes have been made to the electropherogram displays Labeled peak assignments can be displayed for all size standards Labels are retained in both the align by base pair an
18. D 65500 13 81012531 fsa 12531 Sample no export AmpFISTR Yfiler Adva Yfiler wt a a BTTT250 Ra 1250 Sample no expo AmpHISTR Vhia Ades Vie vi CE G amp Wi 6980 NN These samples 15 81500500 fsa 500500 Sample no export AmpFISTR Yfiler Adva Yfiler v1 CE 65 MID 65500 EB pass sizing 16 52500250 ts 500250 Sample no export AmpFISTR filer Adva Yfiler vt CE 05 MID 05500 n 7 83500125 tsa 500125 Sample no export AmpFISTR_Yiilet_Adva Yfiler vt CE 05 HiD 65500 n 18 5450002 tsa 50062 Sample no export AmpFISTR_Ytilet_Adva Yfiler vt CE 65 HiD 65500 a 19 8550031 fsa 50031 Sample no export AmpFISTR Yfiler Adva Yfiler vt CE 65 Mib 65500 n 20 855000 fsa 5000 Sample no export AmpFISTR Yfiler Adva Yfiler v1 CE 65 MID 68500 21 B7lad er tes ladder Allelio Ladder no export AmpFISTR Yfiler Adva Yfiler v1 CE 05 MID 05500 22 B8125125 fsa 125125 Sample no export AmpFISTR_Ytilet_Adva Yfiler vt CE 05 HID 65500 n 23 8912502 tsa 12562 Sample no export AmpFISTR filer Adva Yfiler vt CE 65 HiD 65500 _ Figure 1 Size quality status 18 User Bulletin Export Combined Table Format Two Export Two display options are available to export samples that do not pass Display Options sizing with samples that pass sizing One line per marker This option displays information for each marker on a separate line for a given sample In Figure 2 below for example lines 2 through 15 display the information for each marker in sample file A1012531 fsa E
19. Installation procedures on page 58 have not resolved the problem you may need to uninstall the GeneMapper JD software then contact Technical Support 1 Log onto the local domain of your computer as a user with Administrator privileges page 59 2 Uninstall the software page 59 3 Complete the Troubleshooting Checklist then contact Technical Support page 61 To uninstall the GeneMapper D software you must Logonto the local computer not a network domain Have Administrator privileges on the local computer that is have complete and unrestricted access to the local computer This procedure is for a standalone configuration only This procedure removes the GeneMapper D Software v3 2 and the Oracle Database Standard Edition v8 1 7 To uninstall the software 1 Save and close all applications including the GeneMapper D software and windows before proceeding with the uninstall 2 Select Start gt Settings gt Control Panel 3 Double click Add or Remove Programs Installation Procedures and New Features for GeneMapper ID Software v3 2 59 GeneMapper ID Software 60 Select GeneMapper ID v3 2 then click Change Remove In the Welcome window select Remove then click Next Atthe prompt click OK to confirm the uninstall The uninstaller removes all GeneMapper JD Software v3 2 and Oracle Database Standard Edition v8 1 7 files and settings from the computer When the uninstall is complete th
20. User Bulletin GeneMapper ID Software SUBJECT In This User Bulletin Overview November 30 2004 Installation Procedures and New Features for GeneMapper D Software v3 2 This user bulletin includes the following topics section 1 Installation Procedures ERR 3 Section 2 New Features All AmpFZSTR Kits 17 Section 3 New Features and Procedures Yfiler Kit 25 Appendix A Verification Testing 2 RR KK 4 Appendix B Troubleshooting the Installation 57 GeneMapper JD Software v3 1 has been upgraded to v3 2 This user bulletin Provides GeneMapper JD Software v3 2 installation requirements and procedures e Describes the new features in GeneMapper ID Software v3 2 and where applicable provides procedures for using them Describes verification testing of GeneMapper D Software v3 2 Applied Biosystems GeneMapper ID Software 2 User Bulletin Section 1 Installation Procedures Section 1 Installation Procedures This section covers Supported Instruments and AmpFZSTR Kits 4 4 Installation Requirements yay a uer RR x Rd 6 Installation Procedures 4355333 543315352 3 42 eee ae esas 10 Installation Procedures and New Features for GeneMapper ID Software v3 2 3 GeneMapper ID Software Supported Instruments and AmpF ZSTR Kits Instruments GeneMapper ID Software v3 2 is compatible with the
21. Yfiler_AdvancedMode Yfiler v CE G5 HID GS500 09 B DYS456 15 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vf CE G5 HID GS500 09 B DYS390 24 i Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 0 89 B DYS456 15 Figure 3 One line per sample To create an Export Combined Table 1 After analyzing your samples go to the toolbar and select File gt Export Combined Table to open the Export Combined Table window 7 E port Combined Table X Look in a GeneMapper J AYES E app Export File As i Config Tab delimited text txt b C Database amp docs Merge nr Example Data One line per marker Desktop C GM3 1 Database Defaults installer JRE IV Include all marker information My Documents oO Other I Panels p Plot Settings DUIS TEE C Size Standards M Table Settings GeneMapper_Log My Network PanellmportLog gt File name Sensttvityseries Ytler Export Combined Table Files of type frav and Comma delimited Text b4 csv Y Cancel User Bulletin Export Combined Table Format To create an Export Combined Table 2 From the Look in drop down list select an appropriate destination folder for the Export Combined Table 3 From the Export File As drop down list select a file type 4 From the Merge panel select the format style Oneline per marker or Oneline per sample Note See page 1
22. at pass sizing are flagged with a green square When you create an Export Combined Table both the passing and low quality samples are exported together as shown in Figure 2 on page 19 and Figure 3 on page 20 The procedure for creating an Export Combined Table is on page 20 sitivityseries_Yfiler gmid Is Logged In BE E 3s Help li 1li EI HI Big e ene sening AmeFLSTR Tobie Hi Balm Samples Genctypes Status Sample File Sample Name Sample Type Specimen Cate Analysis Method Panel Size Standard sQ 2 A111250 tsa 1250 Sample no export AmpFISTR Yfiler Adva Yfiler vt None These samples do 3 A12ntc fra ntc Sample no export AmpFISTR Yfiler Adva Yfiler wt None e vt 4 41500500 fsa 500500 Sample no export AmpFISTR Yfiler Adva Ytileryt None e not pass Sizing 5 A2500250 tra 500250 Sample no export AmpFISTR Yfilet Adva Yfiler v1 None e 6 A3500126 tsa 500125 Sample no export AmpFISTR Yfilet Adva Yfiler_v1 CE 05 HID 05500 i Em A450062 tsa 40062 Sample no export AmpFISTR Yfiler Adva Yfiler v1 n 8 4550031 fsa 50031 Sample no export AmpFISTR filer Adva Yfiler v1 m 9 A85000 fra 5000 Sample no export AmpFISTR Yfiler Adva Yfiler v1 CE 65 MID 65500 n 10 A7ladder fsa ladder Allelio Ladder no export AmpFISTR Yfiler Adva Yfiler vt CE 05 MID G 500 n 1 8125125 f a 125126 Sample no export AmpFISTR filet Adva Yfiler vt CE 05 MID 05500 12 4912502 fsa 12502 Sample no export AmpFISTR filer Adva Yfiler vt CE 65 Hi
23. atures and procedures summary table setting and uploading exported haplotype s for searching profiles with the Yfiler Haplotype Database GeneMapper D Software v3 2 to export haplotypes specifically for searching the Yfiler Haplotype Database for profile match estimation ae See Feature Procedure Description Page New feature Allele calling In GeneMapper ID Software v3 1 allele calling parameters 27 parameters for new were only available for markers with tetranucleotide repeat marker repeat types motifs In GeneMapper D Software v3 2 however allele calling parameters are available for four marker repeat types tri tetra penta and hexanucleotide The four allele calling parameters appear in the Allele tab of the Analysis Method Editor as shown in Figure 6 on page 29 You may enter all related analysis values directly into the Tri Tetra Penta or Hexa column fields which allows you to see all values at once New feature Plus stutter To aid in interpreting genotype profiles two new fields have 27 filtering for the DYS392 been added to the Allele tab of the Analysis Method Editor locus specifically to filter out the DYS392 plus stutter e Plus Stutter Ratio e Plus Stutter Distance Procedure Workaround Laboratories may choose to implement a workaround for the for the DYS19 locus DYS19 locus by using the Minus A Ratio and Minus A Distance 2 bp filtering fields in the Allele tab of
24. aying Labeled Peak Assignments for Size Standards Retaining Labels in Base Pair and Data Point Views 48 The fourth test category evaluated the ability of GeneMapper ZD Software v3 2 to Display labeled peak assignments for all size standards Retain labels in both the align by base pair and align by data point views for the X axis All samples within the Samples view were highlighted and only the orange dye color was selected as shown below rim Iu en The size standards were checked to ensure that all defined size standard peaks were labeled appropriately The electropherogram plots were displayed to verify that labels associated with the peaks were retained when switching back and forth between the align by base pair and align by data point views for the X axis User Bulletin Results for Category 1 Peak Detection and Genotyping Reproducibility Results for Category 1 Peak Detection and Genotyping Reproducibility Single Source Population DNA Samples Genotyper Software v3 7 The first parameter evaluated the Peak Detection and Genotyping category to assess genotyping concordance Applied Biosystems compared the genotype results from data analysis with GeneScan Software v3 7 1 and Genotyper Software v3 7 both running on the Windows NT operating system to GeneMapper ID Software v3 2 using the Advanced algorithm The analysis parameter settings for the software packages were defined accord
25. ble AmpFISTR_ Allele 2 tiler_Upload_Table G_DYS458 G_DYS19 G_DYS385 Y_DYS393 B_DYS380 24 B_DYS383I OL G DYS458 17 G_DYS19 15 G DYS385 111 Y pvsas3 13 Y DYS439 Y DYS635 Y_DYS392 2 3 4 5 Y_DYS391 ls 7 8 9 Y_DYS391 11 Y_DYS439112 Y DYS635 24 R Y GATA F R_DYS437 10 R_DYS438 T gt 11 Progress Status 3 For the remaining upload procedures see or Manual PN 4358101 The Yfiler Haplotype Database http www appliedbiosystems com yfilerdatabase The AmpFSTR Yfiler PCR Amplification Kit User s User Bulletin Creating a Table Setting and Uploading Exported Haplotype s Appendix A Verification Testing This appendix covers TPO 22 A A ace ien iced e E edt Redde Vlde d 42 Matenas and Methods saya xe ss uk au pa e Co e 43 Category 1 Peak Detection and Genotyping Reproducibility 45 Category 2 Algorithm Testing A ya ese VERE ba du EA 46 Category 2 Data Hahdl ti i sa i asa kak Rob cues dn 48 Category d Work lW ss sw sa ca ERRARE ORG IRR S EROR RR 48 Results for Category 1 Peak Detection and Genotyping Reproducibility j 20 264 cite a n Rb y Ra 0k02 4i an Rad en 49 Results for Category 2 Algorithm Testing 53 Results for Category 3 Data Handling 54 Results for Category 4 Workflow lsseleseesess 35 Results SUMMAS j asx dace Wl ea
26. d align by data point views for the X axis Labeled Peak GeneMapper ID Software v3 2 now provides the option to display Assignments for labeled peak assignments for all size standards in the All Size electropherograms That is all defined size standard peaks are Standards labeled in the electropherogram per the size standard definitions This allows you to quickly identify peaks visually and perform a size precision test To display peak assignments for all size standards 1 In the Samples view highlight all sample files in the project 2 Click the Display Plots icon 3 From the Plot Setting drop down list select AmpFLSTR Genotyping 4 Hide all dyes except the size standard dye that is red for ROX dye or orange for LIZ dye 5 Select View gt Show Size Standard Label 6 Verify that all values for the 250 bp fragment peaks are within 0 5 bp 22 User Bulletin Changes to the Electropherogram Displays To display peak assignments for all size standards continued T If desired select File gt Print to print the electropherogram plots The examples below show both labeled and unlabeled peak assignments Pe EE vew Ters Aides heb pasera re 5R Gevorg JEN esh laa Ifa STE E RM suis Eua 9 dewle Nun Tod 5Q0 sQ x D azo so e p Gw bea fos ET ETI boo Beos cn kx iia E 1
27. d Haplotype s Using the Table Setting Editor you can create a table setting in GeneMapper D Software v3 2 to export haplotypes specifically for searching the Yfiler Haplotype Database for profile match estimation Database Online The Yfiler Haplotype Database online search tool searches for Search Tool haplotypes generated with the Yfiler kit The online search tool allows you to Estimate the frequency of a given Y chromosome haplotype in specified populations Frequency calculations are based on the haplotype data generated from the 17 loci included in the Yfiler kit This data was compiled from more than 3000 samples from a range of populations Estimate the frequency of haplotypes in a number of reference populations Search complete or partial profiles generated with the Y filer kit e Compare the discrimination capacity of the Y filer kit relative to the recombination of Ystr loci Workflow 1 Use the Table Setting Editor to create a table setting in GeneMapper D Software v3 2 below 2 Upload the exported haplotype s into the Yfiler Haplotype Database for profile match estimation page 40 Create a Table Define custom Samples and Genotypes views for displaying the Setting Yfiler kit data To create a table setting 1 From the GeneMapper Manager select the Table Settings tab 2 Click New to open the Table Setting Editor Installation Procedures and New Features for GeneMa
28. d data analysis Applied Biosystems documented three observations when comparing the results produced from GeneScan Software v3 7 1 and Genotyper Software v3 7 both running on the Windows NT operating system to the results produced from GeneMapper ID Software v3 2 Of the 272 loci examined 267 loci produced concordant results between the software packages and 5 loci alleles produced non concordant results These observations are further described on page 51 Figure 2 below shows the genotyping concordance results when comparing the analyzed data from GeneScan Software v3 7 1 and Genotyper Software v3 7 both running on the Windows NT operating system to the results from GeneMapper D Software v3 2 Genotyping Concordance 98 195 17 805 1 083 u Observation 1 E Observation 2 O Observation 3 Figure 2 Genotyping concordance results User Bulletin Results for Category 1 Peak Detection and Genotyping Reproducibility Observation 1 267 98 20 of the loci alleles compared produced concordant genotype calls Observation 2 Three 1 0896 of the loci alleles were non concordant because these loci alleles fell just below the 50 RFU cutoff threshold value in GeneMapper JD Software v3 2 and were not genotyped Observation 3 Two 0 72 of the loci alleles were non concordant because the alleles analyzed with Genotyper Software v3 7 did not filter the stutter or the Minus A The label 1s removed from Peak A
29. ddition the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities 63 Copyright 2004 Applied Biosystems All rights reserved For Research Use Only Not for use in diagnostic procedures 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 The GeneMapper D Software has not undergone specific developmental validation for human identification applications Human identification laboratories analyzing single source or parentage samples that choose to use the GeneMapper D Software for data analysis should perform their own developmental validation studies 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 Purchase or receipt of this software does not include or guarantee any training by persons belonging to Applied Biosystems or Applera Corporation
30. e PN 4338775 4 User Bulletin Supported Instruments and AmpF 4STR Kits Chemistry Kits GeneMapper ID Software v3 2 is specifically designed to work with the following AmpF STR kits La AmpF STR Yfiler PCR Amplification Kit AmpF STR Identifiler PCR Amplification Kit AmpF STR SGM Plus PCR Amplification Kit AmpF STR Profiler Plus ID PCR Amplification Kit AmpF STR Profiler Plus PCR Amplification Kit AmpF STR COfiler PCR Amplification Kit AmpF STR SEfiler PCR Amplification Kit AmpF STR Profiler PCR Amplification Kit AmpF STR Blue PCR Amplification Kit AmpF STR Green I PCR Amplification Kit Installation Procedures and New Features for GeneMapper ID Software v3 2 5 GeneMapper ID Software Installation Requirements Computer The computer specifications for GeneMapper ID Software v3 2 are Specifications listed in the table below Please note the following The Minimum Requirements column lists the lowest specifications that permit the installer to install the GeneMapper JD software The minimum requirements may not provide optimal performance The Recommended Requirements column lists the requirements that are recommended by Applied Biosystems System Component Minimum Requirements Recommended Requirements Computer e Intel Pentium Ill processor e Intel Pentium IV processor 540 MHz 22 8 GHz 256 MB of RAM 512 MB of RAM e 2 GB hard drive free space e 40 GB EIDE hard drive e
31. e Maintenance Complete page opens Select Yes I want to restart my computer now then click Finish Look for the x GeneMapper folder and delete it if it still exists sometimes the folder get left behind after an uninstall Complete the Troubleshooting Checklist on page 61 User Bulletin Troubleshooting Checklist Troubleshooting Checklist Before you contact Applied Biosystems Technical Support for troubleshooting assistance complete the Troubleshooting Checklist pages 61 to 62 Checklist Table 8 Troubleshooting Checklist Check Information for Technical Support Summarize the problem Have you been able to repeat the problem If yes list the steps that you perform 1 AE SED Olen NE Applied Biosystems personnel that you have contacted 1 Field Applications Specialist J Field Service Engineer 1 Technical Support 1 Sales Representative L Order Administration U Other Computer specifications Operating system e Version Processor Memory e Hard disk space Hard disk configuration Installation Procedures and New Features for GeneMapper ID Software v3 2 61 GeneMapper ID Software 62 Table8 Troubleshooting Checklist continued Check Information for Technical Support Software installed 4 Data Collection software version L Status of Data Collection Services L GeneMapper ID software version 4 Other Applied Biosys
32. ecorded Size Peak height Data point Spectral pull up PQV activated Seventy eight 78 spectral pull up peaks were identified As shown in Figure 5 on page 54 97 44 76 of these pull up peaks were correctly flagged by GeneMapper D Software v3 2 The remaining 2 56 2 of pull up peaks that were not flagged were produced by off scale data If a spectral pull up peak 1s caused by an off scale allele peak the spectral pull up flag is not triggered for that peak This is because the ratio of pull up to off scale peaks cannot be calculated since the peak height for off scale data cannot be determined Installation Procedures and New Features for GeneMapper ID Software v3 2 53 GeneMapper ID Software Applied Biosystems recommends that you carefully review all off scale yellow PQV flags Applied Biosystems recommends that you dilute or re run samples to obtain on scale data to ensure the PQVs reported by data analysis are accurate and to reduce spectral separation that is pull up 97 4496 El Spectral pull up flagged W Spectral pull up not flagged Figure 5 Results for the spectral pull up PQVs flagged Results for Category 3 Data Handling Export Combined Projects with their associated settings that is analysis methods table Table Format settings plot settings matrices if applicable and size standards consisting of samples that passed sizing as well as samples that did not pass sizing were exported The
33. el to open the Control Panel window 3 Double click Add or Remove Programs to open the Add or Remove Programs dialog box 4 Select the GeneMapper software program then follow the prompts to uninstall remove the GeneMapper software 5 If prompted to do so restart the computer 6 Continue with Install the Software below To install GeneMapper D Software v3 2 l Log in to the local computer as an Administrator IMPORTANT If you do not have Administrator privileges log off of the computer and log back in as a user with Administrator privileges Installation Procedures and New Features for GeneMapper ID Software v3 2 11 GeneMapper ID Software 12 To install GeneMapper D Software v3 2 continued 2 Insert the GeneMapper ID Software v3 2 CD into the CD ROM drive The installer launches automatically displaying the Main Menu ED GeneMapper D Software v3 2 Note If the installer does not launch automatically a On the desktop right click the My Computer icon and select Explore to open the My Computer window b Double click the CD drive to open the GeneMapper ID v3 2 folder c Double click the Setup exe file to launch the installer Click Installation Readme to view the InstallationReadme txt file on the GeneMapper ID Software v3 2 CD Note The InstallationReadme txt file may contain installation information that is more current than the in
34. er vi CE G5 HID GS500 09 95 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 og 97 A3500125 fsa 500125 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 09 98 A450062 fsa 50062 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler v CE G5 HID GS500 0 9 99 A450062 fsa 50062 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler vi CE G5 HID GS500 Figure 2 One line per marker Installation Procedures and New Features for GeneMapper ID Software v3 2 19 GeneMapper ID Software One line per sample This option displays the information for each sample on just one line In Figure 3 below for example line 2 displays information for Sample Name 12531 The subsequent lines display information for different samples E Efe Ed t view Insert Format Tools Data Window Help Adobe POF ri Ara 0 B Z u S SR S AS EELA Sample Name Creating an Export Combined Table 20 E F 9 1 H K L Sample Type Specimen Category Analysis Method Panel Size Standard SQ Marker Allele 1 Allele 2 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler v None 0 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler_v1 None 0 Sample no export AmpFISTR Yfiler AdvancedMode Yfiler_v1 None 0 Sample no expor AmpFISTR Yfiler AdvancedMode Yfiler v None 0 Sample no expor AmpFISTR_Yfiler_AdvancedMode Yfiler_v1 None 0 Sample no export AmpFISTR_
35. es columns from the sample table and the genotype table and exports them as a single table You now have two display options when exporting samples Oneline per marker One line per sample This is similar to the Make Allele table in the Genotyper Software Changes to the electropherogram displays The software now provides the option to display labeled peak 37 assignments for all size standards This allows you to quickly identify peaks visually and perform a size precision test The labeled peak assignments are printable When switching from the align by base pair to the align by data point views for the X axis the labels associated with the peaks are now retained in both views Installation Procedures and New Features for GeneMapper ID Software v3 2 17 GeneMapper ID Software Export Combined Table Format GeneMapper JD Software v3 2 can export data in the Export Combined Table format This new format Allows you to track a samples in an electrophoresis run That is when exported from the Samples view samples that do not pass sizing are exported along with samples that pass sizing Provides two display options one line per marker and one line per sample Size Quality As shown in Figure 1 below the size quality status is displayed in the Status inthe SQ column of the Samples view Samples View Samples that do not pass sizing are flagged with a red circle Samples th
36. es were examined and the percent stutter recorded The 27 population samples consisted of 432 n 4 n 5 and n 6 stutter peaks 27 DYS19 n 2 stutter peaks 27 DYS392 n 3 stutter peaks User Bulletin Category 2 Algorithm Testing Spectral Pull Up Laboratories that have implemented the ABI PRISM 3100 Genetic PQV Analyzers into their workflow to electrophorese DNA samples may observe pull up peaks within 2 data points in a different color from the main allele peak which is causing the pull up peak To this end Applied Biosystems has made modifications to the analysis method to flag spectral pull up peaks in the range of 2 data points The spectral pull up PQV flag was evaluated to ensure that a peak meeting specified criteria for spectral pull up is appropriately activated The two criteria required to flag a peak as spectral pull up are as follow The peak is 5 or as specified by the value in the Pull up ratio field in the Peak Quality tab of the Analysis Method Editor of the main allele peak causing the pull up The peak is within the 2 data points range from the main allele peak in a different color Note After installing GeneMapper D Software v3 2 laboratories should create new analysis methods specifically for use with GeneMapper JD Software v3 2 Creating new analysis methods will ensure that spectral pull up peaks within 2 data points from the main allele peak are flagged appropriately S
37. for data processing Select the Use marker specific stutter ratio if available checkbox When this checkbox is selected the software uses the stutter ratios defined in the panel These values are provided in the panels supplied by Applied Biosystems To filter out the reproducible DYS19 tetranucleotide stutter the Minus A Ratio and Minus A Distance fields can be used Additionally two new fields specifically developed to filter out the DYS392 trinucleotide repeat plus stutter have been added to the Analysis Method Editor Plus Stutter Ratio and Plus Stutter Distance Figure 6 on page 29 shows allele calling parameters that can be used with GeneMapper JD Software v3 2 User Bulletin Plus Stutter Filtering and 2 bp Filtering Workaround Analysis Method Editor HID i lxi General Allele Peak Detector Peak Quality Quality Flags Bin Set ampFLSTR_Yfiler_Binset_v1 v Use marker specific stutter ratio if available 4 Marker Repeat Type Tri Tetra Penta He xa Cut off Value oo Minus Ratio oo Minus Distance o D oo Minus Stutter Ratio foo Minus Stutter Distance From 225 25 Fl ho a Plus Stutter Ratio Plus Stutter Distance TTT Wiii olt Amelogenin Cutoff Range Filter Figure 6 Allele calling parameters Note The circled values shown in Figure 6 above are based on developmental validation studies conducted at Applied Biosystems and should o
38. formation in this user bulletin User Bulletin Installation Procedures To install GeneMapper D Software v3 2 continued 4 Click Install GeneMapper ID Software v3 2 to start the InstallShield Wizard InstallShield Wizard Welcome to the InstallShield Wizard for GeneMapperlD 3 2 The InstallShield Wizard will install GeneMapperlD 3 2 on your computer To continue click Next 5 Follow the onscreen instructions to install the software IMPORTANT During installation DOS commands are executed and the DOS window is opened Do not delete close or click in the DOS window If you click in it press the Esc key 6 When the installation is complete click Finish 7 If prompted to do so restart the computer 8 Continue with Register the Software on page 14 Installation Procedures and New Features for GeneMapper ID Software v3 2 13 GeneMapper ID Software Register the To register GeneMapper D Software v3 2 Software 1 Locate the registration code on the Getting Started Card in the software package 2 IMPORTANT Keep the registration code in a place where you can easily retrieve it You will need the registration code the first time you start the GeneMapper JD software below In addition if you need to reinstall the software at any time you are prompted for the registration code again 3 Complete the registration card and return it to Applied B
39. ing to Applied Biosystems default analysis parameters with a defined peak amplitude threshold PAT of 50 RFUs As shown in Figure 1 below a side by side comparison between Genotyper Software v3 7 and GeneMapper ID Software v3 2 was evaluated to ensure the consistency of genotype results where the evaluation criteria was that all samples give concordant genotypes After the trained scientist completed data analysis each population sample tested gave 10096 concordant genotype calls between the two software programs see Table 6 on page 50 GeneMapper D Software v3 2 m W LULL nn was ai aya 888 8 WT ej j i NN A m HU UU ES X Figure 1 Example of the Yfiler kit allelic ladder analyzed with Installation Procedures and New Features for GeneMapper ID Software v3 2 Genotyper Software v3 7 left and GeneMapper D Software v3 2 displaying concordant results right 49 GeneMapper ID Software Mixture Samples 50 As shown in Table 6 below each sample type tested gave concordant genotype calls between the two software programs Table 6 Genotype concordance between Genotyper Software v3 7 and GeneMapper D Software v3 2 Alele Source Namber of Numberot Conordant Population samples 80 1222 100 Positive and negative 5 60 100 controls Allelic ladders 6 137 10096 After the trained scientist complete
40. ion Kit was used to amplify each sample type for the verification testing Sample Types Single source DNA Samples Eighty 80 DNA samples from four 4 population groups Mixture Samples Mixtures of male and male DNA were amplified These samples were mixed in defined ratios of 1 1 3 1 10 1 and 15 1 respectively Additionally mixtures of male and female DNA were amplified These samples were mixed in defined ratios of 1 1000 1 2000 1 4000 and 1 8000 respectively Note The human genomic DNA samples were quantified using Quantifiler Human DNA Quantification Kit and Quantifiler Y Human Male DNA Quantification Kit The samples were amplified using a GneAmp PCR System 9700 with a silver 96 well block The recommended cycling conditions were used as outlined in the AmpF STR Yfiler PCR Amplification Kit User Manual PN 4358101 The amplified samples were injected on three or more ABI PRISM instrument platforms Installation Procedures and New Features for GeneMapper ID Software v3 2 43 GeneMapper ID Software Instruments and Table 4 below lists the instruments Data Collection software versions computer operating systems and run modules that were used to process the samples for verification testing Software Table4 Forensic validated instrument platforms Data Instrument Collection BEN xa Run Module Software y ABI Prism 310 v3 0 Microsoft Windows NT9 e GS STR Pop4 1 ml
41. iosystems 4 Continue with Start the Software below Start the To start GeneMapper D Software v3 2 for the first time Software 1 Log in to the local computer 2 On the desktop click Start gt Programs gt Applied Biosystems gt GeneMapper gt GeneMapper ID v3 2 The first time you start the GeneMapper ID software the Product Registration dialog box opens GeneMapper ID v3 2 Product Registration Your Name Organization Registration Code Note If the GeneMapper JD software fails to start see Troubleshooting the Installation on page 57 14 User Bulletin Installation Procedures To start GeneMapper D Software v3 2 for the first time 3 Register the software a In the Product Registration dialog box enter your name organization and registration code b Click OK The software verifies the registration code then displays the Login dialog box Q Login to GeneMapper ID v3 2 GeneMappere D Software v3 2 Password Database Host genemapper1 v d 1999 2004 Applera Corp All Rights Reserved Installation Procedures and New Features for GeneMapper ID Software v3 2 15 GeneMapper ID Software 16 To start GeneMapper D Software v3 2 for the first time 4 The first time you launch the GeneMapper D software complete the Login dialog box as follows
42. l 3 Figure 3 DYS439 Marker Genotyper Software v3 7 E8 Genotyper 3 7 Plots Yfiler_ 1 4 GTA 5 xi s File Edit Analysis Category Table Views Macro Window Help lj x 3000 2000 1000 D1015 1a fsa GeneMapper D Software v3 2 Plot File Edt View Tools Alleles Help Plot Setting ampri STR Genotypna Peres fr BIBT MNT ES aal eR i EJ d AL a FO J PE Ji i Foe Name rend sue sa Figure 4 DYS456 Marker 52 User Bulletin Results for Category 2 Algorithm Testing Results for Category 2 Algorithm Testing Stutter Evaluation Twenty seven 27 population DNA samples were examined consisting of 432 n 4 n 5 and n 6 stutter peaks 27 DYS19 n 2 stutter peaks 27 DYS392 n 3 stutter peaks The results were as follows All n 4 n 5 and n 6 stutter peaks were below the stutter percent as defined in the panel and were properly filtered The DYS19 locus n 2 stutter peak was below the stutter percent as defined in the Allele tab of the Analysis Method Editor and were properly filtered The DYS392 locus n 3 stutter peak was below the stutter percent as defined in the Allele tab of the Analysis Method Editor and were properly filtered Spectral Pull Up Twenty eight 28 single source population samples were evaluated PQV for spectral pull up For each pull up peak the following was r
43. lysis Method Editor as shown in Figure 6 on page 29 You may enter all related analysis values directly into the Tri Tetra Penta or Hexa column fields which allows you to see all values at once Plus Stutter Filtering and 2 bp Filtering Workaround The following have been reported Plus stutter at the DYS392 locus 2 bp stutter at the DYS19 locus Further descriptions of these loci are provided on page 28 Allele calling parameters that can be used as workarounds are provided on page 28 Installation Procedures and New Features for GeneMapper ID Software v3 2 27 GeneMapper ID Software Plus Stutter DYS392 2 bp DYS19 Stutter Allele Calling Parameters 28 The DYS392 trinucleotide repeat locus displays the typical 3 bp stutter but also a larger 3 bp stutter Sequencing analysis of this 3 bp stutter revealed that the product contains an additional repeat unit relative to the true allele peak Based on developmental validation studies conducted by Applied Biosystems the highest percent stutter observed for any DYS392 allele was 7 9 It has been reported that the DYS19 tetranucleotide repeat locus displays the typical 4 bp stutter but also a smaller 2 bp stutter Based on developmental validation studies conducted by Applied Biosystems the highest percent stutter observed for any DYS19 locus was 10 21 The Allele tab of the Analysis Method Editor is used to set allele calling parameters
44. lysis method or AmpFISTR Yfiler ClassicMode if you are creating an HID Classic analysis method Installation Procedures and New Features for GeneMapper ID Software v3 2 31 GeneMapper ID Software Table 3b Analysis method settings Allele tab Tab Settings Allele Analysis Method Editor HID E xj General Allele Peak Detector Peak Quality Quality Flags Bin Set ampFLSTR_Yfler_Binset_v1 v Use marker specific stutter ratio if available 4 Marker Repeat Type Hexa Cut off Value o 0 MinusA Ratio bo MinusA Distance lo T7 o 0 Minus Stutter Ratio lo 0 Minus Stutter Distance s 25 Bzs Plus Stutter Ratio lo 0 Plus Stutter Distance lo lo 0 Amelogenin Cutoff Range Filter Notes for the Allele tab checkbox is selected The software uses the stutter ratios defined in the panel Ratio Distance fields 1 Be sure to select the Use marker specific stutter ratio if available checkbox When this The stutter ratios include all loci except for the DYS392 3 stutter and the DYS19 2 stutter The stutter ratios are defined in the Analysis Method Editor under the Allele tab if applicable 2 See Plus Stutter Filtering and 2 bp Filtering Workaround on page 27 for a discussion of the Tetra column values in the Minus A Ratio Distance fields and Tri column values in the Plus Stutter 32 User Bulletin Creating HID Analysis Methods for the Yfiler
45. nly be used as reference values Each laboratory should perform their own internal validation studies to determine the appropriate values to enter The DYS19 workaround is not locus specific All peaks for the tetranucleotide loci falling within the range specified in the Minus A Ratio and Minus A Distance fields will be filtered Installation Procedures and New Features for GeneMapper ID Software v3 2 29 GeneMapper ID Software Creating HID Analysis Methods for the Yfiler Kit Use the Analysis Method Editor to set analysis parameter values for analyzing the Yfiler kit data Note The size distribution for the Yfiler kit is 100 to 330 bp Asa result the 450 bp size standard peak does not need to be included in the size standard definition for analysis Workflow l Import the Yfiler kit panels and bin sets See the GeneMapper ID Software Version 3 1 Human Identification Analysis Tutorial PN 4335523 for procedures on importing panels and bin sets Create a new HID Advanced analysis method for use with the AmpFISTR Yfiler kit below Create a new HID Classic analysis method for use with the AmpFISTR Yfiler kit page 36 Create the To create the HID Advanced analysis method HID Advanced Analysis Method 30 l Select Tools gt GeneMapper Manager to open the GeneMapper Manager Select the Analysis Methods tab then click New to open the New Analysis Method dialog box New Analysis Method
46. pectral Pull UP PQV Study To test the functionality of the spectral pull up PQV twenty eight 28 samples from the single source population study were electrophoresed on both the ABI PRISM 310 and 3100 Genetic Analyzers that is the same PCR product was electrophoresed on two different instruments and were evaluated using the following criteria Each analyzed sample was evaluated for the presence of pull up peaks by noting whether or not the spectral pull up PQV was flagged The data point that is 0 data point 1 data point or 2 data points of the pull up peak relative to the main allele peak was recorded The percent height of the pull up peak relative to the main allele peak was recorded that is 596 of the main allele peak causing the pull up Installation Procedures and New Features for GeneMapper ID Software v3 2 47 GeneMapper ID Software Category 3 Data Handling Export Combined Table Format Printing Labeled Size Standard Peaks The third test category evaluated the Export Combined Table format and the size standard printing functionality The purpose for evaluating the Export Combined Table format was to verify that samples that do not pass sizing that 1s low quality samples are exported along with samples that pass sizing In GeneMapper JD Software v3 2 the ability to display and print labels on the size standards in different plot configurations was tested Category 4 Workflow Displ
47. pper ID Software v3 2 37 GeneMapper ID Software 38 To create a table setting continued 3 Select the General tab and complete it as follows a Enter a Name of your choosing b If desired enter a Description Table Setting Editor Ex General Samples Genotypes Table Settings Desorption Name AmpFISTR Yfier Upload Table LZ xl Select the Samples tab and complete it as follows a In the Column Settings section deselect all options b In the Font Settings section leave the default values P Table Setting Editor x General Samples Genotypes Samples Table Settings Column Settings ort Settings Show Column Fitering Content r T Fort Arisi x 1 m Seus Show All Records Na j sft 2 17 SeweFie Show All Records 3 m Sample Name Show all Records 4 Sample D Show All Records 5 m Comments Show All Records 6 Sample Type snow AllRecords NA 7 m Specimen Category Show All Records N A 8 7 Analysis Method Show All Records Blue senec _sew m x cmn User Bulletin Creating a Table Setting and Uploading Exported Haplotype s To create a table setting continued 5 Select the Genotypes tab and complete it as follows a In the Column Settings section select Sample Name Marker Allele Deselect all of the other options b In the Font Settings section
48. re data produced during the Yfiler kit developmental validation This study was conducted to verify that the same mixture samples that is PCR product gave concordant genotype calls between the GeneScan Genotyper software and the GeneMapper D software applications Installation Procedures and New Features for GeneMapper ID Software v3 2 45 GeneMapper ID Software The mixture samples were electrophoresed on three different instruments and consisted of five 5 male male and five 5 male female mixture samples Table 5 below lists the mixture ratios that were used in the mixture experiment Table5 Mixture ratios Male Male Male Female 1 1 1 1000 3 1 1 2000 10 1 1 4000 15 1 1 8000 Category 2 Algorithm Testing Stutter Evaluation 46 The second test category evaluated the functionality of GeneMapper ID Software v3 2 to accurately filter out stutter based on the Marker Specific Stutter ratio specified in the panel and in the Allele tab of the Analysis Method Editor In the Allele tab of the Analysis Method Editor one of the parameters that can be set to filter out stutter is the Use marker specific stutter ratio if available check box Each allele within a locus displays a percent stutter that is reproducible The Use marker specific stutter ratio if available check box was selected in order to use the stutter ratio information from the panel Using GeneMapper JD Software v3 2 27 population sampl
49. rovides the innovative products services and knowledge resources that make this new Integrated Science possible Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches 150 countries on six continents For sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com Applera 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 Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 11 2004 Applied Biosystems Part Number 4352543 Rev A Stock Number 112UB06 01
50. ss Enter If A Connected to message is displayed the Oracle database was installed correctly Proceed with Configure the Database Manually on page 58 Ifthe Oracle database was not installed correctly an error message appears Complete Table 8 Troubleshooting Checklist on page 61 then contact Technical Support Configure the Ifthe Oracle database was installed correctly perform the following Database steps in the Command Prompt window to configure the database Manually manually To configure the database 1 Return to the open Command Prompt window it should still be open from step 4 above 2 Atthe SQL prompt type exit to exit the SOL Plus application 3 At the drive prompt type ed d x GeneMapper database where x is the drive where the GeneMapper JD software is installed then press Enter 58 User Bulletin Uninstall the Software 4 At the drive prompt type ifadb x oraclegm oradata ifa where x is the drive where the GeneMapper JD software is installed then press Enter f Succeeded messages are displayed the database is configured correctly Proceed to Start the Software on page 14 If Error messages are displayed the database is not configured correctly Proceed to Uninstall the Software on page 59 Uninstall the Software Workflow Log Onto the Computer Uninstall the Software If the software installation is not successful and the Troubleshoot the
51. tems software Computer login information User privileges Local or networked domain Software configuration installed 4 Instrument Li Standalone Instrument and instrument computer information Model Data Collection software version e Status of Data Collection Services Other Applied Biosystems software e Capillary length e Capillary lot number Run module Dye set Chemistry kit or reagent with version number Be prepared to send to Technical Support e Exported panels Exported bins e Exported size standard definition e Exported analysis method e Sample fsa files GeneMapper_log txt e PanellmportLog txt e Printed results User Bulletin How to Obtain Support How to Obtain Support Be sure to complete the Troubleshooting Checklist page 61 before contacting Technical Support Installation Procedures and New Features for GeneMapper ID Software v3 2 For the latest services and support information for all locations go to http www appliedbiosystems com then click the link for Support At the 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 a
52. tes that human identification laboratories can successfully adopt GeneMapper ID Software v3 2 Installation Procedures and New Features for GeneMapper ID Software v3 2 55 GeneMapper ID Software 56 User Bulletin Results Summary Appendix B Troubleshooting the Installation This appendix covers Troubleshoot the Installation KK RR RR KK 58 Uninstall the SONGS x ec characte iar x n hana ay hen k eda 59 Troubleshooting Checklist 12 22 i wan a Pan RE RR 61 How do Obtain SUpport aa kb kw k Wi kah a Re TE Ak E 63 Installation Procedures and New Features for GeneMapper ID Software v3 2 57 GeneMapper ID Software Troubleshoot the Installation Workflow Ifthe installation appears to be successful but the GeneMapper JD software fails to start and reports the error Failed to connect to database perform the troubleshooting procedures in this appendix in the order shown below 1 Check the Oracle database installation page 58 2 Configure the Oracle database manually page 58 Check the Oracle Check to see if the Oracle database instance was installed correctly Database Installation To check the Oracle database installation 1 Select Start gt Programs gt Accessories gt Command Prompt 2 Type sqlplus then press Enter You should see SQL Plus Release 8 1 7 0 0 3 Type the user name system then press Enter 4 Type the password manager then pre
53. the Analysis Method Editor These fields can be used to filter out the 2 bp stutter that is observed at the DYS19 locus Procedure Creating HID Use the Analysis Method Editor in GeneMapper D Software 30 analysis methods for the v3 2 to set analysis parameter values for analyzing the Yfiler kit Yfiler kit data Procedure Creating a Using the Table Setting Editor you can create a table setting in 37 26 User Bulletin Allele Calling Parameters for New Marker Repeat Types Allele Calling Parameters for New Marker Repeat Types Peak Detection The peak detection analysis parameters allow you to specify the Analysis minimum peak height to be detected for analysis This in turn Parameters controls the number of peaks analyzed Peaks falling below the parameters specified are displayed in the electropherogram but are not labeled and will not be genotyped In the Allele tab of the Analysis Method Editor a number of parameters can be set to control allele calling including Bin set Marker specific stutter ratio Amelogenin cutoff Marker repeat type New Marker In GeneMapper JD Software v3 1 allele calling parameters were only Repeat Types available for markers with tetranucleotide repeat motifs In GeneMapper JD Software v3 2 however allele calling parameters are available for four marker repeat types tri tetra penta and hexanucleotide The four allele calling parameters appear in the Allele tab of the Ana
54. v3 2 is compatible only with the Oracle Databases database installed with ABI PRISM 3100 3100 Avant Genetic Analyzers Data Collection Software v2 0 Be sure there is no other Oracle client or Oracle server on the computer GeneMapper JD Software v3 2 is not supported on any other Oracle client or server configurations Special Considerations The version of the Oracle database in GeneMapper D Software v3 2 is an embedded license for use by five named users IMPORTANT To accommodate more than five users additional GeneMapper JD software or Oracle database licenses must be purchased TCP IP has to be installed before installing GeneMapper ZD Software v3 2 Installation Procedures and New Features for GeneMapper ID Software v3 2 7 GeneMapper ID Software Compatibility with 3100 3100 Avant Genetic Analyzers The table below describes compatibility of GeneMapper ID Software v3 2 with the Data Collection software for the ABI PRISM 3100 3100 Avant Genetic Analyzers 3100 Genetic Analyzer Data Collection Version 3100 Avant Genetic Analyzer Data Collection Version Compatible with Instrument Computer 1 1 1 0 No 2 0 2 0 Yes a GeneMapper D Software v3 2 can only exist with the Oracle database installed by 3100 3100 Avant Genetic Analyzer Data Collection Software v2 0 IMPORTANT To install GeneMapper ID Software v3 2 on a computer connected to a 3100 3100 Avant
55. x Select analysis type C pp C SNaPshot C Microsatellite OK Cancel Select HID then click OK to open the Analysis Method Editor with the General tab selected Select the analysis method settings shown in Table 3a on page 31 through Table 3e on page 35 IMPORTANT You must select your settings on all the tabs before you click OK to save the analysis method and return to GeneMapper Manager User Bulletin Creating HID Analysis Methods for the Yfiler Kit Analysis Method IMPORTANT The values shown in Table 3b on page 32 through Settings Table 3e on page 35 are based on developmental validation studies conducted at Applied Biosystems and should only be used as reference values Each laboratory should perform their own internal validation studies to determine the appropriate values to enter Table 3a Analysis method settings General tab Tab Settings General Analysis Method Editor HID ER xl General Allele Peak Detector Peak Quality Quality Flags Analysis Method Description Description Analysis Type HID Name JamprISTR_Yfier_AdvancedMode Instrument OK Car cel Enter a name of your choosing here See the Notes below Notes for the General tab 2 Select your instrument from the drop down list 1 Enter a name of your choosing For example enter AmpFISTR Yfiler AdvancedMode if you are creating an HID Advanced ana
56. y Flags r Signal level Homozygous min peak height 200 0 Heterozygous min peak height j 00 0 Heterozygote balance Min peak height ratio oz Peak morphology Max peak width basepairs j 5 r Pull up peak Pull up ratio Joos Allele number Max expected alleles b Factory Defaults OK Cancel Notes for the Peak Quality tab The values shown in the Peak Quality tab have been chosen based on empirical data generated at Applied Biosystems and should only be used as reference values Each laboratory should perform their own internal validation studies to determine the appropriate values to enter 34 User Bulletin Creating HID Analysis Methods for the Yfiler Kit Table 3e Analysis method settings Quality Flags tab Tab Settings Quality Flags Analysis Method Editor HID xj Quality weights are between 0 and 1 Quality Flag Settings Spectral Pull up os Control Concordance fi 0 Broad Peak os Low Peak Height fo 3 Out of Bin Allele os Otf scale 0 8 Overlap jos Peak Height Ratio 0 3 PQY Thresholds Sizing Quality From lo 75 1010 From 0 0 to 0 25 Genotype Quality From b 75 to1 0 From 0 0 to 10 25 Factory Defaults Notes for the Quality Flags tab The weighted values in the Quality Flag Settings section were ranked on a scale from most important to least important This ranking was performed by the Applied Biosystems HID Group
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