Home

GeneMapper® ID Software Version 3.2: Human Identification Analysis

1. GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 27 Chapter 2 Casework Analysis To complete analysis continued 5 Click Hide Green Dye click id Show Yellow Dye and scroll through all samples qr Samples Plot alx File Edit View Tools Alleles Help HID Genobping E Panes f x mim mie BR wee Hae ie whe Mops 8 Sample Name Panel sao sa Sample cotier a x 075820 400 200 300 00 600 o 10 Samplet Pretilr Plus v x m DESETE D138317 D75320 100 200 300 00 2000 4000 j J J m m 12 Sample rofier Pus v xm S88 piss 5520 400 200 300 400 2000 i Li li mE E sl 6 Select File gt Close Plot Window to close the Samples Plot window and return to the Project window 7 Select File gt Save Project to save all changes 2 28 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Concordance Usefulness Concordance Requirements Checking Concordance for Shared
2. 1 14 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Methods Table 1 2 HID Advanced analysis method settings continued Tab Settings Quality Flags Quality flag settings PQV thresholds GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 15 Chapter 1 Software Setup Analysis Tables Overview In this tutorial you define a custom view of Samples and Genotypes tables for viewing HID tutorial data For subsequent analysis with your own samples edit this table setting or create a new table setting Creating a Table To create a table setting Setting 1 From the GeneMapper Manager select the Table Settings tab 2 Click New to open the Table Setting Editor with the General tab selected 3 Enteraname in the text box For this tutorial type HID Table 1 16 GeneMapperQ ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Analysis Tables To create a table setting continued 4 Select the Samples tab and make the following selections Column settings Show 1 3 6 13 17 18 22 23 Hide 2 4 5 14 16 19 21 24 25 Note The box in the Show column indicates whether columns are shown or hidden in the table Check the box to show the column and deselect the box to hide the column Font settings Font Arial
3. 0 e eee eee eee eee 3 9 To examine the allelic ladder calls 0 00 0 0 e eee 3 9 To examine data and edit labels 00 0 0 e cease 3 10 To expert the table sere EEWesRUMUNVEDERENO SOR 3 13 To set CODIS export fields 0 0 ees 4 3 To modify columns veya tice eae eR eA Re dA SO ede 4 5 To export the CODIS table lle eere 4 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial A 5 Appendix A Additional Information Genotyping Samples Manually To genotype samples manually 1 Select one lane or injection of the allelic ladder to use for genotyping Note Applied Biosystems studies have shown that it does not matter which lane or injection of allelic ladder is selected if the alleles in the allelic ladder samples are within 0 5 bp of each other 2 Compare the base pair size obtained for each sample allele peak to the sizes obtained for the allelic ladder peaks 3 Assign genotypes to those sample allele peaks falling within 0 5 bp of the corresponding allelic ladder peak Note For the allele designation for each allelic ladder peak refer to the appropriate user guide for your AmpF STR PCR Amplification kit A 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Converting Macintosh Sample Files Appendix Overview This appendix describes how to use sample file conversio
4. 0 0 2 0 c eee eee 1 5 To create analysis methods for HID Classic 1 8 To create a table setting 6 cece ee es 1 16 To create HID Genotyping plot settings 4 1 19 To view and set options 6 0 eee ees 1 27 To adjust the Project window 00 0 c cence ee eens 2 4 To add samples to the project 0 0 cece eens 2 5 To apply analysis settings 0 0 0 0 ccc eee eens 2 7 To analyze the project n 0 eee ees 2 14 To examine the size standard 1 0 0 0 ccc eee ee es 2 15 To examine the 250 bp peak 0 1 eee 2 18 To examme data oo ceocneexenes Bow Rare wie WE EDEN ES 2 20 To editlabels 26235 Boe tes hee PLE ete niece laa the 2 25 To view allele history and comments 005 2 25 To complete analysis ise 2 25 To check concordance for shared markers 2 28 To export the tablez eoi iiem bh matin te Evexecihessbress 2 30 To check concordance for shared markers 2 28 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Database Analysis Procedures CODIS Export Procedures Lists of Tables and Procedures in This Tutorial To adjust the Project window 2 0 0 ccc eee eee 3 3 To add samples to the project 0 0 c eee ee 3 4 To apply analysis settings 00 6 ccs 3 6 To analyze the project 0 0 0 cece teens 3 8 To examine the size standard
5. o 4x gt a s wl ny 5655 200 0 0 0 300 0 340 0 Skip the 250 bp peak ES 5743 350 0 11 6140 400 0 g Click OK to save the size standard close the Size Standard Editor and return to the Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 11 Chapter 2 Casework Analysis 2 12 To apply analysis settings continued 9 Set the size standard for the samples a Click the Size Standard column header to select the column Size Standard Click here to select the column b Select Edit gt Fill Down to apply the size standard to all samples GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Casework Project Analyzing the To analyze the project Project l Click J Analyze and the Save Project dialog box opens 2 Type Casework Project and click OK to initiate analysis and save each analyzed sample to the project The status bar displays progress of analysis Asacompletion bar extending to the right with the percentage indicated With text messages on the left The table displays the row of the sample currently being analyzed in green or red if analysis failed for the sample See Figure 2 3 Note Auto saving takes place after analysis of every 10 sample files is completed The Gen
6. GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 31 Chapter 1 Software Setup 1 32 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Casework Analysis This chapter covers Casework Workflow 00 ccc cette eee 2 2 Setting Up a Casework Project 00 cece eee 2 3 Examining and Editing Results 0 00 0 c cence 2 14 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 1 Chapter 2 Casework Analysis Casework Workflow Description In this chapter you perform analysis of tutorial casework samples using the software settings from Chapter 1 Software Setup Casework Overview of the tutorial for analyzing a casework project Analysis Tutorial 1 Overview 2 SO 99 c GEN 10 Add samples to be analyzed to a new project page 2 5 Apply analysis settings to the samples in the project page 2 7 a Select the analysis method b Create a custom size standard definition for your data using the Classic peak detection algorithm c Select the size standards for the samples Analyze the project page 2 14 Examine the size standard page 2 15 a Examine the size standard peak assignments b Examine the 250 bp size standard peak Examine data page 2 20 a Examine allelic ladder calls b Examine allele calls Edit labels page 2 25 View allele history and comments page
7. Size 11 Table Setting Editor x General Samples Genotypes Samples Table Settings T Column Settings Font Settings Show Column Fittering Content fort SY 1 Status Show allRecords NIA on S 2 Sample File Show All Records m 3 p Sample Name Show All Records 4 j Sample ID Show All Records 5 Comments Show All Records 6 p Sample Type Show All Records N A 7 p Specimen Category Show All Records N A 8 p Analysis Method Show All Records f GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 17 Chapter 1 Software Setup To create a table setting continued 5 Select the Genotypes tab graphic below and make the following selections Column settings Show 2 4 8 14 16 17 19 24 29 32 33 35 Hide 1 3 9 13 15 18 20 23 30 31 34 36 38 Number of Alleles 2 Note To display columns for more alleles this value can be increased Font settings Font Arial Size 11 Table Setting Editor 6 Click OK to save the table setting close the Table Setting Editor and return to the GeneMapper Manager 1 18 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Plots Overview Creating HID Genotyping Plot Settings Plots In this tutorial you create five custom vie
8. a Use the default setting of no export for allelic ladders and controls Note Exporting sample types designated as allelic ladders or controls generates an error message b Select Convicted Offender for Sample3 Sample4 and SampleS Sample Name Sample Type Specimen Category ID Control Positive Control no export ID Ladder Allelic Ladder Ino export ID_Neg_Cntri Negative Control no export Sample3 Sample Convicted Offender Sample4 Sample Convicted Offender Samples Sample Convicted Offender 4 5 Chapter 4 CODIS Export Exporting the Note GeneMapper ID software exports a composite genotype for CODIS Table samples containing concordant genotypes for shared markers from the same sample For example 13 locus STR profile with sample amplified using both AmpFZSTR Profiler Plus and AmpF STR COfiler kits If you attempt to export nonconcordant profiles the software reports an error message because CODIS will not accept the file Resolve discrepancies to export a composite profile To export the CODIS table 1 Create a new folder called Exported Tables and place it in the Tutorial Data folder X Applied Biosystems GeneMapper Example Data Exported Tables Note X is the drive where you installed GeneMapper D software EM AppliedBiosystems Cg GeneMapper C app E Config H E Database E docs 3 Example Data x fExported Tables Hid G Microsatellite mcg SNaPsh
9. c Use the Edit gt Fill Down feature to place Identifiler vl in each sample row 3 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Database Project To apply analysis settings continued 4 Select the size standard for the samples a Click the first empty None cell in the Size Standard column and select CE G5 HID GS500 from the drop down list b Click the Size Standard column header to select the column Size Standard Click here to select the column _G5_HID_GS500 c Select Edit gt Fill Down to apply the size standard to the selected samples GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 7 Chapter 3 Database Analysis Analyzing the To analyze the project Project 1 Click f Analyze to open the Save Project dialog box 2 Type Database Project and click OK to initiate analysis and save each analyzed sample to the project The status bar displays progress of analysis Asacompletion bar extending to the right with the percentage indicated With text messages The table displays the row of the sample currently being analyzed in green or red if analysis failed for the sample See Figure 3 2 Note Auto saving takes place after analysis of every 10 sample files and after analysis is completed f GeneMapper ID v3 1 Database Project
10. GeneMapper D Software Versions 3 1and 3 2 Human Identification Analysis Tutorial Applied Biosystems O Copyright 2004 Applied Biosystems All rights reserved For Research Forensic or Paternity Use Only Not for use in diagnostic procedures NOTICE TO PURCHASER PLEASE REFER TO THE GENEMAPPER ID SOFTWARE VERSION 3 1 USER GUIDE FOR LIMITED LABEL LICENSE OR DISCLAIMER INFORMATION 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 ABI PRISM AmpF STR Applied Biosystems COfiler GeneMapper GeneScan LIZ and ProfilerPlus are registered trademarks and AB Design Applera YFiler and ROX are trademarks of Applera Corporation or its subsidiaries in the U S and or certain other countries AppleScript and Macintosh are registered trademarks of Apple Computer Inc Microsoft Windows and Windows NT are registered trademarks of Microsoft Corporation All other trademarks are the sole property of their respective owners Part Number
11. ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Methods To create analysis methods for HID Classic continued 3 Select the settings shown in Table 1 1 on page 1 10 IMPORTANT You must select your settings on all the tabs before you Click OK to save the analysis method and return to GeneMapper Manager GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 9 Chapter 1 Software Setup HID Classic Table 1 1 HID Classic analysis method settings Settings Tab Settings General Name HID Classic Allele Analysis Method Editor HID AmpFLSTR Bins v1 Note Stutter values included with kit panels are the same as those included in Genotyper template version 7 Values listed are simple ratios rather than percent differences For specific information on these values see the appropriate user guide for your AmpF4STR PCR Amplification kit Note The values in the current macros do not match the values in the user manual Genotyper template version 7 applies only to Macintosh computers 1 10 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Methods Table 1 1 HID Classic analysis method settings continued Tab Settings Peak Detector Analysis Method Editor HID Partial Range Y Partial Sizes 3275 5400 400 eceee N
12. Genotype Show 2 5 10 15 18 19 and 20 Header Hide 1 6 9 16 and 17 Sizing Show 1 8 Table Font Arial size 11 Labels Label 1 Allele call Label 2 Label 3 and Label 4 None Show data type prefixes deselected Show type of edit deselected Invert mutant labels deselected Label Color Dye Color Border Label Font Arial size 11 Display Settings General Sample Header Genotype Header Sizing Table Labels Display Settings When Opening The Plot Window C Usethe display settings last used for this plot Use these display settings For both Sample and Genotype plots Panes 1 EST faa FL fe ale Af S X Axis Basepairs zl Y Axis Scale individually X IV Toolbar IV Show Off scale For Sample plot only m m m will xt For Genotype plot only Marker Margin 3 bp GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 23 Chapter 1 Software Setup Creating Overlay To create the Overlay GS500 ROX Dye plot settings GS500 ROX Dye Overlay GS500 Table 1 6 Overlay GS500 ROX Dye plot settings 1 24 Plot Settings 1 From the GeneMapper Manager select the Plot Settings tab 2 Click New to open the Plot Settings Editor with the General tab selected 3 Select the settings shown in Table 1 6 Overlay GS500 ROX Dye plot settings 4 Click OK to save the plot settings and
13. as fs so ishzhe fiajashefas Bikses 6 2 1s Gs fai 23 3 be Note If the electropherogram plots display No room for labels then do one or more of the following to view the labels Reduce the number of panes displayed Remove the ladder from the view Increase the screen resolution Expand the top window by placing the cursor on the line then click and drag GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 19 Chapter 2 Casework Analysis To examine data continued 3 Examine the allelic ladder calls and verify that the allelic ladder was called correctly 4 View the electropherogram plots and notice that there are three allele calls for Sample2 COfiler v1 panel at the D16S539 locus D165539 fo 14 To zoom in on a particular marker click and drag to create a rectangle around the marker of interest Release the mouse to zoom in 5 View the D16S539 alleles for Sample2 COfiler_v1 panel more closely in a single pane a Select the D16S539 labels 1 Place the cursor to the left of the peaks within the plot Ee 11 2 Click and drag
14. 2 Human Identification Analysis Tutorial 3 1 Chapter 3 Database Analysis Database Workflow Description Cutoff Value Setting Database Analysis Tutorial Overview 3 2 In this chapter you perform analysis of tutorial database samples using the software settings from Chapter 1 Software Setup The HID Advanced analysis method created in this tutorial for processing database samples removes labels from each peak with a height less than 20 of the highest peak in a marker s allele size range cutoff value selected from the Allele tab of the analysis method does not include any condition regarding the base pair size of the peak with a removed label relative to a higher peak This option is provided for laboratories that wish to use one general value for removing labels from all loci It can be used when a high level of filtering specificity is not required as in the typing of single source samples for example database samples Overview of the tutorial for analyzing a database project 1 Add samples to be analyzed to the project page 3 4 2 Apply analysis settings to the samples in the project page 3 6 a Select the analysis method b Select the size standards for the samples 3 Analyze the project page 3 8 4 Examine the size standard page 3 9 a Assess whether samples pass the sizing criteria b Check the size standards for any samples that do not pass the sizing criteria 5 Examine the allelic ladde
15. 4357520 Rev A 11 2004 Contents Preface Chapter 1 Chapter 2 Chapter 3 Chapter 4 How to Use This Tutorial 0 000 000 ccc RR How to Obtain More Information 00 0000 cc eee How to Obtain Support 00 000 ee Software Setup Before You Start 33a uo setae eO e ace abd RA Panels and Bins 3 veda Gut RP hers ete wee woes HID Analysis Methods 0 00 cece eee Analysis Tables screen ee xn e ente Plots is pLtied wee sk uRerZ enEnbUsqatacorig gu E wes HID Analysis Options orara riir er eiiie n eae eee Casework Analysis Casework Workflow 0200 0c ee eee Setting Up a Casework Project 000 ccc eee eee Examining and Editing Results lille Database Analysis Database Workflow 0 000 cece res Setting Up a Database Project 2 000 0c eee eee Examining and Editing Results 0 0 0 eee eee eee CODIS Export About GODIS voee ec ede Sa SA ees See awa tas GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial lii CODIS Export Manager sss ere 4 3 CODIS Table Export 0 0000 ee 4 5 Appendix A Additional Information Size Standard Definitions llle A 2 Peak Detection Algorithms leslie A 3 Lists of Tables and Procedures in This Tutorial A 4 Genotyping Samples Manually 00000 eee eee eee A 6 Appendix B Converti
16. B 1 Appendix B Converting Macintosh Sample Files To install the sample file conversion programs on a Macintosh computer continued 2 Double click the CD ROM icon A CD ROM window displays containing files and folders 3 Locate and double click the CONVFOLD folder Inside this folder are two files CONVPROG HQX and README TXT which contain the installation instructions 4 Copy the CONVPROG HQX file to your local hard drive by clicking on the file dragging the file over to the local hard drive icon and dropping it in 5 Decompress the CONVPROG HQX file by dragging and dropping it onto a program called Stuffit Expander Note You can download a free version of Stuffit Expander from http www stuffit com expander Note Decompressing the CONVPROG HQX file creates a folder on the local hard drive This folder contains the conversion programs and the SimpleText file About Conversion Programs This file is a seven page document that describes in detail how to use the conversion programs why they are necessary solutions to common problems and possible alternative programs B 2 GeneMapper ID Software Version 3 1 Human Identification Analysis Tutorial Converting Macintosh Sample Files Converting To convert Macintosh computer sample files for use on a Macintosh computer running Microsoft Windows operating system Sample Files to Microsoft 1 Double click the icon to start the
17. COfiler CODIS v1 Identifler CODIS v1 1 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Panels and Bins To import panels and bin sets continued 6 View the markers and display the Bin view a Select the Profiler Plus v1 folder in the navigation pane to display the list of markers it contains in the right pane b Double click the Profiler Plus v1 folder in the navigation pane to display the list of markers below it c Select D381358 in the navigation pane to display the Bin view for the marker in the right pane File Edit Bins View EXE E LIU MY ln Set verc sins v1 a Loo McrosaTeLuTe_yY E E AmpFLSTR_Panels_v 41 42 13 14 18 15 216 16 2117 17 2 18 18 2119 20 Ei AmpFLSTR_Panels_v se Z 08 08 07 D21814 D18S51 D5S818 D135317 05 D75820 06 04 03 02 01 93 9 101 105 109 113 117 121 125 129 133 137 141 145 149 153 D381358 x Cancel Apply 7 Click Apply to add the Profiler Plus vl panel to the project window 8 Click OK to close the Panel Manager IMPORTANT If you close the Panel Manager without clicking OK the panels and bins will not be available for analysis What s Next You have now imported the necessary panel marker and bin information that you need for this tutorial and subsequent analysis You are ready to continue setting
18. Dono Sampie ro expo m 2 m Dadder Allelic Ladder no export m C 3 By lD_Neg_Cntii Negative Contre no export m 1 a m mee Sample Convieted Offer m 5 M Samples Sample Convicted Offer m 1 g e Samples Sample Convicted Otter HID im n Green vi Profier vi Profier Plus vi COfier vi SGM Plus vi Identifier vi SEfier vi Profiler Plus CODIS vi COfier CODIS v1 identifier CODIS v Note In the example above the first four samples are Cofiler and the last four samples are Profiler Plus GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 7 Chapter 2 Casework Analysis To apply analysis settings continued 3 Create a new size standard custom definition a Click the first empty None cell in the Size Standard column b Select New Size Standard from the drop down list c Specify the parameters below Select Dye and Analysis Method x C Basic or Advanced Classic Dye Red Analysis Method poces Sizing method Classic Dye Red Analysis Method HID Classic Select Sample CO Control fsa Note If you want to use another sample to make the size standard definition click Select Sample and then browse to the location of the sample file For this tutorial use the CO Control fsa sample already displayed d Click OK to access the Size St
19. GeneMapper app E Config Database E docs 3 Example Data Hid E Casework CMM Select the Databasing folder Z3 Microsatellite SNaPshot Note If you make an error in moving a file to the list select the files to remove from the Samples to Add list and click Clear Click Add to import the files into the project and close the dialog box The samples are displayed in the Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 5 Chapter 3 Database Analysis Applying Analysis To apply analysis settings Settings 1 Make sure that HID Table is selected from the Table Setting drop down list 2 Select the analysis method for the samples a Click the first empty None cell in the Analysis Method column in the Samples tab b Select HID Advanced from the drop down list c Click the Analysis Method column header to select the column Analysis Method Click here to select the column HID A need d Select Edit gt Fill Down to apply the analysis method to the selected samples 3 Select the appropriate panel for the samples a Click on the first empty None cell in the Panel column and open the AmpFZSTR Panels v1 folder b Double click on the Identifiler v1 panel from the drop down list This places the Identifiler v1 panel in the first sample row
20. More than one kit with shared markers A specimen category is selected for each sample to be exported Samples designated as a positive control negative control or allelic ladder cannot be exported A sample must have at least one allele call Allele calls contain acceptable characters numbers decimal points letters X and Y for Amelogenin allele calls and the symbols less than lt and greater than gt GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial CODIS Export Manager CODIS Export Manager Overview In this section use the CODIS Export Manager to view and set values for three fields required for exporting samples to CODIS Specimen Types Source Lab ID Destination Lab ID Setting CODIS For this tutorial you create a Source Lab ID and a Destination Export Fields Lab ID For future CODIS export procedures CODIS laboratories should use their assigned Source Lab ID and Destination Lab ID To set CODIS export fields 1 Select Tools gt CODIS Export Manager 2 View the Specimen Types The specimen types included in GeneMapper D Software version 3 1 are currently accepted by CODIS When CODIS accepts a new specimen type you can add the specimen type to the software by typing it in the text box and then clicking Add Specimen Types Alleged Father Alleged Mother Biological Child v no export Add Delete GeneMapper ID
21. Y Axis Scale individually gt v Toobar Iv Show of scale For Sample plot only ME mmu BES Mal For Genotype plot only Marker Margin F bp 1 26 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Options HID Analysis Options Overview In preparing GeneMapper ID software to analyze tutorial data from AmpF STR kits view and set options for Startup of GeneMapper JD software Analysis settings when adding samples to a project Analysis displays Users of GeneMapper ID software Viewing and Note These options are active only for the user currently logged into Setting Options the software To view and set options 1 Select Tools gt Options to open the Options dialog box 2 From the Startup tab view the default startup options Project Open Blank Project C Open Previous Project Note Later you may select Open Previous Project to open the last project you analyzed using GeneMapper D software GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 27 Chapter 1 Software Setup To view and set options continued 3 Select the Add Samples tab to view the default Add Samples options iSelect a Panel ol Note For subsequent analyses you may change these settings to set the same analysis method size standard 310 377
22. prepare fresh matrix A right arrow bracket 7 separates successive commands you select from a drop down or shortcut menu For example Select File gt Open gt Project Right click the sample row then select View Filter gt View All Runs GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Preface User Attention Words Two user attention words appear in Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Provides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical Examples of the user attention words appear below Note The size of the column affects the run time Note The Calibrate function is also available in the Control Console IMPORTANT To verify your client connection to the database you need a valid Oracle user ID and password IMPORTANT You must create a separate Sample Entry Spreadsheet for each 96 well microtiter plate How to Obtain More Information Related Documentation Send Us Your Comments vi The following related documents are available GeneMapper ID Software Version 3 1 User Guide PN 4338775 GeneMapper ID Software Version 3 2 User Bulletin PN 4352543 AmpF amp TR Yfiler PCR Ampl
23. the When using the Classic peak detection algorithm and at least three Size Standard size standard peaks match the software assigns a Sizing Quality SQ value of 0 5 which corresponds to a yellow triangle Check In this procedure you verify that the size standard peak assignments are correct and override the SQ value to display a green square Pass To examine the size standard 1 Scroll to the right side of the table to see the yellow sizing qualities 2 Select Edit gt Select All and click Size Match Editor to view the size standard for all samples 3 Notice that the Sizing Quality value equals 0 5 Size Matches size Calling curve Quality Sizing Quality 0 5 Override SQ 150160 200 46 139 300 340350 400 20004 75 4600 1200 800 400 tt R 4th ae es a i H 3500 3700 3900 4100 4300 4500 4700 4300 5100 5300 5500 5700 5900 6100 2 14 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To examine the size standard continued 4 View the peak assignments for each sample a Press the down arrow key to scroll through the samples on the left side of the Size Match Editor screen b Confirm that the size for the peaks in the HID Classic GS500 250 size standard GeneScan 500 ROX Size Standard is correctly assigned for each sample 5 Select Edit gt Override All SQ to ov
24. up the software GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 7 Chapter 1 Software Setup HID Analysis Methods Overview In this tutorial you create two analysis methods suitable for Human Identification HID analysis HID Classic Used in Chapter 2 Casework Analysis for processing casework This training analysis method includes GeneScan analysis parameters for Macintosh computers and maker specific stutter percentages HID Advanced Used in Chapter 3 Database Analysis for processing database samples This training analysis method includes GeneScan analysis parameters for the Microsoft Windows NT operating system and a 20 stutter filter similar to Kazam 209 Note These analysis methods are examples for training When analyzing your own data adjust the analysis range and peak amplitude thresholds for your samples and validation Creating Analysis To create analysis methods for HID Classic Methods for HID Classic 1 Select Tools GeneMapper Manager to open the GeneMapper Manager 2 Create an analysis method called HID Classic a Select the Analysis Methods tab and click New to open the New Analysis Method dialog box New Analysis Method x Select analysis type c Ba C SNaPshot C Microsatellite OK Cancel b Select HID and click OK to open the Analysis Method Editor with the General tab selected 1 8 GeneMapper
25. 0 Tm Ta 60 0 200 E EJ EU EJ 300 9m EJ EU ion eee te u En A a al d 5 12 T Cour Menit v D1954333 7 WWA Pox DISSET 300 Tm LJ LJ T5 UJ E 74 E 7 300 EJ EJ 360 800 D s b s bs Ls I Conirdl eid E rn Fe 400 120 a0 387 d 200 a EJ s EJ 307 J ur 350 800 v A Ee 3 all s Note GeneMapper JD software remembers the last plot used in the Samples Plot window and Genotypes Plot window independently 7 Continue with troubleshooting a Observe that there are no other indications of a mixture in the sample b Select View gt Raw Data for further examination 3 12 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To examine data and edit labels continued 8 Override the genotype for the tri allelic sample a Return to the Samples Plot window and click id Genotypes Table b Select the row containing the red octagon in the GQ column c Right click and then click Yes in the dialog box d Observe that the GQ flag changed from a red octagon Low Quality to a green square Pass and that the other flags changed to gray triangles to indicate that the sample was edited OS BIN PHR LPH SPU AN BD CC ovl Ga A m Close the Samples Plot window and save the project Exporting the You may export the table data as a tab delimited text file that can be Table O
26. 1 Human Identification Analysis Tutorial Index A Add Allele Comment dialog box 2 30 Add Samples options 1 28 adding alleles 2 30 casework samples 2 5 database samples 3 4 user names 1 31 Advanced peak detection algorithm A 3 Allele Changes selecting 2 29 Allele Number AN 3 10 alleles adding 2 30 deleting 2 29 viewing comments 2 25 viewing history 2 25 allelic bin definitions 1 2 allelic ladder analysis method for 1 2 examining calls 2 21 3 9 finding plots 3 9 sample type 1 2 AmpFISTR_Panels_v3 folder 1 6 analysis method for allelic ladders 1 2 HID_Advanced settings 1 13 HID_Classic settings 1 10 selecting 2 7 3 6 Analysis Method Editor 1 8 1 12 analysis options 1 29 analyzing casework project 2 14 database project 3 8 Applied Biosystems GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial contacting V Services and Support v Technical Communications iV Technical Support v applying analysis settings casework project 2 7 database project 3 6 Automatic Analysis option 1 29 B Basic peak detection algorithm A 3 bin sets importing 1 6 viewing 1 7 Bin view displaying fora marker 1 7 bold text when to use ili C casework analysis adding samples 2 5 analyzing 2 14 applying analysis settings 2 7 checking concordance 2 28 editing labels 2 25 examining allelic ladder calls 2 21 examining data 2 20 examining the 250 bp peak 2 18 examining the size standard 2 15
27. 2 25 Complete analysis page 2 25 Check concordance for shared markers page 2 28 Export the table optional page 2 30 2 2 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Casework Project Setting Up a Casework Project Adjusting the As you examine the Project window you may need to adjust the Project Window window to see as many of the table columns as possible The amount of resizing needed depends on the number of columns displayed and on the size and screen resolution of your monitor In general perform the following steps to view all columns in the Project window Adjust column width by placing cursor on lines between columns and then dragging File Edit Analysis View Tools Help Be BH S fave siting Samples Genotypes Status Jat ple File ample Name ample ID Comments Sample Type Specimen Category Analysis Method Panel Size Stant lej e jlojc zlol we o Figure 2 1 Adjusting the column width Note Altered column widths are not saved when you close the window To adjust the Project window 1 Click the square in the upper right corner of the window to maximize the window Ix GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 3 Chapter 2 Casework Analysis To adjust the Project window continued 2 Deselect S
28. E S mm 3 Click ji Display Plots to open the Genotypes Plot window and select the HID Genotyping plot from the drop down list below the menu bar 3 10 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To examine data and edit labels continued 4 Observe that there are three alleles for the marker am E EJ E Ej oe B B AU v 2 Bg e Staying within the bounds of the electropherogram select the three peaks by clicking to the left of the first peak and then dragging to the right of the last peak before releasing GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 11 Chapter 3 Database Analysis To examine data and edit labels continued 6 Observe the peaks within the context of a sample a With the peaks selected in the Genotypes Plot window return to the Project window b Select the Samples tab to open the Samples Plot window displaying the HID Genotyping plot File Edit View Tools Alleles Help Plot Setting AmpFLSTR Genotyping A Panes fs al E Luft p E ad fig defi s P l soo sQ Dasi Dz1s1r D78820 CSFIPO 20 us 280 E E g E 200 00 k Eo biu De 3 TD Cora raenittitr v m pssi3ss me pi3s317 D16S539 D281338 1 40
29. GS500 ROX Dye plot a With all samples still selected click Ali Display Plots to display the Samples Plot window b Select the Overlay GS500 ROX Dye plot from the drop down list below the menu bar e Samples Plot File Edit View Tools Alleles Help Plat Setting overlay GS500 ROX Dye M ll i ME ooo MEN is here to display fi gef c ee e uds ps b the list of plots Zoom in on the 250 bp peak a Place the cursor to the left of the 250 bp peak along the top x axis until the cursor changes to a magnifying glass 300 200 Q b Click and drag to create a box and release when the box includes the 250 bp peak d amp ore A Semet usus Note If you zoom in inaccurately move the cursor toward the x axis until the cursor changes to a magnifying glass and then double click to restore the plot to full view GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 17 Chapter 2 Casework Analysis To examine the 250 bp peak continued 3 Select the 250 bp peak by clicking it 20 The selected peak is highlighted 4 Select View gt Table Filter gt Show Selected Rows and verify that the values in the Size column are approximately 246 bp expected for this set of data However not all instruments will produc
30. GS500 standards are provided for use with the Advanced peak detection algorithm See Size Standard Definitions on page A 2 for more information To apply analysis settings 1 Select HID Table from the Table Setting drop down list at the top of the project window 2 Select the analysis method for the samples a Click the first empty None cell in the Analysis Method column in the Samples view b Select HID Classic from the drop down list c Click the Analysis Method column header to select the column Analysis Method Click here to select the column None None None None d Select Edit gt Fill Down to apply the HID Classic analysis method to all samples GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Casework Project To apply analysis settings continued 3 Select the appropriate panel for the sample Samples with a CO prefix use the COfiler v1 panel and samples with the PP prefix use the Profiler Plus Plus vlpanel GeneMapper ID v3 1 databasing gmid Is Logged In la xi le Edt Analysis View Tools Help i N iU fE e Table setting amprLsTR Table m Era OBS P5 LU 8 8 S Project Samples cenctypes oetebasing Status Sample Name Sample Type Specimen Cate Analysis Metho Size Standard Matix sao SFNF SNF sO a i
31. Label Font Arial size 11 rud Plot Settings E ditor Basepairs Scale individually p 1 20 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Plots Creating HID To create HID Sizing plot settings Sizing Plot Settings 1 From the GeneMapper Manager select the Plot Settings tab Click New to open the Plot Settings Editor with the General tab selected Select the settings shown in Table 1 4 HID Sizing plot settings Click OK to save the plot settings and to close the Plot Settings Editor Note Do not click OK until after you select settings on all tabs Click Done to close the GeneMapper Manager if you have finished creating all plot settings HID Sizing Plot Settings Table 1 4 HID Sizing plot settings Tab Settings General Name HID Sizing Sample Header Show 2 3 4 and 6 Hide 1 and 5 Genotype Header Show 2 5 10 15 18 19 and 20 Hide 1 6 9 16 and 17 Sizing Table Show 1 8 Font Arial size 11 Labels Label 1 Allele call Label 2 Label 3 Label 4 None Show data type prefixes deselected Show type of edit deselected Invert mutant labels deselected Label Color Dye Color Border Label Font Arial size 11 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 21 Chapter 1 Software Setup Table 1 4 HID Sizing plot
32. Markers Examining and Editing Results Checking concordance can be useful for comparing a sample amplified using kits with shared markers Requirements for performing a concordance check Add the sample to a project in the local GeneMapper database Note A sample added from outside of the GeneMapper database has no results associated with it for comparison Samples to be compared must have the same sample name or user defined value Note The concordance check in this tutorial compares markers shared between samples with the same sample name Laboratories with automated processes for naming samples can still perform this procedure by typing in a shared name for two or more samples in the UDI column You can also use this option when setting up a sample sheet by typing after the panel name in the comment field for example Profiler Plus v1 sample 1 To check concordance for shared markers 1 In the Project window select the Genotypes tab 2 Select Analysis gt Non concordant Samples to Top Note No samples are highlighted indicating that there are no discrepancies in genotypes for shared markers of the same sample amplified with AmpF STR Profiler Plus and AmpF STR COfiler kits GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 29 Chapter 2 Casework Analysis To check concordance for shared markers continued 3 For this tutorial introduce a discrep
33. Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 4 3 Chapter 4 CODIS Export To set CODIS export fields continued 3 Add a Source Lab ID a Type TutSrceID in the text box b Click Add Note The Source Lab ID cannot exceed nine characters Source Lah IDs srclab TutSrcelD fi utSrcelD Add Delete 4 Add a Destination Lab ID a Type TutDestID in the text box b Click Add Note The Destination Lab ID cannot exceed nine characters Destination Lab IDs destlab rutDestiD 5 Click OK to save the changes and close the CODIS Export Manager 4 4 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial CODIS Table Export CODIS Table Export Overview CODIS Specimen Number Modifying Columns GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial In this section 1 Modify columns for samples that will be exported 2 Export a table for CODIS The CODIS Specimen Number up to 24 characters is accessed from The Sample Name field if the UD1 column is not used The UDI column if the UD1 column is used Note For more information about the UD1 column see page 2 28 To modify columns 1 Open the project a Select File gt Open b Select Database Project 2 For each row make the appropriate setting in the Specimen Category column
34. U UDI for CODIS Specimen Number 4 5 for shared names 2 28 4 5 user attention words defined iv username adding 1 31 Users options 1 30 Z zooming in Samples Plot window 2 18 Size Standard Editor 2 11 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Index 5 Index 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 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 provides the innovative products services and knowledge resources that make this new Integrated Science possible 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 Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of www appliedbiosystems com Applied Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in USA 11 2004 Part Number 4357520 Rev A an Applera business
35. ak Height Ratio PHR and Allele Number AN columns and a red octagon Low Quality in the Genotype Quality GQ column Sample Name RunName Panel Marker Dye Allele 1 Allele 2 JAE Com amp E Com ADO AE os ein PHR LPH sPU AN BD cC Jovi oo 1 Samples 11 li J tt 2 ID Ladder Databasing Identifier v3 D21811 B 24 242 IX mm la mi 3 Sample3 Databasing Identifier va D18851 Y i5 fie mm mm mi 4 ID Ladder Dafabasing ldentifler v3 D18851 Y T t x mm n mA 5 ID Ladder Databasing ldentifler v3 D381358 G 12 13 Pad mm En 6 ID_Ladder_ Databasing identifier v3 D168539 6 5 8 x mm n mi 7 ID Ladder Databasing Identifier va D281338 G 15 fie x m m mi 8 ID Ladder Databasing Mentifler vs TPOX Y 6 7 x C C m 9 D Ladder Databasig denWerys Desii7aja e x mm m mmi 10 ID Ladder Databasing identifier v3 FGA R i7 fis Ix n L mA 11 ID Ladder Databasing ldenfifler v3 D198433 Y 9 10 x mm n mm mm 12 ID Ladder Databasing Identifler v3 WWA v nu 12 IX mm mm mm 13 IDLadder Databasing ldentiflIer v3 CSFIPO B 6 7 x mim n mm mm 14 ID Ladder Databasing identifier va TH0 G 4 5 IX mm m mm mm 15 ID Ladder Databasing identifier v3 D135317 o 8 8 x mm n mm 16 ID Ladder Databasing identifier v3 AMEL R x Y mm m mmm mm 17 ID Ladder Databasing ldentiller v3 D58818 R 7 8 x mm
36. ancy a Select the row for Sample 1 Profiler Plus v1 panel containing the D3S1358 locus Note The navigation pane contains a folder for each panel AmpF ZSTR kit analyzed Selecting a marker in the navigation pane displays all samples containing that marker b Click lll Display Plots to open the Genotypes Plot window c Select allele 15 by clicking the label or the peak and then right click and select Delete from the pop up menu to delete the allele Note If you select multiple labels or peaks and then select Delete the software prompts you with a warning that the corresponding alleles will be deleted d Type Concordance Test in the Delete Allele Comment dialog box and click OK e Notice that the label is deleted us 126 Note Show deleted labels by selecting Allele Changes from the View menu 4 Select File gt Close Plot Window to return to the Project window 2 30 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To check concordance for shared markers continued 5 Select Analysis gt Non concordant Samples to Top and notice that rows 1 and 2 are highlighted and brought to the top These samples contain the D3S1358 marker with nonconcordant genotypes e Allele 1 Allele 2 AE Com AE Com ADO AE os BIN PHR LPH sPU aN BD cc Jovi ca 5 16 BEEBE E H amp SE LM HMM MESE EM N 6 C
37. and release when the box contains the desired viewing range Always drag along the x axis that contains the numbers The x axis changes depending on the type of plot c Move the cursor toward the x axis until the cursor changes to a magnifying glass and then double click to restore the plot to full view 7 Explore the Size Standard Editor a Select a peak in the electropherogram and notice that the corresponding row in the table is highlighted b Select a peak in the table and notice that the corresponding peak in the electropherogram is highlighted 2 10 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Casework Project To apply analysis settings continued Peak C b Press Enter e Press Enter Data Points Size 8 Assign sizes to the peaks of the size standard 75 100 139 150 160 200 0 skip the 250 peak 300 340 350 400 Note Do not assign a size for the 250 bp peak This peak can be used as an indicator for precision within a run a Click the first peak in the electropherogram to select it c Type the fragment size for the selected peak in the corresponding cell in the table d Press the down arrow key to move to the next peak cell f Repeat steps c through e for all fragments sizes 3391 75 0 3623 100 0 3984 139 0 4074 150 0 4157 160 0 4511 4908 5350
38. andard Editor 2 8 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Casework Project To apply analysis settings continued The Size Standard Editor shows the electropherogram and a table of peaks for the dye color and sample selected rSize Standard Description Template File Info Name JH classic 6500 250 f CO Control fsa Run Date amp Time 0002 11 30 00 00 00 0 pce 0 ee Method ates Size Standard Table Data Points 3391 3623 3984 4074 4157 For more information about setting size standard parameters see the GeneMapper ID Software Version 3 1 User Guide 4 Enter a name for the size standard HID Classic GS500 250 5 If needed adjust the size of the Size Standard Editor window a Position the cursor over a border or corner of the Size Standard Editor until the cursor changes to sizing arrows b Click and drag the sizing arrows to achieve the desired size GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 9 Chapter 2 Casework Analysis To apply analysis settings continued 6 Zoom in and out of the Size Standard Editor electropherogram for easy viewing a Place the cursor along the x axis until the cursor changes to a magnifying glass b Click and drag to create a box
39. cate and open the folder containing the panels and bins a Select Panel Manager in the navigation pane Panel Manager File Edit Bins View if i mL NL NN amp iPanel Manager Select this l b Select File gt Import Panels to open the Import Panels dialog box GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 5 Chapter 1 Software Setup To import panels and bin sets continued 4 Import AmpFLSTR Panels v1 a Select AmpFLSTR Panels v1 txt b Click Import Note Importing this file creates a new folder in the navigation pane of the Panel Manager AmpFISTR Panels v1 containing the panels and associated markers 5 Import AmpFLSTR Bins vl txt a Select the AmpFLSTR Panels v1 folder in the navigation pane F Panel Manager File Edit Bins View of m M NU b Select File gt Import Bin Set to open the Import Bin Set dialog box c Select AmpFLSTR Bins vl1 txt d Click Import Note Click Apply or OK to make this file associate the bin set with the panels in the AmpFISTR Panels v1 folder Panel Manager File Edit Bins View wf gt lt el B Bin Set famprLsTR_Bins_v1 7 E Panel Manager Panel Name Comment Green v1 Profiler v1 Profiler Plus v1 CoOfiler v1 SGM Plus v1 Identifiler v1 SEfiler v1 Profiler Plus CODIS v1
40. d when you close the window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 3 Chapter 3 Database Analysis Adding Samples You should have a blank untitled Project window open To create a project select File gt New Project f GeneMapper ID v3 1 test gi Edit Analysis View Tools Ctri N Save Project Cts Save Project As Add Samples to Project Ctrl K Export Table Ctri E Export Table for CODIS Page Setup Print Ctrl P Log Out Exit AltsF4 Figure 3 1 New Project To add samples to the project 1 From the Project window select File gt Add Samples to Project to navigate to the disk or directory containing the tutorial sample files The initial view of the dialog box is for local disk access For more information on the GeneMapper JD software database see the GeneMapper ID Software Version 3 1 User Guide 2 Navigate to the Databasing folder X AppliedBiosystems GeneMapper Example Data HID Databasing Note X is the drive where you installed GeneMapper D software For subsequent analysis using your data navigate to the disk directory containing your files 3 4 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Database Project To add samples to the project continued 3 Select the Databasing folder and click Add To List 3 AppliedBiosystems
41. e Last Used plot settings Used Plot Settings 1 From the GeneMapper Manager select the Plot Settings tab 2 Click New to open the Plot Settings Editor with the General tab selected 3 Select the settings shown in Table 1 7 Last Used plot settings 4 Click OK to save the plot settings and to close the Plot Settings Editor Note Do not click OK until after you select settings on all tabs 5 Click Done to close the GeneMapper Manager if you have finished creating all plot settings GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 25 Chapter 1 Software Setup Last Used Plot Table 1 7 Last Used plot settings Settings Tab Settings General Name Last Used Sample Show 2 3 4 and 6 Header Hide 1 and 5 Genotype Show 2 5 10 15 18 19 and 20 Header Hide 1 6 9 16 and 17 Sizing Show 1 8 Table Font Arial size 11 Labels Label 1 Allele call Label 2 Label 3 and Label 4 None Show data type prefixes deselected Show type of edit deselected Invert mutant labels deselected Label Color Dye Color Border Label Font Arial size 11 Display Select this radio button Settings Plot Settings Editor eheral Sample Header Genotype Header Sizing Table Labels Display Settings Use these display settings For both Sample and Genotype plots Panes 1 he Ta pu wi uf E X Axis Basepairs be
42. e a 246 migration of the 250 peak yeiSample Pe Sample File Na Marker Allele i Data Point D RJ R7 R7 R7 R7 R7 R7 R7 Note This peak was not defined in the size standard The 250 bp peaks should size consistently and overlap In a typical run the 250 bp peaks all fall within a size window of approximately 1 bp Temperature fluctuations in the laboratory may cause variations gt 1 bp Note Laboratory temperature fluctuations can cause size shifts For the ABI PRISM 310 Genetic Analyzer only if the temperature of the laboratory fluctuates inject the appropriate AmpF STR allelic ladder approximately every 10 injections or 5 h 5 Close the sample plot What s Next You have now confirmed the sizing precision and you are ready to view and edit the plots and allele calls 2 18 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results Examining Data To examine data 1 With all samples still selected in the Project window select the HID Genotyping plot from the drop down list below the menu bar of the Samples Plot window 2 Click Hide All and then click m Show Blue Dye 7 Samples Plot File Edit View Tools Alleles Help Plot Setting HID Genotyping ZE Poesh AMA e E A fic gef afe ds SES Sample Name Pana sQo sa asfishs ipshisp p 2022 24
43. ed to be identified as Allelic Ladder in the Sample Type column in a project Failure to make this setting for ladder samples results in failed analysis Allelic bin definitions are stored in the AmpF STR panels in the Panel Manager Lanes or injections containing the allelic ladder should be analyzed with the same analysis method and parameters used for samples Alleles not found in the AmpFZSTR Allelic Ladders do exist These off ladder alleles may contain full and or partial repeat units An off ladder allele is defined as an allele falling outside of the 0 5 bp bin window of any known allelic ladder allele or virtual bin Note If a sample allele peak is called as an off ladder allele then run the sample again to verify the result 1 2 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Before You Start The marker specific stutter ratios included in the kit panels and cutoff value used in the tutorial serve as a tool and a guideline Base final conclusions on careful examination of the STR profiles Note GeneMapper ID Software version 3 1 has undergone a verification process defined by Applied Biosystems However human identification laboratories that choose to use GeneMapper ID Software to analyze forensic paternity databasing and single source samples should perform their own appropriate validation studies Software Setup Perform the following tasks before you analyze fragme
44. erride of the values due to the deletion of the allele call Completing Complete the analysis of all of the samples by viewing the dyes Analysis individually in the HID Genotyping plot To complete analysis 1 Return to the Project window and select Edit gt Select All 2 Click ill Display Plots to open the Samples Plot window 2 26 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To complete analysis continued 3 With the samples plot still open reselect the HID Genotyping plot from the drop list to refresh the window with the original settings Note that it may appear as though it is already selected but you need to open the box and select it again 4 Click All Hide All and click J Show Green Dye and scroll through all samples Samples Plot n x File Edit View Tools Alleles Help Plot Setting HD Genotyping AA Panes Foe PRT a erp acu 1 E d ce haf ka IET 4s P ss Sample Name m B esti J 120 w p2 2942 apa ofis 2163 2165 rsfa 2 ez Bal B6 ra 3 5
45. erride the SQ value for all samples 6 Notice that the Sizing Quality is changed to 1 07 which indicates that user verified the size standard Sizing Quality Size Matches size Calling Curve Sizing Quality lt 1 0 gt 2400 439150160 200 300 350 400 20004 75 100 340 1600 1200 800 400 0 tment a ate t fom 3500 3700 3900 4100 4300 4500 4700 4900 5100 5300 5500 5700 5900 6100 7 Click Apply then click OK to close the Size Match Editor and return to the Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 15 Chapter 2 Casework Analysis To examine the size standard continued 8 Notice that after overriding the SQ values The SQ flags are changed to green squares Pass The Sizing Quality Override SQO column is checked sao srNr Sa x m m x m m xm m xm m x m m xm m xm m x m m 9 Define a new size standard for the affected samples and then reanalyze the sample if one of the following occurs Size standard peak assignments are incorrect for one or more of the samples in a subsequent analysis Fewer than three peaks are matched and a red flag is displayed 2 16 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results Examining the To examine the 250 bp peak 250 bp Peak 1 Display the Overlay
46. examining 250 bp peak 2 18 allelic ladder calls 2 21 3 9 data 2 20 3 10 size standard 2 15 3 9 export file type for CODIS 4 7 exporting casework project table 2 30 CODIS table 4 6 database project table 3 13 F finding allelic ladder plots 3 9 G GeneMapper Manager 1 8 Genotype Quality GQ 1 29 3 10 3 13 genotype overriding 3 13 Genotypes Plot window displaying 2 29 2 30 3 9 3 10 Genotypes table Index 2 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial displaying 2 23 Genotypes Table icon 2 23 settings 1 18 genotyping samples manually A 6 H HID analysis considerations 1 2 HID Genotyping plot displaying 2 20 2 26 3 9 3 10 3 12 settings 1 19 HID Sizing plot settings 1 21 HID Table creating 1 16 displaying 2 7 3 6 HID_Advanced analysis method cutoff value setting 3 2 selecting 3 6 settings 1 13 HID Classic analysis method creating 1 8 1 12 selecting 2 7 settings 1 10 Hide Allicon 2 26 history viewing for alleles 2 25 Import Panels dialog box 1 5 IMPORTANTS description iv importing panels and bin sets 1 5 italic text when to use ili L labels deleting 2 29 selecting 2 21 2 25 showing deleted 2 29 using 20 filter to remove 3 2 viewing 2 20 Last Used plot settings 1 25 Low Quality to Top icon 3 10 M Macintosh file conversion B 1 Mac to Win AppleScript 1 3 magnifying glass 2 11 2 18 marker displaying Bin view of 1 7 menu co
47. exporting the table 2 30 genotyping samples manually A 6 overview 2 3 viewing allele history and comments 2 25 checking concordance 2 28 Classic peak detection algorithm A 3 CMF 1 0 file type 4 7 Index 1 CMF 3 0 file type 4 7 CODIS export manager 4 3 exporting CODIS table 4 6 modifying columns 4 5 requirements 4 2 setting CODIS export fields 4 3 specimen number 4 5 table export 4 5 Web site 4 2 columns resizing 2 5 3 3 Combine Dyes icon 2 21 concordance checking 2 28 CODIS requirement 4 6 requirements 2 28 usefulness 2 28 conventions bold text iii IMPORTANTS iv in this guide iii italic text iii menu commands iii Notes iv user attention words iv converting Macintosh files to Windows format B 1 custom size standards 2 3 cutoff value 1 3 3 2 D database analysis adding samples 3 4 analyzing 3 8 applying analysis settings 3 6 editing labels 3 10 examining allelic ladder calls 3 9 examining data 3 10 examining the size standard 3 9 exporting the table 3 13 overview 3 2 Databasing folder 3 4 Delete Allele Comment dialog box 2 29 Destination Lab ID adding 4 4 selecting 4 7 Display Plots icon 2 18 2 25 2 29 2 30 3 9 3 10 Documentation PDF versions iV related iV Don t Bring Controls to Top icon 2 21 Duplicate homozygous alleles check box 1 29 E editing labels casework project 2 25 database project 3 10 E mail address Technical Communications 1V errors displayed at top of table 1 29
48. for each size standard Table A 1 Size standard fragment sizes Size Standard Fragment Sizes bp 377 F HID GS500 75 100 139 150 160 200 250 300 340 350 400 377 G5 HID GS500 75 100 139 150 160 200 250 300 340 350 400 450 CE F HID GS500 75 100 139 150 160 200 300 340 350 400 CE G5 HID GS500 75 100 139 150 160 200 300 340 350 400 450 A 2 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Peak Detection Algorithms Peak Detection Algorithms Available Basic Contains limited parameters that may not provide enough Algorithms user control over data analysis for desired results Classic Includes the same parameters and the same size caller and produces the same results as GeneScan Software version 3 1 2 designed for use with the Macintosh operating system Advanced Provides the most user control over data analysis Includes the same parameters as and produces similar results to GeneScan software designed for use with the Microsoft Windows NT operating system with the exception of the smoothing function Smoothing in GeneMapper D software applies to both the electropherogram and data table The Advanced algorithm also includes a new size caller with a quality value based on the fit of the size standard definition to the actual size standard in the sample PQV System The Process Component Based Quality Value PQV syste
49. gmid Is Logged In file Edit Analysis view Tools Help 3 Project a E Datavasing Analyzing Samples He a RE LE LL mi Bg Bi Samples Genotypes Status Sample F Sample N Sample IC Comment Sample T Specimer Analysis Panel Size Star Matrix Run Nam Instrumer Instrumer ID Contrc ib Contrc None pee Jro export HID_Adv Identifier CE G5 Databasir ABI3100 demo 31 ID Ladde ID_Ladde None Alelic La no export HD Advildentifiler CE_G5_ Databasit ABI3100 demo 31 l ID Neg c ID Neg C None Negative no export HD AdviIdentifi CE G5 F Databasir ABI3100 demo 31 ID amp Samples None Sample Jno expor HID_Adve identi Databasit ABI3100 demo 31 3 8 Figure 3 2 Database Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results Examining and Editing Results Overview Sizing Quality Examining the Size Standard Examining the Allelic Ladder Calls In this section you examine the size standard and data then edit labels The advanced peak detection algorithm includes a sizing quality SQ value to assess the sizing of a sample You can override the SQ value assigned by the software and or reassign incorrect size standard peaks using the Size Match Editor Overriding the SQ value sets the value
50. how Navigator from the View menu to hide the navigation pane This action expands the Samples and Genotypes tabs to the width of the Project window Select Show Navigator from the View menu to restore the navigation pane Resize columns by dragging the separating lines a Position the cursor over the line separating two columns until the cursor changes to sizing arrows b Click and drag the sizing arrows Dragging to the left narrows the column to the left Adding Samples You should have a blank untitled Project window open To create a blank project if a blank project window is not open or if an existing project is already open select File gt New Project F GeneMapper ID v3 1 test g LM Edit New oject Ctrl N Open Project Ctrieo Save Project Ctri S Analysis View Tools Save Project As Add Samples to Project Ctrl K Export Table Ctri E Export Table for CODIS Page Setup Print Ctrl P Log Out Exit Figure 2 2 New Project To add samples to the project l From the Project window select File gt Add Samples to Project to navigate to the disk or directory containing the tutorial sample files The initial view of the dialog box is for local disk access For more information on the GeneMapper JD software database see the GeneMapper ID Software Version 3 1 User Guide 2 4 GeneMapper ID Software Versions 3 1 and 3 2 Hu
51. ification Kit Users Manual PN 4358101 Portable document format PDF versions of this tutorial and the user guide are also available on the GeneMapper JD software installation CD PDF versions of the other tutorials are available on the Applied Biosystems Web site See How to Obtain Support on page v Applied Biosystems welcomes your comments and suggestions for improving its documents You can e mail your comments to techpubs appliedbiosystems com GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial How to Obtain Support How to Obtain Support 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 addition the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial vii Preface viii GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Software Setup This chapte
52. lick ii Display Plots to open the Genotypes Plot window 7 Restore the original allele call a Select the peak without the label by clicking it b Right click the selected peak and select Add Allele Call from the pop up menu c Type Concordance restored in the Add Allele Comment dialog box and click OK 8 Select File gt Close Plot Window to return to the Project window and select File gt Save Project to save the changes Exporting the You may export the table data as a tab delimited text file that can be Table Optional used with spreadsheet software Note To export a table for the CODIS database go to Chapter 4 CODIS Export To export the table 1 Select File gt Export Table from the Project window 2 Select a location for the file 3 Enter Casework Table for the file name 4 Click Export Table 5 Using Microsoft Excel software or equivalent spreadsheet software open the exported table file GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 31 Chapter 2 Casework Analysis 2 32 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Database Analysis This chapter covers Database Workflow 1 20 0 0 cece eee ee 3 2 Setting Up a Database Project n on 0 00 eee 3 3 Examining and Editing Results esses 3 9 GeneMapper ID Software Versions 3 1 and 3
53. m Description monitors the major components of the size calling and allele calling process The quality values Are reported by GeneMapper ID software as an aid to flag criteria related to sample preparation PCR separation detection and analysis for each marker Are weighted by the user and represented as green squares Pass yellow triangles Check and red octagons Low Quality Do not affect the genotypes called by the software and can be manually overridden by the user The final conclusions made by the examiner of the STR profile override and take precedence over any assignments made by the POV system GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial A 3 Appendix A Additional Information Lists of Tables and Procedures in This Tutorial A 4 Tables Software Setup Procedures Casework Analysis Procedures Concordance Procedure Table 1 1 HID Classic analysis method settings 1 10 Table 1 2 HID Advanced analysis method settings 1 13 Table 1 3 HID Genotyping plot settings 1 19 Table 1 4 HID Sizing plot settings 005 1 21 Table 1 5 Overlay GS500 LIZ Dye plot settings 1 23 Table 1 6 Overlay GS500 ROX Dye plot settings 1 24 Table 1 7 Last Used plot settings 0 00 ce eee ee 1 26 Table A 1 Size standard fragment sizes 004 A 2 To import panels and bin sets
54. man Identification Analysis Tutorial Setting Up a Casework Project To add samples to the project continued 2 Navigate to the Casework folder X Applied Biosystems GeneMapper Example Data HID Casework Note X is the drive where you installed GeneMapper ID software For subsequent analysis using your data navigate to the disk directory containing your files 3 Select the Casework folder and click Add To List at the bottom of the screen Eg GeneMapper zd Config zd Database zd Example Data H Hid H E Casework Select the Casework folder Databasing C3 Microsatellite EL SNaPshot Note The casework folder appears in the Samples To Add box on the right Note If you make an error in moving a file to the list select the files to remove from the Samples to Add list and click Clear 4 Click Add to import the files into the project and close the dialog box The samples are displayed in the Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 5 Chapter 2 Casework Analysis Applying Analysis Settings In this procedure you select the analysis method for the samples create a new size standard custom definition and set the size standard for the samples Note The definitions for the 377 F HID GS500 377 G5 HID GS500 CE F HID GS500 and CE G5 HID
55. matrix panel and or sample type for all samples Select the alternative radio button and then select the setting from the drop down list 1 28 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Options To view and set options continued 4 Select the Analysis tab to set the Analysis options Automatic Analysis Automatically bring low quality samples to the top Quality Metrics Display Symbols C Numbers Mif only one labelled allele in a genotype then duplicate the label Duplicate homozygous alleles a For the Automatic Analysis option deselect the Automatically bring errors to the top of the table check box Note Later you can select the check box to display samples with analysis errors at the top of the Project window automatically b Set the Quality Metrics Display option to Symbols Note Changing this option to Numbers affects only the Sizing Quality SQ column in the Samples view and the Genotype Quality GQ column in the Genotypes view The Quality Metrics Display option is part of the Process Component Based Quality Value PQV system for more information see PQV System Description on page A 3 and the GeneMapper ID Software Version 3 1 User Guide c Deselect the Duplicate homozygous alleles check box GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis T
56. mmands conventions for describing iii modifying columns for CODIS 4 5 MSDSs obtaining v N navigation pane hiding restoring in the Project window 2 5 3 3 Panel Manager 1 5 nonconcordant samples to top 2 28 2 30 Notes description iv O off ladder alleles 1 2 options setting 1 27 Overlay LIZ Dye plot settings 1 22 Overlay ROX Dye plot displaying 2 18 settings 1 24 P Panel Manager 1 5 window commands 1 4 panels importing 1 6 Panes drop down list 2 21 PDF versions of documents iV peak detection algorithms A 3 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Index 3 Peak Height Ratio PHR 3 10 peaks examining 2 21 selecting 2 22 plot settings creating 1 19 HID Genotyping plot 1 19 HID Sizing plot 1 21 Last Used plot 1 25 Overlay LIZ Dye plot 1 22 Overlay ROX Dye plot 1 24 Preface ili Process Component Based Quality Value PQV system 1 29 A 3 Profiler_Plus_v3 folder 1 7 Project window adjusting 2 4 3 3 displaying casework samples 2 6 displaying database samples 3 5 pull up ratio 2 23 Q Quality Metrics Display option 1 29 R raw data viewing 2 24 3 12 Related documentation iv S sample files converting from Mac to NT B 1 converting to fsa format 1 3 samples adding to casework project 2 5 adding to database project 3 4 Samples Plot window closing 2 27 displaying 2 18 2 25 3 12 zooming in 2 18 Samples table settings 1 17 Sample
57. mple THO1 or vWA The marker information contains the e Name Min and max size Dye color Marker specific sutter ratio e 9947A control alleles e Allelic ladder alleles Bin An expected location for a particular allele within a marker Binset Collection of expected locations for markers contained within a panel or kit 1 4 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Panels and Bins Importing Panels Use this procedure to import panels and bin sets into the and Bin Sets GeneMapper database for subsequent analysis and to view imported panels markers and bins Import the panels and bin sets the first time you use the software and when updated versions of panels and bin sets are provided To import panels and bin sets l Start the GeneMapper JD software a Select Start gt Programs gt Applied Biosystems gt GeneMapper gt GeneMapper ID b In the login box leave the Password box empty if this is the first time you are launching the software If not enter your password c The first time you start the software you are prompted to change the password When the password dialog box opens Leave the Old Password box blank Type a the New Password Type the new password again to verify it The GeneMapper Project window opens with a blank untitled project Select Tools gt Panel Manager to open the Panel Manager Lo
58. n programs to prepare Macintosh computer generated fragment analysis sample files for transfer to a Microsoft Windows based format and vice versa Converting Macintosh Sample Files About Converting Applied Biosystems created two conversion programs that prepare Sample Files sample files for transfer from a Macintosh computer to computers running Microsoft Windows NT operating systems and vice versa These sample file conversion programs run only on a Macintosh computer The sample file conversion programs do not perform the file transfer from computer to computer They set attributes of the files so that they can be used on the destination computer For example when transferring a fragment analysis sample file from a Macintosh computer to a computer running the Windows operating system a file extension is required and the conversion program adds fsa to the sample file name For more detailed information on how these conversion programs function refer to the SimpleText file entitled About Conversion Programs located in the same folder as the sample file conversion programs Installing To install the sample file conversion programs on a Macintosh Conversion computer Programs 1 Insert the GeneMapper ID software CD ROM into your Macintosh computer s CD ROM drive An icon displays for the CD ROM on the right hand side of the screen GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial
59. ng Macintosh Sample Files Appendix Overview 2 0c eee B 1 Converting Macintosh Sample Files llsssss B 1 Index iv GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Preface How to Use This Tutorial Purpose of This The Applied Biosystems GeneMapper ID Software Versions 3 1 Tutorial and 3 2 Human Identification Analysis Tutorial provides example workflows for using GeneMapper ID Software versions 3 1 and 3 2 The tutorial consists of casework analysis and database analysis using data provided with the software from AmpF STR PCR Amplification Kits The settings included in this tutorial should serve as a guideline for subsequent analysis For detailed information on the features and capabilities of GeneMapper ID Software version 3 2 including support of the AmpFZSTR Yfiler PCR Amplification Kit please refer to the GeneMapper ID Software Version 3 2 User Bulletin PN 4352543 Audience This tutorial is intended for novice GeneMapper JD software users who use the software to analyze forensic casework and single source or parentage samples amplified with the AmpF STR PCR Amplification Kits Text Conventions This guide uses the following conventions Bold indicates user action For example Type 0 then press Enter for each of the remaining fields e Italic text indicates new or important words and is also used for emphasis For example Before analyzing always
60. nt sample Tutorial Overview _ fsa files for HID the first time 1 Import panels and bins into the Panel Manager page 1 5 2 Create an analysis method with the appropriate bin set option page 1 8 Define custom views of analysis tables page 1 16 Define custom views of plots page 1 19 View and set HID analysis options page 1 27 ON no 3x O2 If necessary convert any GeneScan software sample files generated on the Macintosh platform to the fsa format using the Mac to Win AppleScript software provided with GeneMapper ID software Conversion is described in the GeneMapper ID Software Version 3 1 User Guide GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 3 Chapter 1 Software Setup Panels and Bins Overview In this tutorial you import panels and bin sets in the form of text files txt extension provided for use with the AmpFZSTR kits and included with the GeneMapper ID software For information on creating new panels see the Panel Manager Window Commands section in the GeneMapper ID Sofiware Version 3 1 User Guide Definitions The following table lists some terms and definitions that are used often in this tutorial Term Definition Kit Collection of panels For example an AmpFZSTR kit is a panel Panel Collection of markers A primer set specific to an AmpF STR kit For example Identifiler has 16 markers Marker A loci or primer pair For exa
61. o create analysis methods for HID Advanced continued 2 Select the settings shown in Table 1 2 HID Advanced analysis method settings IMPORTANT You must select your settings on all the tabs before you Click OK to save the analysis method and return to GeneMapper Manager HID Advanced Table 1 2 HID Advanced analysis method settings Settings Tab Settings General Name HID Advanced Allele Analysis Method Editor HID General Allele Peak Detector Peak Quality Quality Flags Bin Set ampFLSTR_Bins_v1 bd Marker Repeat Type PM Use marker specific stutter ratio if available Cut off Value Minus amp Ratio Minus amp Distance From To Stutter Ratio Stutter Distance From To Tetranucleotide 2 0 0 IU Note For more information about the Cutoff Value setting see page 3 2 Amelogenin Cutoff 0 25 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 13 Chapter 1 Software Setup Table 1 2 HID Advanced analysis method settings continued Tab Settings Peak Detector Analysis Method Editor HID Partial Range v Partial Sizes 2700 7500 450 Note The Analysis Partial Range is defined for tutorial database sample files Note For more information see Peak Detection Algorithms on page A 3 Peak Quality Analysis Method Editor HID
62. ot 2 Return to the GeneMapper JD software Project window and select File Export Table for CODIS The Export CODIS Data dialog box opens 4 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial CODIS Table Export To export the CODIS table continued 3 Make the following selections a Look in X GeneMapper Example Data Exported Tables Note X is the drive where you installed GeneMapper ID software b Export File As CMF 3 0 xml Note GeneMapper JD software supports CMF 1 0 dat file types for export c Source TutSrceID d Destination TutDestID e File name default Database Project Note The default file name for CODIS export is the project name f Export CODIS Data for Database Project x a Exported Tables x f E Look in ry Export File As EMF 3 0 mb 7 rCODIS Laboratory IDs Source Desktop TutsrcelD m Destination TutDestID z My Documents iud My Computer TE atabase Project Export Files of type cons formats CMF 1 0 CMF 3 0 dat xml x Cancel RENGE File name GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 4 7 Chapter 4 CODIS Export To export the CODIS table continued 4 Click Export The file is exported to the Exported Table
63. ote The Analysis Partial Range is defined for tutorial casework sample files Note For more information see Peak Detection Algorithms on page A o 3 Peak Quality Analysis Method Editor HID GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 11 Chapter 1 Software Setup Table 1 1 HID Classic analysis method settings continued Tab Settings Quality Flags Quality flag settings Quality weights are between 0 and 1 Quality Flag Settings Spectral Pull up fo 8 Control Concordance fi 0 Broad Peak os Low Peak Height fos Out of Bin Allele fos Off scale Js Gueits fos Peak Height Ratio fos PQV thresholds PQV Thresholds Sizing Quality From ors to10 From 0 0 to o2s Genotype Quality From pss to10 FromoO 0te 0 25 Factory Defaults Creating Analysis To create analysis methods for HID Advanced Methods for HID Advanced 1 In the GeneMapper Manager create an analysis method called HID Advanced a Select the Analysis Methods tab and click New to open the New Analysis Method dialog box New Analysis Method x Select analysis type c Bp C SNaPshot C Microsatellite OK Cancel b Select HID and click OK to open the Analysis Method Editor with the General tab selected 1 12 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Methods T
64. otypes tab becomes available after analysis f GeneMapper ID v3 1 Database Project gmid Is Logged In Fil Edit Analysis wy Tools Help SS E E mc G Bil B Project Samples Genotypes B Status Sample F Sample N Sample IC Comment Sample T Specimer Analysis Panel Size Star Matrix Run Nam Instrumer Instrumer Run Date ID_Contre ID Contrc None Pere Jre expori HD Adv Identifller CE G5 Databasir ABI100 demo 31 2002 06 ID Ladde ID Ladde None Allelic Len no export HID Adv Identifiler CE G5 F Databasir ABI3100 demo 31 2002 06 1 2 3 D Nea c ID Nea None Negative no exporl HID Adv Identifiler CE G5 F Databasir ABIS100 demo 31 2002 06 4 ID Sampl Sample3 None Sample noexpor HID Adv Identifiler CE G5 F Databasir ABI3100 demo 31 2002 06 e e 5 313100 demo 31 ID Sampl Sample5 Sample noexporn HID Adv Identifiler Databasir ABIS100 demo 31 2002 06 Analyzing Samples Figure 2 3 The Database Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 13 Chapter 2 Casework Analysis Examining and Editing Results Overview You can display electropherogram plots from the Samples and Genotypes tabs of the Project window to examine the data These procedures start with the Samples tab of the Project window assuming that analysis is complete Examining
65. program Windows Files Sample File Win to Mac The following dialog box opens cjuo bate roses a za b G Hard Disk ToolKit 12 17 98 v G parent Today b u Contains Windows files Today gt Oj rest of System stuff 12 11 99 b 2 Sequencing Analysis 3 4 1 5 17 00 b a System Folder 12 11 99 Where are the files to convert to Windows format Rew open Cne Goose Note On Macintosh computers running operating system 8 0 or less this dialog box has a different appearance For more information refer to the SimpleText file About Conversion Programs see the Note in step 5 above 2 Using the triangle shaped icons to the left of the folder names navigate to the folder that contains the fragment analysis sample files you want to convert 3 Select the folder by single clicking its name 4 Click Choose at the bottom of the dialog box If there are no problems the program performs the task and quits automatically When you open the folder the sample files have the file extension fsa Note To convert sample files created on a computer running the Microsoft Windows operating system for use on a Macintosh computer follow steps 1 3 above in Step 1 double click the Sample File Win to Mac icon GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial B 3 Appendix B Converting Macintosh Sample Files B 4 GeneMapper ID Software Version 3
66. ptional used with spreadsheet software Note To export a table for the CODIS database see Chapter 4 To export the table l In the Genotypes tab view select File gt Export Table Select a location for the file Enter Database Table for the file name Click Export Table Using Microsoft Excel software or equivalent spreadsheet software open the exported table file GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 13 Chapter 3 Database Analysis 3 14 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial CODIS Export This chapter covers About CODIS te ee erret et e 4 2 CODIS Export Manager l l ees 4 3 CODIS Table ExpOrt 2 oieiRaeeX ec eRekkeerEeSWeeihee 4 5 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 4 1 Chapter 4 CODIS Export About CODIS GeneMapper ID GeneMapper ID software can export data from the analysis in a Software format suitable for the FBI Laboratory Combined DNA Index Features System CODIS For more information about CODIS see http www fbi gov hq lab codis index1 htm CODIS Creation of CODIS CMF files from GeneMapper ID software Requirements requires that Genotypes and specimen categories for shared markers are identical for each sample tested with AmpF STR Profiler Plus Kit COfiler PCR Amplification Kit
67. r calls page 3 9 6 Examine data and edit labels page 3 10 a Assess whether sample markers pass the genotyping criteria b Examine peaks for any sample markers that do not pass the genotyping criteria 7 Export the table optional page 3 13 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Setting Up a Database Project Setting Up a Database Project Adjusting the As you examine the Project window you may need to adjust the Project Window window to see as many of the table columns as possible The amount of resizing needed depends on the number of columns displayed and on the size and screen resolution of the monitor used to run the GeneMapper D software In general perform the following steps to view all columns in the Project window To adjust the Project window l Click the square in the upper right corner of the window to maximize the window m Deselect Show Navigator from the View menu to hide the navigation pane This action expands the Samples and Genotypes tabs to the width of the Project window Select Show Navigator from the View menu to restore the navigation pane Resize columns by dragging the separating lines a Position the cursor over the line separating two columns until the cursor changes to sizing arrows b Click and drag the sizing arrows Dragging to the left narrows the column to the left Note Altered column widths are not save
68. r covers Before You Start 22 cell ARE REECOIMG REDI ey 1 2 Panels and Bins s soccer LUE ede eg 1 4 HID Analysis Methods 0 00 c cece cee ene 1 8 Analysis Tables 2 euisque Ee eR neat 1 16 Plots etri stas t tas Sot uia eee uote baci 1 18 HID Analysis Options 0 0 0 00 0 1 26 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 1 1 Chapter 1 Software Setup Before You Start Considerations When using GeneMapper ID Software version 3 1 to perform for HID Analysis Human Identification HID analysis with AmpF STR kits consider the following HID analysis requires the presence of at least one allelic ladder sample per project Your laboratory can use multiple ladder samples in an analysis provided individual laboratories conduct the appropriate validation studies Samples are genotyped according the to the allelic bins calculated from ladder s within the same run folder When multiple run folders are imported into a project each sample is genotyped according to the ladders with the respective run Allelic ladder samples in a single run folder are considered to be from a single run When the software imports multiple run folders into a project only ladders within a single run folder are used for calculating allelic bin offsets and subsequent genotyping Multiple ladders within a single run folder are averaged by the software to create bin offsets Allelic ladder samples ne
69. s folder T Exploring D AppliedBiosystems GeneM apper E xample D ataXE xported T ables File Edit View Tools Help 3 Exported Tables E fal xs AES x x agaa All Folders Contents of D AppliedBiosystems GeneMapper E xample Dat AppliedBiosystems ajf Name Size Type Modi cC GeneMapper K Database Project ml 17KB XML Document 8 13 app zy Config Database E does Example Data 3 E ported Tables Hid Microsatellite cg SNaPshot x gt 1 objects selected 16 8KB 4 8 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Additional Information This appendix covers Size Standard Definitions nona 0 0000 c cece eee A 2 Peak Detection Algorithms 000 cece eee eee A 3 Lists of Tables and Procedures in This Tutorial A 4 Genotyping Samples Manually onana anaana 00 0 eee eee A 6 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial A 1 Appendix A Additional Information Size Standard Definitions Size Standard The definitions for the following size standards are provided with Definitions GeneMapper JD software version 3 1 for use with the Advanced Provided algorithm 377 F HID GS500 377 G5 HID GS500 CE F HID GS500 CE G5 HID GS500 Fragment Sizes The table below lists the fragment sizes
70. s table displaying 2 24 Save Project dialog box 2 14 3 8 Separate Dyes icon 2 25 Services and Support obtaining V setting CODIS export fields 4 3 setting options 1 27 shared markers checking concordance 2 28 CODIS requirement 4 6 Show Allicon 2 21 Show Green Dye icon 2 26 Size Match Editor icon 2 15 size standard creating custom definition 2 9 definitions A 2 examining 2 15 3 9 incorrect peak assignments 2 17 setting 2 13 3 7 shifts 2 19 Size Standard Editor adjusting view 2 11 displaying 2 10 Sizing Quality SQ 3 9 overriding 2 16 Quality Metrics Display option 1 29 viewing 2 15 2 17 Sizing Quality Override SQO 2 17 Sizing Table icon 2 22 software setup converting sample files 1 3 creating analysis method 1 8 1 12 creating plot settings 1 19 creating table setting 1 16 importing panels and bin sets 1 5 overview 1 3 setting options 1 27 Source Lab ID adding 4 4 selecting 4 7 specimen number CODIS 4 5 Index 4 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial specimen type 4 3 Spectral Pull Up SPU 2 22 2 23 spike in raw data 2 24 startup options 1 27 stutter ratio 1 3 stutter values 1 10 T table export for CODIS 4 6 tab delimited text file 2 30 3 13 table filter using 2 19 2 22 table setting editor 1 16 selecting 2 7 3 6 Technical Communications contacting iv Technical Support contacting V temperature fluctuations 2 19 training information on V
71. settings continued Tab Settings Display Settings General Sample Header Genotype Header Sizing Table Labels Display Settings When Opening The Plot Window C Use the display settings last used for this plot Use these display settings f For both Sample and Genotype plots Panes 4 lt Jeti H lupe pF 3 X Axis Basepairs zl Y Axis Scale individually E I Toolbar IV Show Off scale For Sample mm mu mm Impp Ee a Ma For Genotype plot only Marker Margin B bp Creating Overlay To create the Overlay GS500 Liz Dye plot settings GS500 LIZ Dye Plot Settings 1 From the GeneMapper Manager select the Plot Settings tab 2 Click New to open the Plot Settings Editor with the General tab selected 3 Select the settings shown in Table 1 5 Overlay GS500 LIZ Dye plot settings 4 Click OK to save the plot settings and to close the Plot Settings Editor Note Do not click OK until after you select settings on all tabs 5 Click Done to close the GeneMapper Manager if you have finished creating all plot settings 1 22 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Plots Overlay GS500 Table 1 5 Overlay GS500 LIZ Dye plot settings LIZ Dye Plot Settings Tab Settings General Name Overlay GS500 LIZ Dye Sample Show 2 3 4 and 6 Header Hide 1 and 5
72. sions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To examine data continued 10 Observe the raw data a Select View gt Raw Data b Zoom in on the data point position 4898 and observe that the allele 9 peak corresponds to a spike Spike at data point d uU w position 4898 11 Select View gt Samples to view the Samples tab of the Project window GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 25 Chapter 2 Casework Analysis Editing Labels To edit labels 1 Click a On the Samples Plot on the lower taskbar of your computer screen to return to the previous plot window b Click s to separate dyes 2 Click within the plot but not on a peak to deselect previously selected peaks 3 Select the label for allele 9 by clicking the label or the peak 4 Right click the label and select Delete 5 Type spike in the Edit Allele Comment dialog box 6 Click OK Viewing Allele To view allele history and comments History and Comments 1 In the Samples Plot window right click the label for the edited allele and select History to view changes 2 Click OK to close the history 3 View the row for the locus D16S539 for Sample2 COfiler v1 panel in the Genotypes table and observe that The PQVs are displayed as gray triangles indicating that there is an ov
73. than 1 Dye Sample Pe Sample File Na Marker Allele Size Area Data Point 434 Height 127 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 2 23 Chapter 2 Casework Analysis To examine data continued 8 With the peaks still selected click sd Genotypes Table and observe that the spectral pull up SPU PQV is a green square Pass os BIN PHR LPH sPU aN BD cc Jovi o Raa nM A Bo SPU PQV is a green square Note The SPU PQV denotes no peak above the analysis threshold and no peak below the 0 05 pull up ratio set on page 1 11 within 1 data point of allele 9 9 Observe the other PQVs and note that PHR peak height ratio and the AN allele number are flagged yellow e PHR Indicates that the peak height ratio between the 9 11 12 peaks are not as expected In the Analysis Method Peak quality tab we set a 70 ratio Any ratio less than 70 flags the PQV yellow In this case the peak height of the 9 peak is 127 and the peak height fo the 11 peak is 2265 This is an unacceptable ratio of 5 696 AN Indicates that there are more than 2 alleles In theAnalysis Method Peak Quality tab we set the maxium expected alleles at 2 A marker with more than 2 alleles flags the PQV yellow When these two components PHR and AN are both flagged yellow the overall genotype quality is flagged red 2 24 GeneMapper ID Software Ver
74. to 1 0 the override is indicated by a check mark in the SQO column To examine the size standard l Examine the flags in the SQ column to assess sizing quality 2 Observe that all flags in the SQ column are green squares indicating that all samples passed the sizing criteria To examine the allelic ladder calls 1 Select the Genotypes tab 2 Find plots for all allelic ladders a Select Edit gt Find b In the Find what field type ladder c From the In column drop down list select Sample Name d Click Find All e Close the dialog box 3 Display the HID Genotyping plot a Click Display Plots to display the Genotypes Plot window b Select the HID Genotyping plot from the drop down list below the menu bar GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial 3 9 Chapter 3 Database Analysis To examine the allelic ladder calls continued 4 Verify that the allelic ladder is called correctly for each marker Note Deselecting Controls to Top will display all panes chosen from Genotypes plots 5 Close the Genotypes Plot window Examining Data To examine data and edit labels and Editing Labels l Click Low Quality to Top Note This option can be set as a default in Analysis options see page 1 29 2 Select Sample5 Marker CSF1PO which displays yellow triangles Check in the Pe
75. to close the Plot Settings Editor Note Do not click OK until after you select settings on all tabs 5 Click Done to close the GeneMapper Manager if you have finished creating all plot settings Rox Dye Plot Settings Tab Settings General Name Overlay GS500 ROX Dye Sample Show 2 3 4 and 6 Header Hide 1 and 5 Genotype Show 2 5 10 15 18 19 and 20 Header Hide 1 6 9 16 and 17 Sizing Show 1 8 Table Font Arial size 11 Labels Label 1 Allele call Label 2 Label 3 and Label 4 None Show data type prefixes deselected Show type of edit deselected Invert mutant labels deselected Label Color Dye Color Border Label Font Arial size 11 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Plots Table 1 6 Overlay GS500 ROX Dye plot settings continued Tab Settings Sein Settings General Sample Header Genotype Header Sizing Table Labels Display Settings When Opening The Plot Window C Use the display settings last used for this plot c Use these display settings For both Sample and Genotype plots Panes 1 he E zr a Mi Fc de ue d X Axis Basepairs Y Axis Scale individually V Toolbar MV Show Off scale For Sample plot only ele m sla eed d u For Genotype plot only Marker Margin b bp Creating Last To create th
76. to the right to create a box 3 Release when the box includes the three peaks R LI s b Select 1 from the Panes drop down list in the toolbar Note Panes for the selected peaks are presented in the Project window c Click Aj Don t Bring Controls to Top 6 Examine the peak for allele 9 Click lili Combine Dyes and click 4 Show All 2 20 GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Examining and Editing Results To examine data continued 7 Observe that the allele 9 peak is not caused by spectral pull up a Select the 250 bp size standard peak and the allele 9 peak by clicking within the plot and dragging to create a box that includes these peaks 2m 20 R b Click Sizing Table and select View gt Table Filter gt Show Selected Rows c View the peak location in the graph and note that the blue peak for allele 9 is shifted to the left of the red peak for the 250 bp size standard 241 242 248 244 245 246 24 248 249 250 251 252 253 254 255 256 257 258 co 4 3 2400 2200 2000 1800 1600 d View the data point values for the selected peaks and note that the data point for allele 9 4898 differs from the data point for the 250 bp size standard 4906 by more
77. utorial 1 29 Chapter 1 Software Setup 1 30 To view and set options continued 5 IMPORTANT We do not recommend creating new users since the software license is limited to 5 users Select the Users tab to view the Users options Startup Add Samples Analysis Users GeneMapper Users User Name Created On Show New User GHRHHUEPASSYVBIO Column Contents User Name The user name that Pis used to log into GeneMapper JD software is shown amid in the example above Created On The date a particular user either _ registered or chose a name on this tab Show indicates whether the user name is resented at GeneMapper JD software ogin Deselect the box in the Show column to hide the name at GeneMapper JD software login GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial HID Analysis Options To view and set options continued 6 To add a user name click New User to open the New User dialog box and then a Type a user name of your choice into the New User Name text box b Type a password and confirm the password in the corresponding text boxes c Click OK to add the user name and close the dialog box 7 Click OK to exit Options and implement the changes you made on all Options tabs IMPORTANT If you click Cancel to exit you discard any changes made on the Options tabs
78. ws of electropherogram plots HID Genotyping HID Sizing Overlay GS500 LIZ Dye Overlay GS500 ROX Dye Last Used To create these custom views follow the table steps and the software settings for each view To create HID Genotyping plot settings 1 From the GeneMapper Manager select the Plot Settings tab 2 Click New to open the Plot Settings Editor with the General tab selected 3 Select the settings shown in Table 1 3 HID Genotyping plot settings 4 Click OK to save the plot settings and to close the Plot Settings Editor Note Do not click OK until after you select settings on all tabs 5 Click Done to close the GeneMapper Manager if you have finished creating all plot settings HID Genotyping Table 1 3 HID Genotyping plot settings Plot Settings GeneMapper ID Software Versions 3 1 and 3 2 Human Identification Analysis Tutorial Tab Settings General Name HID Genotyping Sample Hide 1 and 5 Header Show 2 3 4 and 6 1 19 Chapter 1 Software Setup Table 1 8 HID Genotyping plot settings continued Tab Settings Genotype Show 2 5 10 15 18 19 and 20 Header Hide 1 6 9 16 and 17 Sizing Show 1 8 Table Labels Label 1 Allele call Label 2 Label 3 and Label 4 None Show data type prefixes deselected Show type of edit selected Invert mutant labels deselected Label Color Dye Color Border

GeneMapper® ID Software Version 3.2: Human Identification Analysis

Contents

Download Pdf Manuals

Related Search

Related Contents

GeneMapper&reg; ID Software Version 3.2: Human Identification Analysis

Contents

Download Pdf Manuals

Related Search

Related Contents

GeneMapper® ID Software Version 3.2: Human Identification Analysis