GeneMapper™ ID Software Version 3.1 Human Identification Analysis User Guide © Copyright 2003, Applied Biosystems. All rights reserved. For Research, Forensic or Paternity Use Only. Not for use in diagnostic procedures. Notice to Purchaser: License Disclaimer. Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly, or by estoppel. GeneMapper ID Software version 3.1 has undergone a verification process defined by Applied Biosystems. However, human identification laboratories analyzing forensic, paternity, databasing, and single-source samples that choose to use GeneMapper ID Software for data analysis should perform their own appropriate validation studies. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document. Purchase or receipt of this software does not include or guarantee any training by persons belonging to Applied Biosystems or Applera Corporation. ABI PRISM, AmpFlSTR, AmpFlSTR COfiler, Applied Biosystems, Genotyper, Identifiler, LIZ, Profiler, Profiler Plus, SEfiler, SGM Plus, and SNaPshot are registered trademarks, and AB (Design), AmpFlSTR Blue, AmpFlSTR Green, Applera, GeneMapper, GeneScan, POP-6, Primer Focus, ROX, and TAMRA 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. This product includes software developed by the Apache Software Foundation (http://www.apache.org/). Copyright © 1999-2000 The Apache Software Foundation. All rights reserved. This product includes software developed by the ExoLab Project (http://www. exolab.org/). Copyright © 2000 Intalio Inc. All rights reserved. JNI Registry is Copyright © 1997 Timothy Gerard Endres, ICE Engineering, Inc., http://www.trustice.com. Microsoft Windows NT and Microsoft Excel are registered trademarks of Microsoft Corporation. Oracle is a registered trademark of Oracle Corporation. All other trademarks are the sole property of their respective owners. Applera Corporation is committed to providing the world’s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. Printed in the USA, 12/2003 4338775 Rev. C DRAFT December 17, 2003 12:31 am, RevisedGeneMapperTitle.fm Contents Preface How to Use This Guide . ix How to Obtain More Information . x How to Obtain Support . xi Chapter 1 About GeneMapper™ ID Software Overview of GeneMapper ID Software . 1-2 Steps Required to Use GeneMapper ID Software . 1-5 Organization of the User Guide . 1-6 Chapter 2 Getting Started with GeneMapper ID Software Hardware Requirements . 2-2 Installing the GeneMapper ID Software . 2-3 Registering GeneMapper ID Software . 2-6 Logging Onto and Logging Out of the GeneMapper ID Software . 2-7 Chapter 3 Using the Project Window Main GeneMapper ID Project Window . 3-2 Overview of the Project Window . 3-3 Navigating in the Project Window . 3-12 Chapter 4 Using Panel Manager Panel Manager Overview . 4-2 Panel Manager Window Commands . 4-7 Formats of Panel and Bin Text Files . 4-22 ™ GeneMapper ID Software v3.1 User GuideDRAFT iii December 17, 2003 2:21 am, GeneMapper3.0TOC.fm Panel Table View . 4-34 Marker Table View . 4-36 Bins View - Microsatellites Only . 4-39 Chapter 5 Using GeneMapper Manager Introduction . 5-2 Section 5.1 Projects Tab . 5-3 Section 5.2 Analysis Methods Tab . 5-9 Section 5.3 Table Settings Tab . 5-27 Section 5.4 Plot Settings Tab . 5-41 Section 5.5 Creating and Evaluating a Matrix . 5-53 Section 5.6 Size Standards Tab . 5-65 Chapter 6 Options Dialog Box Introduction . 6-2 HID Analysis Options . 6-3 Startup Tab . 6-4 Add Samples Tab . 6-5 Analysis Tab . 6-7 Users Tab . 6-9 Chapter 7 Analyzing and Interpreting Data Introduction . 7-2 Considerations for HID Analysis . 7-2 Analyzing Samples Files . 7-3 Interpreting Sample PQVs, Sizing Quality, and Precision . 7-11 Size Match Editor . 7-14 Size Calling Curve . 7-19 Viewing Sample Data . 7-23 ™ ivDRAFT GeneMapper ID Software v3.1 User Guide December 17, 2003 2:21 am, GeneMapper3.0TOC.fm Genotypes Table . 7-27 Interpreting Genotype PQVs and Genotype Quality . 7-30 Concordance Checks . 7-32 Chapter 8 Using Plot Windows - Samples and Genotypes About the Plot Window . 8-2 Plot Window Toolbars . 8-4 Plot Window Menus . 8-5 Chapter 9 Exporting Table Data Introduction . 9-2 Exporting Samples and Genotypes Table . 9-2 About CODIS . 9-5 CODIS Export Manager . 9-6 CODIS Table Export . 9-8 Chapter 10 Printing Data Printing Data . 10-2 Page Set Up Options . 10-4 Printing Sizing Plots Similar to Genescan Using the Predefined AmpFlSTR Sizing Plot Setting . 10-7 Printing Genotype Plots Similar to Genotyper Using the Predefined AmpFlSTR Genotyping Setting . 10-8 Appendix A Process Quality Values Overview of Process (Component-Based) Quality Values (PQV) . A-2 Using Process (Component-Based) Quality Values . A-3 ™ GeneMapper ID Software v3.1 User GuideDRAFT v December 17, 2003 2:21 am, GeneMapper3.0TOC.fm Appendix B Software Genotyping Algorithms GeneMapper ID Software Genotyping Algorithms . B-2 Basic Mode - Peak Detection Algorithm Settings . B-6 Classic Mode - Peak Detection Algorithm Settings . B-7 Advanced Mode - Peak Detection Algorithm Settings . B-12 Peak Detection: Polynomial Degree and Peak Window Size Parameters . B-17 Optimizing Peak Detection Sensitivity: Example 1 . B-20 Optimizing Peak Detection Sensitivity: Example 2 . B-22 Optimizing Peak Detection Sensitivity: Example 3 . B-24 Peak Detection: Slope Threshold for Peak Start and Slope Threshold for Peak End Parameters . B-25 Slope Threshold Examples . B-27 Size Calling Methods for Classic and Advanced Modes . B-29 Appendix C Project Window Software Interface Overview of the Project Window . C-2 Project Window Menus . C-10 Project Window File Menu Dialog Boxes . C-27 Printing Tables and Electropherograms . C-34 Add Samples to Project Dialog . C-37 Project Window Edit Menu Dialog Boxes . C-45 Appendix D GeneScan Size Standards Introduction . D-2 GeneScan 120 Size Standard . D-3 GeneScan 350 Size Standard . D-4 GeneScan 400HD Size Standard . D-5 GeneScan 500 and GeneScan 500(-250) Size Standards . D-7 Appendix E Converting Macintosh Sample Files Converting Macintosh Sample Files . E-2 ™ viDRAFT GeneMapper ID Software v3.1 User Guide December 17, 2003 2:21 am, GeneMapper3.0TOC.fm Appendix F Transferring Data and Backing Up Data Transferring Data . F-2 Backing Up Data and Cleaning the Database . F-7 Appendix G Sample Sheets and Plate Records Information from the Data Collection Sample Sheet or Plate Record . G-2 Appendix H Troubleshooting Sheet Troubleshooting Sheets . H-2 Appendix I GeneMapper ID Software Verification Summary of GeneMapper ID Software Verification . I-2 AmpFlSTR Kits, Samples, Instrumentation, Hardware, and Software Used for Verification Testing . I-4 Results of Verification Testing . I-7 Conclusion . ..