Home

GeneMapper® ID-X Software Version 1.1 (Mixture Analysis Tool

1. 57 Step 2 Review the Results ofthe Extraction 58 Step 3 Determine Genotype Combinations to Include in Statistical Calculations 0 0 0 cee eens 63 Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion 05 71 Step 5 Review the Results of Random Match Probability and Combined Probability of Inclusion Exclusion Calculations 72 Step 6 Calculate and Review Likelihood Ratio Results 74 GeneMapper D X Software Version 1 1 Getting Started Guide 55 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns E Overview Overview About Analysis of 2 Contributor Samples Where Both Contributors 56 are Unknown In This Chapter When analyzing 2 contributor mixtures where both contributors are unknown the software extracts the possible genotype combinations for each contributor and assesses each combination according to the peak height ratio thresholds set in the Mixture Analysis Method and the residual threshold specified by the software The software Generates all possible genotype combinations at each marker Calculates the residual values and peak height ratios for all combinations Computes an average minor contributor mixture proportion Mx from 3 peak and 4 peak data across a profile which serves as the basis for comparison of all genotype combinations generated Automatically selects com
2. Likelihood Ratio LR Calculation LR Statistics Summary LR Pr E Hp Pr E Hd where Pr probability E evidence pipebar given Hp prosecution hypothesis Hd defense hypothesis LR Analysis Summary sample H4 H28 1 5 analyst gmidx Reference Sample s seleetoneor more Ret 1 H4 H28 0 1 eference use C1 Major Only Reference 1 H4 H28 0 1 Reference 2 None Hypothesis 1 _ Hp Mixture of Ci H4 H28 O0 1 and one unknown unrelated person Ha Mixture of two unknown unrelated people Reference 2 None Reference 2 not selected only relevant hypotheses are displayed Hypotheses select one or more Database B Identifiler UM Population African American Theta 0 01 LR 5 4484E 5 5 9836E 19 9 1056E13 Notes e Calculate Statistics WE Mixture Analysis Parameters Samples Plot Cancel Back Next Finish The software calculates the Likelihood Ratio based on the following alternate hypotheses H H4 H28 1 5 originates from a mixture of H28 and one unknown unrelated person e H H4 H28 1 5 originates from a mixture of two unknown unrelated people The observed profile is 9 1056E13 or 91 trillion times more likely to occur if it originated from reference H28 and one unknown unrelated person than from a mixture of two unknown unrelated people You can also calculate a Likelihood Ratio based on the hypothesis that both c
3. I Select reference s and hypotheses 1 and 2 contributors 2 and 2 3 contributors 1 and 2 contributors Review RMP statistics Review CPI CPE statistics Review LR statistics Optional Export results then print GeneMapper ID X Software Version 1 1 Getting Started Guide 5 Chapter 1 Getting Started Using this Guide for Mixture Analysis Using this Guide for Mixture Analysis Overview This guide is designed to familiarize you with the key features and functions of the GeneMapper ID X Mixture Analysis Tool and to take you through an example mixture analysis workflow The workflow is presented in a tutorial format starting in Chapter 3 Prepare for Mixture Analysis The tutorial uses the example data provided with the Mixture Analysis Tool Refer to Chapter 2 Understanding the Software for information on how to access the example data Once you complete the tutorial you will understand how the Mixture Analysis Tool works and you will be able to create your own settings and evaluate your own mixture and single source data IMPORTANT How you use the Mixture Analysis Tool in your laboratory and the settings you create depend on the mixture analysis and interpretation guidelines established by your internal validation process Chapter Description Software Chapter 2 Understanding the Mixture analysis methods e
4. 0000 EE COCO EE OOO EE Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next gt Finish 2 Inthe previous example review sample H4_H28_1_1 and select Filter by Marker D3S1358 GeneMapper ID X Software Version 1 1 Getting Started Guide 89 waa Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Step 1 Assign Known Genotypes Selected Genotype Combinations The C1 Major contributor in the Selected Genotype Combinations table is a 16 17 as noted below and matches the known whereas the C2 Minor contributor is a 15 16 Marker c1 Major Inconclusiw C2 Minor Inconclusi Known Genotype ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 D351358 1617 n 1616 r Eas 0 534 0 003 0 979 0 979 I B di Unselected Genotype Combinations Note In the Unselected Genotype Combinations table there are three genotype pairs that pass all PQV metrics Residual Status PHR Status and IQ and yet are not included in the Selected Genotype Combinations table shown below Patterns 2 and 3 do not contain a genotype that matches the known contributor and therefore do not meet the criteria for known filtering Pattern 1 is the inverse Major 15 16 and Minor 16 17 ofthe selected pattern Major 16 17 and Minor 15 16 In approximate 1 1 mixtures where both patterns have high Inclusion Quali
5. Marker C1 Major Inconclusis C2 Minor Inconclusis Known Genotype ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 D351358 15 16 n 17 F1 v B os 0 001 0 994 0 542 2 0351358 15 17 r 16 16 v B W 0202 0 229 N A e e 3 p3si3s8 16 17 ri 15 15 v B ima 0 203 o231 NA amp e cm 4 pas1358 15 17 n 16 F1 Vv 0 476 0 236 0 229 0 125 s p351358 16 17 n 15 F1 F Bp 0 479 0 238 0 231 01249 e Select 6 D351358 15 17 r 15 16 v r 0 813 0 252 0 817 0 817 B 7 0351358 16 17 r 15 16 v n 0 813 0 254 0 809 0 809 mH Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel Back Next gt Finish Note When you assign one possible genotype combination as inconclusive for any marker the software automatically checks the Inconclusive box for all other possible genotype combinations at that marker in both the Unselected and Selected Genotype Combinations tables 68 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 3 Determine Genotype Combinations to Include in Statistical Calculations 2 In the Mixture Analysis Results Viewer click the Notes button The Sample Notes dialog box is displayed Sample Notes H4 H28 1 5 X Date Time User Action P008 08 21 10 29 59 omid Pattern 17 F1 15_16
6. Select All Select All Analyzed Samples Select All Unanalyzed Samples Clear All 10 out of 10 samples analyzed in Genemapper ID X loaded successfull Sample Details Cancel Back Next gt Finish Note Note that all 10 samples loaded successfully GeneMapper ID X Software Version 1 1 Getting Started Guide 49 LA Chapter 4 Segregate Samples r Step 3 Create a New Mixture Analysis Method 2 Click Select All to select all of the samples check marks appear in each checkbox 3 In the Mixture Analysis Method column click the first sample click New then select MA Test Method from the drop down menu 4 Click on the Mixture Analysis Method column header and press Ctrl D to apply the MA Test Method mixture analysis method to all samples Create an MA You can also create new mixture analysis methods by selecting New Method using the from the Mixture Analysis Method column drop down menu then Column Drop following the directions in Create a Mixture Analysis Method using Down Method the Mixture Analysis Manager on page 45 Alternate Method 50 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples wu Step 4 Segregate the Samples Step 4 Segregate the Samples After you ve applied the MA Test Method mixture analysis method to all samples the Mixture Analysis Sample Selection dialog box should appear as shown below Mixture Analysis Sa
7. F monu naa e Table Setting 310 Data Analysis Jaana Samples filtered Analysis Summary Genotypes Status Sample Name Sample Type Analysis Method Panel Size Standard Custom Control ARNM SOS SG SSPK Mx OMR h Tas Sample HD Fut Range 75 SGM Plus v1X CE F HID GS500 75 450 None m m m mm 2 AAIS Sample HD FulRange 75 SGM_Plus_v1X CE_F_HID_GS500 75 450 None B m mm 3 Sample ia x Fy 50 fw E E 3 is 4 H4_H28_1_0 Sample HID FulRange 75 SGM Plus v1X CE F HD GS500 75 450 None B 5 H4 H28 1 1 Sample HD FulRange 75 SGM Plus vIX CE F HID GS500 75 450 None B 6 H4 H28 12 Sample HID Ful Range 75 SGM Plus v1X CE F HID GS500 75 450 None E m m 7 H4 H28 1 3 Sample HD_Ful Range 75 SGM Plus vIX CE_F_HID_GS500 75 450 None m ma A B 8 H4 H28 1 5 Sample HID FulRange 75 SGM Plus v1X CE F HD GS500 75 450 None T m B 9 H4 H28 1 9 Sample HD FulRange 75 SGM Plus viX CE F HID GS500 75 450 None B 10 H4_H28_AA18_1 Sample HD FulRange 75 SGM Plus vIX CE F HID GS500 75 450 None m B li I 32 Note The MIX PQV flag is yellow for many of the samples indicating that GeneMapper D X Software has identified the samples as potential mixtures In the Samples filtered tab select sample H4 H28 0 1 as shown previously and click the display plots icon in the tool bar GeneMapper D X Software Version 1 1 Getting Sta
8. Selected Mixture Analysis Status Run Folder Sample File Sample Name Mixture Analysis Method 1 I amp MA_PP H4 H28 0 1 001 AO3 fs H4 H28 0 1 MA Test Method 2 v MA CO H4 H28 0 1 001 AOS fs H4 H28 0 1 MA Test Method 3 Iv amp MA PP H4 He8 1 0 013 GO3 fs H4 H28 1 0 MA Test Method 4 Iv amp MA CO H4 H28 1 0 013 GOS fs H4 H28 1 0 MA Test Method 5 Iv amp MA PP H4 H28 1 3 D07 DO3 fs H4 H28 1 3 MA Test Method 6 Vv amp MA CO H4 H28 1 3 007 DOS fs H4 H28 1 3 MA Test Method Select All Select All Analyzed Samples Select All Unanalyzed Samples Clear All 6 out of 6 samples analyzed in Genemapper ID X loaded successfully sample Details Cancel Back Next gt Finish 3 Click Next gt to proceed with sample segregation as shown in the following section GeneMapper ID X Software Version 1 1 Getting Started Guide 103 m n Chapter 7 Analyze Merged Results Step 5 Segregate Samples and Review Profiles Step 5 Segregate Samples and Review Profiles The two samples segregate as minimum 2 Contributor mixtures s Mixture Analysis Sample Segregation by Minimum Number of Contributors loj x GeneMapper ID X Project Mame pro co Test 2 Contributors 1 Contributor 3 or More Contributors Extraction Status Review Status Run Folder Sample File Sample Name Mixture Analysis Methog Known 1 MA PP H4 H28 1 3 007 DO3 fsa H4 H28 1 3 MA Test Method None L L L 2 amp
9. Cannot be used for samples containing alleles with off ladder OL only labels 4 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started Fn GeneMapper ID X Software Mixture Analysis Workflows GeneMapper ID X Mixture Analysis Workflow Prepare for mixture analysis 1 Optional Open the GeneMapper ID X project containing samples for mixture analysis 2 Select Mixture Analysis from the Tools menu 3 Optional Create mixture analysis methods 4 Optional Import population databases to use for statistical calculations 5 Select samples and mixture analysis methods 1 contributor 2 contributors gt 3 contributors i umm n Select analysis View previously Begin new analysis options for saved mixture 1 Optional Import known genotypes statistical analysis results 2 Extract contributors calculations per marker Sc ifie t lik Review analysis results per sample 1 Review genotype combinations and optional known matches 2 Display plots and view peak data 3 Select genotype combinations for statistical calculations 4 Select Sample Review Complete Optional Merge sample analysis results 21 panel 1 Select one panel per marker 2 Review merged marker data for statistical calculations Calculate statistics Select population database s
10. Applied Getting Started Guide KS Biosystems GeneMapper D X Software Version 1 1 Mixture Analysis Tool Note To improve the clarity of graphics in this PDF file use the zoom tool to increase magnification to 15096 or greater GeneMapper ID X Getting Started Guide gt Applied A Biosystems GeneMapper D X Software Version 1 1 Mixture Analysis Tool Getting Started Understanding the Software Prepare for Mixture Analysis Segregate Samples Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Contributor Mixtures with One Known Contributor Analyze Merged Results EA O Copyright 2008 Applied Biosystems Inc All rights reserved For Research Forensic or Paternity Use Only Not for use in diagnostic procedures Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in this document GeneMapper D X Software has undergone a verification process defined by Applied Biosystems However human identification laboratories analyzing forensic casework paternity and databasing samples that choose to use GeneMapper D X Software for data analysis should perform their own appropriate validation studies APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR
11. 0 00 0c cece eee 115 Bibliography a3 sac56 eet sec tetas Rx NR 119 Index casto DO RI OPEP IC EHE E tees 121 GeneMapper D X Software Version 1 1 Getting Started Guide Preface How to Use This Guide Purpose of This Guide Audience Assumptions The GeneMapper ID X Sofiware Version 1 1 Getting Started Guide explains how to perform mixture analysis using the GeneMapper ID X Software Version 1 1 This guide functions as An introduction to the mixture analysis features of GeneMapper ID X Software Version 1 1 A tutorial using example experimental data provided with the GeneMapper D X Software Version 1 1 A guide for your own experiments This guide is written for forensic analysts who perform AmpF STR kit data analysis using the GeneMapper ID X Software and who routinely perform analysis of mixture data This guide assumes that you have Installed GeneMapper ID X Software Version 1 1 as described in the GeneMapper ID X Software Version 1 0 1 1 Installation Guide Used AmpF STR amplification kit data for human identification HID applications Developed a working knowledge of the Microsoft Windows XP operating system Text Conventions This guide uses the following conventions Bold text indicates user action For example Type 0 then press Enter for each of the remaining fields e talic text indicates new or important words and is also used for emphasis For example Before analy
12. 7 VWA 18 18 o 15 15 n im 0 524 0 009 nja N A B 8 D165539 9 10 r 12 12 O p 0 441 0 000 0 994 N A T 9 D165539 10 12 mi 9 12 LI WW lo 5o2 0 006 10 789 0 789 EN Ir 1 a rUnselected Genotype Combinations Fiter on 1Q WAE Fiter on Known Match 3 Marker C1 Major Inconclusiy C2 Minor Inconclusiy Known Genotype ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 prs quie r 17 F1 m Bp 02720072 0 545 0 213 2 D351358 16 17 r 15 F1 r B 0 304 0 075 0 476 0 186 e 3 D351358 16 17 r 15 15 r Bp wa oos 0 476 Na O Em 4 D351358 16 F1 O 15 17 r 0 481 0 091 0 101 0 874 5 D351358 15 17 r 16 F1 Fr B 0 519 0 094 0 874 0 101 e 9 select 6 D351358 15 16 r 17 17 r Bp w 0 098 josewa O e 6 7 D351358 15 16 O 15 17 r B va 0 103 0 369 0 369 e D Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next gt Finish Selected Genotype Combinations Table The Selected Genotype Combinations table shows the list of possible genotype combinations deducible from the mixture that passed the criteria for selection IQ status and were therefore automatically assigned to this table for inclusion in the statistical calculations To exclude geno
13. M major contributor definition 12 major contributor Likelihood Ratio 74 81 markers inclusion frequency definition 12 inconclusive 11 missing 12 menu commands conventions for describing viii merged results analyzing 106 calculating 106 mixture analysis 105 sample analysis 101 viewing 105 minimum allele frequency definition 12 minor contributor definition 12 minor contributor Likelihood Ratio 74 MIT definition 12 Index mixture analysis analyzing merged results 106 calculating statistics 106 launching Mixture Analysis Tool 43 merged results definition 13 method definition 13 parameters definition 13 preparing for 26 103 project definition 13 quality value system 58 selecting Mixture Analysis Tool 43 viewing merged results 105 Mixture Analysis Results Viewer 105 understanding table data 58 working with 58 Mixture Analysis Tool definition 13 launching 43 selecting 43 mixture analysis definition 13 Mixture Interpretation Threshold definition 12 MSDSs obtaining xi N new mixture analysis method using the column drop down method 45 new project adding samples 27 99 creating 27 99 opening 27 O online Help See Help system opening a new project 27 P peak height ratio status definition 14 PHR status definition 14 GeneMapper ID X Software Version 1 0 Getting Started Guide 123 Index population databases calculating statistics 71 106 definition 14 importing 43 Profiler P
14. Residual PHRI PHRZ Residual Status PHR Status IQ Filter by Marker 0351358 1 D351358 15 16 r 16 17 r B 2 0 003 0 920 0 920 j B 2 D351358 15 16 r 17 17 r Bp 0130019 jozos wa gg L B Unselect 6 Review the selected genotype combinations for the D3S1358 marker to assess whether the software successfully evaluated the 2 contributor mixture Use the marker filter or marker header bar selection to review the data for other markers 7 Select the icon indicated below to display the Mixture Analysis Unselected Genotype Combinations table and view the combinations that the software did not automatically select 64 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns a Step 3 Determine Genotype Combinations to Include in Statistical Calculations UER o Mixture Analysis Unselected Genotype Combinations Table For each marker verify whether you agree with the combinations that were NOT selected Use the Select button to manually add genotype combinations to the Selected Genotype Combinations table 8 Click the X icon in the upper right hand corner to exit the Samples Plot and return to the Mixture Analysis Results Viewer 9 Check the Sample Review Complete box to indicate that this sample is ready for statistical analysis The Sample Workflow Completion dialog box is displayed Sample Workflow Completion x The statistical results fo
15. Analysis Summary Genotypes Sample File Sample Name AA18 010 EDO8 f 4418 AA18 D04 BO8 f AA19 H4 H28 0 1 001 H4 H28 D 1 H4 H28 1 0 D1z H4 H28 1 0 H4 H28 1 1 DOz H4 H28 1 1 H4 H28 1 2 DOt H4 H28 1 2 H4 H28 1 3 007 H4 H28 1 3 H4 H28 1 5 DDt H4 H28 1 5 ol Ol 4 of om ef ofn gt H4 H28 1 8 O11 H4 H28 1 8 1 H4_H28_AA18_1 GeneMapper ID X Software Version 1 1 Getting Started Guide 35 Fu Chapter 3 Prepare for Mixture Analysis Step 5 Export and View a Known Genotype Profile 2 Select the Genotypes tab which should now display only the 36 Samples filtered Analysis Summary Genotypes Sample File Sample Name Marker Allele 1 and Allele 2 columns as shown Sample File Sample Name Marker Allele 1 Allele 2 1 4A18_010_E08 fsa AA18 D381358 11 15 2 AA18 D10 E08 fsa AA18 ANA 15 18 3 AA18 D10 E08 fsa AA18 ipiess39 9 11 4 AA18 D10 E08 fsa AA18 D251338 18 23 5 AA18 D10 E08 fsa AA18 AMEL x Y 6 AA18 D10 E08 fsa AA18 D8s1179 14 15 7 AA18_010_E08 fsa AA18 D231811 28 312 8 AA18 D10 E08 fsa AA18 D18551 17 20 9 4418_010_E08 fsa AA18 DISS433 11 122 10 AA18_010_E08 fsa AA18 THO1 7 8 11 AA18 D10 E08 fsa AA18 FGA 21 22 12 AA19 D04 BO8 fsa AA18 D381358 14 15 13 AA18 D04 B08 fsa AA19 vwa 15 16 144 AA19_004_B08 fsa A819 DT6S538 12 15 AA19_004_B08 fsa AA19 251338 19 16 AA19 D04 BO8 fsa
16. H H4 H28 1 5 originates from a mixture of H4 and one unknown unrelated person H H4 H28 1 5 originates from a mixture of two unknown unrelated people The observed profile is 4 7134E4 or 47000 times more likely to occur if it originated from reference H4 and one unknown unrelated person than from a mixture of two unknown unrelated people Hypothesis 5 H H4 H28 1 5 originates from a mixture of H28 and one unknown unrelated person H H4 H28 1 5 originates from a mixture of two unknown unrelated people The observed profile is 9 1056E13 or 91 trillion times times more likely to occur if it originated from reference H28 and one unknown unrelated person than from a mixture of two unknown unrelated people For all hypotheses the software validates the inclusion of the reference profile in the mixture profile If you select a reference that cannot be included in the mixture based on comparison of the contributor genotypes the software displays a message that the validation of inclusion ofthe reference profile in the mixture failed as shown next GeneMapper ID X Software Version 1 1 Getting Started Guide 79 E Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns 80 Step 6 Calculate and Review Likelihood Ratio Results LR Statistics Summary LR Analysis Summary sample H4 H26 1 5 analyst gmidx Reference 1 A19 Reference 2 None Reference 2 not se Ses are displayed
17. Min Peak Height RFU 48 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples VA Step 3 Create a New Mixture Analysis Method Apply a Mixture 1 Select Tools Mixture Analysis from the toolbar or press Analysis Method Ctrl U to Samples Tools Admin Help GeneMapper ID X Manager Ctrl M Panel Manager Ctri J E Report Manager ctrl Q Bl Table Setting Editor Ctri T CODIS Export Manager Im Mixture Analysis Mixture Analysis Manager Add Profile t Profile Manager Profile Comparison VietiTod Editor tandard Editor Ll Size Match Editor s Mixture Analysis Sample Selection r Select Samples and Mixture Analysis Methods Selected Mixture Analysis Status Run Folder Sample File Sample Name Mixture Analysis Method 1 Fi MA SGM AA18 010 EO08 fsa AA18 None 2 r 1 MA SGM AA19 004 BO8 fsa AA19 None 3 r amp MA SGM H4 H28 0 1 001 A07 fs H4 H28 0 1 None 4 r MA SGM H4 H28 1 0 013 GO7 fs H4 H28 1 0 None Lo 5 O amp MA SGM H4 H28 1 1 003 B07 fs H4 H28 1 1 None xl 6 ri amp MA SGM H4 H28 1 2 005 CO7 fs H4 H28 1 2 None s 7 T amp MA SGM H4 H28 1 3 007 D07 fs H4 H28 1 3 None s 8 O amp MA SGM H4 H28 1 5 009 E07 fs H4 H28 1 5 None 3 La 9 ri amp MA_SGM H4 H28 1 9 O11 F07 fs H4 H28 1 9 None L 5 R L Ls i 10 ri t MA SGM H4 H28 AA18 1 1 2 OD H4 H28 AA18 1 1 2 None
18. Known None Selected Genotype Combinations Merged includes markers automatically added from one or more panels Run Folder Sample File Marker ci Major Inconclusiys C2 Minor Inconclusiv y mre io dale heel i ON Y 7 MA CO H4 H28 1 3 007 COfiler v1x D165539 10 12 m 9 10 n 8 MA CO H4 H28 1 3 007 COfiller vix D165539 10 12 ri 9 12 ri 9 MA PP H4 H28 1 3 007 Profller Plus vIX D18551 13 15 rH 12 12 rH 10 MA PP H4 H28 1 3 007 Profiler Plus vIX D18551 13 15 n 1215 ri e Remove Marker 11 MA PP H4 H28 1 3 00 Profile Plus v1X D21511 30 30 rH 33 2 33 2 7 12 MA PP H4 H28 1 3007 Profiler Plus viX D21511 30 30 nr 30 33 2 nr filer_Plus_v1X 8 I I Filer_Plus E Selected Genotype Combinations Unmerged select one panel to add per marker Filter by Marker All Sd Run Folder Sample File Panel Marker ci Major Inconclusiys C2 Minor Inconclusiv f Notes Calculate Statistics Export Mixture Analysi Samples Plot Cancel lt Back Next gt Finish 11 Calculate Statistics or click Finish to return to the GeneMapper ID X Project window Refer to the GeneMapper ID X Software Help for additional information on analyzing merged results GeneMapper ID X Software Version 1 1 Getting Started Guide 109 E Chapter 7 Analyze Merged Results Step 7 Calculate and Analyze the Results 110 GeneMapper D X Software Versio
19. in Marker D351358 removed 2008 08 21 10 30 01 gmdx Minor of Marker D351358 marked Inconclusive The dialog box shows that the software recorded the removal of 5 pattern 17 F1 15 16 from the Selected Genotype Combinations table for marker D3S1358 and that D3S1358 is marked inconclusive for the minor contributor 3 Click Done to exit the dialog box GeneMapper D X Software Version 1 1 Getting Started Guide 69 wu Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 3 Determine Genotype Combinations to Include in Statistical Calculations 4 Check the Sample Review Complete checkbox to signify that Sample Workflow Completion review of the sample and selection of genotypes are finished and the sample is ready for statistical analysis The Sample Workflow Completion dialog box is displayed x The statistical results for the selected sample are calculated based on the current genotype combination and population database selections and are not saved once you exit the Mixture Analysis Results Viewer Do you want to export the statistical results for the selected sample now we Review Remaining Samples 70 1 Click No Note You will calculate statistics in Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion Click the Next Sample gt gt button to move to the next sample in the list Review the data contained in both tables using the
20. ma_co H4_H28_1_3_007_D05 fsa H4 H28 1 3 MA Test Method None 0 Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish 1 Inthe 2 Contributors tab click Next gt to proceed with extraction of contributors 2 Review the results for sample H4 H28 1 3 analyzed with AmpF STR Profiler Plus and COfiler kits then check Sample Review Complete Note You will NOT be able to access merged results for samples where the Sample Review Complete box is unchecked The Sample Workflow Completion dialog box is displayed 104 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results E Step 6 View Merged Results Sample Workflow Completion i x The statistical results for the selected sample are calculated based on the current genotype combination and population database selections and are not saved once you exit the Mixture Analysis Results Viewer Do you want to export the statistical results for the selected sample now 3 Click No Note You will calculate statistics later 4 Select Next Sample gt gt to review the next sample repeat procedure steps 3 and 4 above then proceed to the next section to view the results Step 6 View Merged Results Upon completion of the review of each individual profile click Next gt to proceed to the Mixture Analysis Merged Results Viewer and view the mixture analysis resul
21. 0 1 001 A07 sa H4 H28 0 1 WA H4 H28 0 1 001 A07 sa H4 H28 0 1 D16S539 10 12 H4 H28 0 1 001 AO07 fsa H4 H28 0 1 0251338 17 20 H4 H28 0 1 001 A07 fsa H4 H28 0 1 AMEL x H4 H28 0 1 001 A07 sa H4 H28 0 1 DB8S1178 14 H4 H28 0 1 001 AO07 fsa H4 H28 0 1 D21S11 30 uality Value Details o view individual quality value details select a single row H4 H28 0 1 001 AD7 sa H4 H28 0 1 D18551 13 15 H4 H28 0 1 001 A07 fsa H4 H28 0 1 D198433 14 H4 H28 0 1 001 A07 fsa H4 H28 0 1 THOI 7 93 H4 H28 0 1 001 A07 sa H4 H28 0 1 FGA 21 26 5 Select File Export Table Ctrl E GeneMapper ID X Software Version 1 1 Getting Started Guide 37 vu Chapter 3 Prepare for Mixture Analysis Step 5 Export and View a Known Genotype Profile Export the Table 1 Select File Export Table Ctrl E g BT1 TEST Samples Plot File Edit view Plots Tools Alleles save Pane Ctrl Shift 5 Page Setup amp Print Ctrl P Print Preview Export Table Ctrl E Close Plot Wii Low Escape 2 Select Export File As Tab delimited text txt file Note You can export samples from the GeneMapper ID X Software as tab delimited text files txt or as comma separated values files csv 3 Name the file Known H28 txt 4 Choose Export destination lt drive gt AppliedBiosystems GeneMapperID X Mixture Analysis then click Export Note During the routine
22. 0 231 0 124 amp 6 D351358 15 17 T 15 16 r Bp 0 813 0 252 0 817 0 817 i A 7 D351358 16 17 n 15 16 rn Bg 0 813 0 254 0 809 0 809 di 8 D351358 15 F1 nr 16 17 r E 0521 0268 0 124 0231 o9 o9 9 D351358 16 F1 n 15 17 nm BE 0 524 0 270 0 125 0 229 o9 o9 10 D351358 15 17 O 16 17 r Bp Ma 0 300 0 115 0 115 9 o9 11 D351358 16 17 n 15 17 r Bg We 0 302 0 115 0 115 o9 o9 12 0351358 15 15 oO 16 17 r B WA 0312 na 0 231 o9 amp 13 D351358 16 16 O 15 17 O B wa 0316 N A 0 229 e 9 e 9 amp 14 D351358 17 F1 ri 15 16 r Bg 0 849 0 505 0 542 0 994 BH A 15 0351358 17 17 n 15 16 ri Bg 0 897 0 860 nja 0 9904 ul A Note The combination that you removed from the Selected Genotype Combinations table now appears in row 1 of the Unselected Genotype Combinations table 8 Exit the Samples Plot by clicking the X in the upper right corner then select Filter by Marker All in the Mixture Analysis Results Viewer GeneMapper ID X Software Version 1 1 Getting Started Guide 67 5 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 3 Determine Genotype Combinations to Include in Statistical Calculations Select Genotypes Assume that the D3S1358 marker cannot be interpreted with for Second confidence for the minor contributor for sample H4_H28_1_5 Sample 1 Omit the marker from the statistical calculations by checking the Inc
23. 1 Getting Started Guide Chapter 7 Analyze Merged Results Step 3 Analyze Samples To make your selections click in each cell and select from the drop down list To change an entire column click in the first cell make your selection then click in the column header and press Ctrl D to populate fill down the column Samples Analysis Summar esl Status Sample File Sample Name C analysis Method Custom Control i Run Date amp Time 7 i SE ARNM sos sa M H4 H28 0 1 001 H4 H28 D 1 umm HD TREE WX eO 75 4 None 2008 04 09 19 05 1 C 2 y H4 H28 0 1 001 H4 H28 0 1 Sample HD FulRange 75 COfier v1X CE_F_HID_GS500 75 4 None 2008 04 09 20 25 2 im e 3 y H4 H28 1 0 DIz H4 26 1 0 Sample HD FulRange 75 Profiler Plus v1X CE F HDD GS500 75 4 None 2008 04 09 19 05 16 im e 4 H4 H28 1 0 O1z H4 H28 1 0 Sample HID Full Range 75 COfiler x CE F HID GS500 75 4 None 2008 04 09 20 25 28 m e 9 5 amp H4 H28 1 3 007 H4 H28 1 3 Sample HID Full Range 75 Profiler Plus v x CE F HID GS500 75 4 None 2008 04 09 19 05 1 m o9 5 amp H4 H28 1 3 007 H4 H28 1 3 Sample HID Full Range 75 cotier v1 x CE F HID GS500 75 4 None 2008 04 09 20 25 2 m o9 7 f Ladder 012 F04 Ladder Allelic Ladder HID Ful Range 75 Profiler Plus v1X CE F HID GS500 75 4 None 2008 04 08 19 05 1 m e 8 3 Ladder 012 FO6 Ladder Allelic Ladder HID FulRange 75 COfiler v1X CE F HDD GS50
24. 4 Segregate Samples for information on how to import a ready to use population database To create a custom population database refer to the GeneMapper ID X Software Help Example Data Overview Example data fsa files are installed with the GeneMapper JD X Software v1 1 for use with the mixture analysis tutorial SGM Plus Kit example data are used to demonstrate features of the Mixture Analysis Tool in Chapter 3 through Chapter 6 COfiler and Profiler Plus Kit example data are used to demonstrate additional functionality of the Mixture Analysis Tool in Chapter 7 22 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 2 Understanding the Software Ww Example Data How to Access To perform the exercises described in this guide locate the example the Example Data data files provided as shown below Files File Location Install Configuration Mixture Analysis Sample Files fsa Client install lt drive gt AppliedBiosystems GeneMapperlID X Client Example Data Mixture Analysis Samples Full install lt drive gt AppliedBiosystems GeneMapperlD X Example Data Mixture Analysis Samples Note The drive varies depending on the installation of the GeneMapper ID X Software See the GeneMapper ID X Software Version 1 0 1 1 Installation Guide for more information on installation options GeneMapper ID X Software Version 1 1 Getting Started Guide 23 24 Chapter 2
25. A PARTICULAR PURPOSE IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF 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 TRADEMARKS Applied Biosystems AB Design AmpFZSTR COfiler GeneMapper Identifiler and SGM Plus are registered trademarks of Applied Biosystems Inc or its subsidiaries in the US and or certain other countries This product includes software developed by the Apache Software Foundation This product includes software developed by the ExoLab Project JNIRegistry is copyrighted O by ICE Engineering Inc Microsoft Excel and Windows are registered trademarks of Microsoft Corporation All other trademarks are the sole property of their respective owners 4396773 Rev A 9 2008 Contents Preface t P PPM vii How to Use This Guide 2 0 0 0 cece vii How to Obtain More Information n asana anaana anaana ix How to Obtain Support 2 0 00 0 0c ee xi Chapter 1 Getting Started 0 cc ee 1
26. MA PP H4 H28 1 3 007 Profler Plus vX D135317 8 9 r 9 11 r Remove Marker 5 MA PP H4 H28 1 3 00 Profiler Plus vIX D135317 8 9 r 11 F1 r 6 MA CO H4 H28 1 3 007 COfiler vix D165539 10 12 r 9 9 r I7 MA CO H4 H28 1 3 007 COfiler vix D165539 10 12 r 9 10 r Ifs MA CO H4 H28 1 3 00 COfiler vix D165539 10 12 r 9 12 r a MA PP H4 HZR 1 3 nf Profiler Plis vix 018551 i315 12 12 l Selected Genotype Combinations Unmerged select one panel to add per marker Filter by Marker All Y Run Folder Sample File Panel Marker c1 Major Incondusis C2 Minor Incondusi 1 PREC 2813007 COfiler_v1x D351358 15 16 r 17 17 r 2 MA PP H4 H28 1 3 007 Profler Plus vIX D351358 15 16 r 17 17 r 3 MA PP H4 H28 1 3 007 Profiler Plus v1X D351358 15 16 r 16 17 r Add Marker Mixture Analysis Parameters Notes Calculate Statistics Export Cancel lt Back Next gt Finish Q 10 Select the Profiler Plus results by highlighting the rows in the bottom table and clicking Add Marker The Profiler Plus results move into the Selected Genotype Combinations Merged table as shown next 108 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results ea Step 7 Calculate and Analyze the Results s Mixture Analysis Merged Results Viewer 2 nl xl Sample Name Ha Ho 13 af lt lt Previous 5 Next Sample gt gt Mixture Analysis Results KrP 22 n GPT GPE Sbabstice Disease BE B
27. Peak Height RFU 300 PHR Threshold between 0 and 1 0 54 OK Cancel Help 7 Click OK to save your changes and return to the New Mixture Analysis Method dialog box 8 Click New to create a second PHR threshold and perform the following a Verify the Minimum Peak Height value is 301 Note The default value for a new Minimum Peak Height entry in the Heterozygote PHR settings table the Maximum Peak Height value for the previous row in the table 1 b In the Maximum Peak Height RFU field enter 1000 c In the PHR Threshold between 0 and 1 field enter 0 60 9 Click OK to save your changes and return to the New Mixture Analysis Method dialog box 10 Click New to create a third PHR threshold and perform the following a Verify the Minimum Peak Height value is 1001 Note The default value for a new Minimum Peak Height entry in the Heterozygote PHR settings table the Maximum Peak Height value for the previous row in the table 1 b In the Maximum Peak Height RFU field enter 10000 GeneMapper D X Software Version 1 1 Getting Started Guide 47 VA Chapter 4 Segregate Samples Step 3 Create a New Mixture Analysis Method c In the PHR Threshold between 0 and 1 field enter 0 70 11 Click OK to save your changes and return to the New Mixture Analysis Method dialog box The final mixture analysis test method displays the following settings New Mixture Analysis Method
28. Review Likelihood Ratio Results on page 74 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor wu Step 1 Assign Known Genotypes Mixture Analysis Sample Segregation by Minimum Number of Contributors GeneMapper ID X Project Name SGM_TEST 2 Contributors 1 Contributor 3 or More Contributors Extraction Status Review Status Run Folder Sample File Sample Name Mixture Analysis Methog Known n MA SGM H4_H28_1_1_003_B07 fsa H4 H28 1 1 MA Test Method B MA SGM H4 H28_1 _2_005_C07 fsa H4 H28 1 2 MA Test Method E v MA SGM HA H28 1 3 007 D07 fsa H4 H28 1 3 MA Test Method p p MA SGM H4_H28_1_5_009_ 07 fsa H4 H28 1 S MA Test Method 5 l MA SGM H4 H28 1 9 O11 FO7 fsa H4 H28 1 9 MATestMethod i 0 Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish e or To import another known sample click Import then from the drop down list navigate to the location of a different known genotype profile and click Import The following message is displayed indicating that the review status will change 1f you select a known contributor Mixture Analysis EE xi p The Review status is set to Reviewed for the Mixture Sample H4_H28_1_1 A Do you still want to change its Known Selector No Note This message is displayed only if you previously reviewed a sample and ch
29. Started Guide Preface How to Obtain Support How to Obtain Support For HID support you can send an e mail to HIDTechSupport appliedbiosystems com or call 888 821 4443 option 1 For HID support outside North America contact your local support office 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 Access worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities Search through frequently asked questions FAQs Submit a question directly to Technical Support Order Applied Biosystems user documents MSDSs certificates of analysis and other related documents Download PDF documents Obtain information about customer training Download software updates and patches GeneMapper D X Software Version 1 1 Getting Started Guide Xi Preface How to Obtain Support xii GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started Understanding the Software J Prepare for Mixture Analysis r Segregate Samples Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Contributor Mixtures with One Known Contributor I Analyze Merged Results This chapter covers B Whats New in Analysis Tool E GeneMapper E GeneMapper Getting Started
30. Step 2 Import a Population Database 1 In the Mixture Analysis Manager select the Population Databases tab and click Import 2 Navigate if necessary to lt drive gt AppliedBiosystems GeneMapperID X Mixture Analysis Population Databases and select ABIdentifilerPopulationDatabase csv then click Import s Import Population Database B xj Look in E Population Databases be dos ie EI ABIdentifilerPopulationDatabase csv y Bi STR JFS Database csv My Recent EI STR JF5 D2 D19 Database csv Documents Desktop My Documents DE My Computer em a File name Import My Network Places Files of type csv Files csv X Cancel GeneMapper ID X Software Version 1 1 Getting Started Guide 43 wu Chapter 4 Segregate Samples Step 2 Import a Population Database 3 Select Open to view the AB Identifiler Population Database This database is provided as a default with the GeneMapper ID X Software v1 1 The Open Population Database dialog box allows you to view the number of samples comprising each database the allele frequency data and the minimum allele frequency used for each database g Open Population Database EF Population Database Name as Identifiler UM Population Data Source JampFIsTR Identifiler Kit Users Manual r Populations African American 2 Number of samples in selected marker n 357 Allele Frequency i D165539
31. The profile for 4419 was not found in the mixture H4 H28 1 5 Hypotheses including 4419 are disabled 1 Click Back to return to the Mixture Analysis Sample Segregation dialog box 2 If desired click Yes to save the changes to the current sample IMPORTANT Saved extraction results are overwritten when you reanalyze a sample GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results Calculate the 1 To calculate the Likelihood Ratio for a major contributor only Likelihood Ratio check the Use C1 Major Only box as shown next Based on the Major Contributor Only Mixture Analysis Results Viewer Minimum Number of Contributors 2 E Sample File H4_H28_1_5_009_E07 fsa Panel SGM Plus v1X Run Folder MA SM Sample Name H4 H28 1 5 X lt lt Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major RMP Statistics C2 Minor CPI CPE Statistics LR Statistics Likelihood Ratio LR Calculation LR Pr E Hp Pr E Hd where Pr probability E evidence pipebar given Hp prosecution hypothesis Hd defense hypothesis LR Statistics Summary LR Analysis Summary sample H4 H28 1 5 analyst gmidx Reference Sample s select one or more Reference 1 None Reference 1 None Reference 2 None Hypotheses
32. Understanding the Software Example Data GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis This chapter covers B Overview ssssleseeen RR Ie 26 Getting Started E Step 1 Create a GeneMapper ID X Software Project 27 E Step 2 Import an Analysis Method 28 E Step 3 Analyze Data Using Appropriate Settings 29 hace dox d E Step 4 Review Analysis Results 005 31 E Step 5 Export and View a Known Genotype Profile 35 Chapter 3 Prepare for Mixture Analysis Segregate Samples J Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Contributor Mixtures with One Known Contributor l Analyze Merged Results GeneMapper ID X Software Version 1 1 Getting Started Guide 25 Chapter 3 Prepare for Mixture Analysis 2 Overview Overview Mixture Analysis 26 Preparation In This Chapter This chapter provides a tutorial that proceeds through the steps to prepare samples for mixture analysis within a project You will create a GeneMapper ID X Software project as described in the mixture analysis workflow and perform data analysis and allele editing before selecting and launching the Mixture Analysis Tool from the Tools menu Chapter 4 You will also export a known genotype profile during this process To prepare the data for mixtu
33. available statistical options 4 B bold text when to use vii C C1 Major definition 9 C2 Minor definition 9 Index calculating merged results 106 calculating statistics approaches 113 Combined Probability of Exclusion 72 Combined Probability of Inclusion 72 Combined Probability of Inclusion and Exclusion 71 Likelihood Ratio 72 74 94 population databases 71 Random Match Probability 71 92 client installation 23 COfiler Kit example data 22 sample files 22 combined frequency definition 10 Combined Probability of Exclusion calculating 71 reviewing calculation results 72 statistical approach 114 115 Combined Probability of Inclusion calculating 71 reviewing calculation results 72 statistical approach 114 combining amplification results 99 conventions bold text vii for describing menu commands viii IMPORTANTS viii in this guide vii italic text vii Notes viii user attention words viii CPE definition 10 CPI definition 10 GeneMapper ID X Software Version 1 0 Getting Started Guide 121 Index customer feedback on Applied Biosystems documents x D data analysis 29 disclaimer license ii documentation related ix E example data COfiler Kit 22 how to locate 20 how to use 22 23 Identifiler Kit 22 Profiler Plus Kit 22 SGM Plus Kit 22 example files locating 23 exporting genotypes 35 exporting known genotypes 35 extracting genotypes 57 extraction results reviewing 58 89 ext
34. calculated for the unknown C1 Major contributor s Mixture Analysis Results Viewer Minimum Number of Contributors 2 ixi Sample File H4 H28 1 3 007 _D07 fsa Panel SGM Plus v1X Run Folder MA SGM Sample Name H4 H28 1 3 X lt lt Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major AMPibtatistics finr CPI CPE Statistics LR Statistics Random Match Probability RMP Statistics Summary Contributor 1 Major Random Match Probabilities for Sample H4 H28 1 3 Database AB Identifiler UM Population African American Theta 0 01 Major Contributor Profile Frequency 1 0982E 14 RMP 1 in 91 Trillion African Americans RMP 1 in 9 1056E13 RMP Statistics Details Contributor 1 Major Database Population Marker Alleles Genotype Frequency Combined Frequency 1 AB Identifiler UM African American D351358 15 16 o 1744 0 1744 2 aB Identifiler UM African American vWA 15 18 0 0589 0 0589 3 jag Identifiler UM African American D165539 10 12 0 0410 0 0410 4 AB Identifiler UM African American D251338 17 20 0 0130 0 0130 5 JAB Identifiler UM African American D851179 B 14 0 0928 0 0928 6 AB Identifiler UM African American D21511 30 30 0 0311 0 0311 pa JAB Identifiler UM African American D18551 15 15 0 0169 0 0169 8 s Identifiler UM African American D195433 14 14 0 0458 0 0458 Export Mixture Analysis Parameters Sa
35. contributor genotype of 17 F1 In this case the software analyzes the possibility of allele dropout below the Mixture Interpretation threshold in order to include the combination From the Samples Plot select row 1 in the Selected Genotype Combinations table Click Unselect The combination in row 1 moves to the Unselected Genotype Combinations table and no longer appears in the Selected Genotype Combinations table This removed combination will not be included in the statistical calculations for this sample Note This combination is being removed for the purposes of this demonstration only Select the icon indicated below to display the Unselected Genotype Combinations table ki BER A0 ixture Analysis Unselected Genotype Combinations Table GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns E Step 3 Determine Genotype Combinations to Include in Statistical Calculations Select Filter by Marker D3S1358 to display the results as shown below Marker C1 Major Inconclusis C2 Minor Inconclusiw Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 8 0 001 2 D351358 15 17 r 16 16 r E Wa 0202 0229 N e e 3 D351358 16 17 ri 15 15 mn Bg Wa 0 203 0 231 Na o9 4 D351358 15 17 r 16 F1 r Bp 0 476 0 236 0 229 0 125 e 5 D351358 16 17 n 15 F1 ri E 0 479 0 238
36. for each contributor to the mixture The software can calculate Combined Probability of Inclusion Exclusion in instances involving two or more contributors to a mixture Probability of Inclusion The software computes the probability of inclusion for each marker as Probability of Inclusion f f f fy where f frequency allele 1 f frequency allele 2 f frequency allele 3 N last allele in marker data Combined Probability of Inclusion The software computes the combined probability of inclusion as Combined Probability of Inclusion II Marker Probability of Inclusiong where II product 1 marker index GeneMapper D X Software v1 1 Getting Started Guide Appendix A Statistical Analysis and Algorithms m Statistical Approaches m For example Probability of Inclusion for Marker D3 0 01 Probability of Inclusion for Marker D5 0 025 Combined Probability of Inclusion 0 01 0 025 0 00025 If the ethnic group U S Hispanic then Combined Probability of Inclusion 0 00025 for U S Hispanic Stated otherwise 1 0 00025 4000 1 in 4 thousand U S Hispanics Combined Probability of Exclusion Combined Probability of Exclusion 1 0 Probability of Inclusion Using the above example Combined Probability of Inclusion 0 00025 for U S Hispanic Combined Probability of Exclusion 1 0 0 00025 0 99975 which is expressed as a percentage of the population ex
37. jo jo217 W amp amp S D351358 r gt r1 BE 07640164 0 920 0 920 A Select 6 p351358 16 16 n 15 17 n 16 17 Ma 0166 na o309 8 e amp 7 D351358 r Dn Bp 0 394 0 168 0 217 0 128 e e 8 D351358 15 17 Dn 16 16 n 16 17 BE w 0206 o309 N e e Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel Back Next gt Finish e 4 Select Filter by Marker vWA The five genotype combinations are listed in the Selected Genotype Combinations table In all cases the C1 Major contributor is a type 15 18 whereas four different possible genotypes are listed for the C2 Minor contributor 15 18 15 F1 18 Fl Fl Fl and F1 F2 The known 15 18 contributor is not excluded from any of these possibilities GeneMapper ID X Software Version 1 1 Getting Started Guide 91 non Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor a Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor Selected Genotype Combinations Marker C1 Majory Inconclusiss C2 Minor Inconclusiw Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 VWA N A 0 000 10 975 0 975 I d d 2 VWA 0 089 0 006 0 934 0 934 I d 3 VWA 0 087 0 008 0 890 0 890
38. panels extracting the potential genotypes of the contributors 2 person mixtures only and performing statistical analysis on a composite profile generated from replicate results from the same sample or from results generated from the same sample using different AmpF STR9 kits Mixture Analysis Method A collection of user defined settings that determine the sample segregation and extraction thresholds used by the Mixture Analysis tool to analyze potential mixture samples transferred from a GeneMapper D X Software project Mixture Analysis Parameters The heterozygote Peak Height Ratio PHR settings and Mixture Interpretation Threshold MIT as defined in the mixture analysis method and used to perform sample segregation and extraction on selected mixture samples within the Mixture Analysis tool Mixture Analysis Project The mixture analysis results for a group of samples transferred into the Mixture Analysis tool from a GeneMapper D X Software project Mixture Analysis Tool Part of the GeneMapper D X Software containing specific functionality to assist in the analysis interpretation and statistical analysis of DNA mixtures Mx Mixture Proportion A measure of the relative proportion of the minor contributor in a 2 person mixture sample as described by Gill et a 1998 see Bibliography GeneMapper D X Software Version 1 1 Getting Started Guide 13 mm Chapter 1 Getting Started Glossary of Term
39. prompted to save changes Click Yes to save the changes Add Samples to 1 Inthe Project window Select Edit Add Samples to Project the Project Ctrl K 2 Navigate to lt drive gt AppliedBiosystems GeneMapper ID X Example Data Mixture Analysis and select MA SGM 3 Click Add to List in the lower left hand side of the window to add the sample files to the project then click Add to close the dialog box From the Table Setting drop down list select 31XX Data Analysis GeneMapper ID X Software Version 1 1 Getting Started Guide 27 Chapter 3 Prepare for Mixture Analysis Step 2 Import an Analysis Method Step 2 Import an Analysis Method Analysis methods define the peak detection sizing genotyping and quality assessment parameters applied during analysis of sample data In this step you will import the analysis method configured specifically for use with the GeneMapper D X Software example data provided and with the procedures outlined in this guide IMPORTANT The values used in this guide may not be suitable for analyzing data generated in your laboratory You must optimize and validate these values as part of an internal validation study In the GeneMapper D X Project window 1 Select Tools gt GeneMapper ID X Manager 2 In the Analysis Methods tab select Import 3 Navigate to lt drive gt AppliedBiosystems GeneMapper ID X Example Data Mixture Analysis GSG Analysis Method and select HI
40. the GeneMapper ID X Software The Mixture ID X Software Mixture Analysis Workflows 4 ID X Software Mixture Analysis Workflows 4 B Using this Guide for Mixture Analysis 6 GeneMapper D X Software Version 1 1 Getting Started Guide 1 Chapter 1 Getting Started What s New in the GeneMapper ID X Software The Mixture Analysis Tool What s New in the GeneMapper D X Software The Mixture Analysis Tool GeneMapper ID X Software is an automated genotyping software solution for all human identification HID data analysis needs including forensic casework databasing and paternity testing GeneMapper D X Software v1 1 contains a new Mixture Analysis Tool designed to Help the forensic analyst interpret DNA mixtures Evaluate autosomal DNA mixtures and 1 contributor single source samples Y STR data cannot be evaluated using the tool e Save the mixture analysis results to the GeneMapper ID X Software project Note The Mixture Analysis Tool supplements but does not replace mixture interpretation by an experienced analyst The Mixture Analysis Tool is accessible from the Tools menu in a GeneMapper ID X Software project For all samples in a project the tool performs the following functions Identifies samples that are eligible for Mixture Analysis Samples are assessed according to sample type analysis status and allele label status Note Only analyzed samples with green or ye
41. workflow you may prefer to export known genotypes to the run folder containing the sample file associated with the known profile 5 Navigate to drive VAppliedBiosystems GeneMapperID X Mixture Analysis and open the exported file using Excel to view the exported data shown below Sample File Sample Name Marker Allele1 Allele 2 H4_H28_0_1_001_A07 fsa H4 H280 1 D3S1358 15 16 H4 H28 0 1 O01 AU7 fsa H4 H28 01 WA 15 18 H4 H28 0 1 001 AU7 fsa H4 H280 1 D165539 10 12 H4 H28 D 1 D01 AQ7 fsa H4 H280 1 D281338 17 20 H4 H28 D 1 DO1 AO7 fsa H4 H280 1 AMEL X H4 H28 0 1 D01 AQ7 fsa H4 H280 1 D8S1179 14 H4 H28 0 1 D01 AQ7 fsa H4 H280 1 D21511 30 H4 H28 0 1 D01 AQ7 fsa H4 H280 1 D18551 13 15 H4 H28 0 1 D01 AQ7 fsa H4 H280 1 D195433 14 H4 H28 0 1 D01 AQ7 fsa H4 H280 1 THO 7 9 3 H4 H28 D 1 001 AU7 fsa H4 H280 1 FGA 21 26 38 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis Step 5 Export and View a Known Genotype Profile 6 Return to the GeneMapper D X Project window select the Samples tab and in the Samples table select single source sample H4 H28 1 0 then display the Samples Plot using the display plots icon Jul in the toolbar 7 Repeat Select Samples for Viewing step 4 on page 37 through Export the Table step 5 to export this known sample as Known H4 txt The exported known samples will be used later during mixture extraction and Likelihood Ratio calculatio
42. 0 75 4 None 2008 04 08 20 25 25 m e 9 y NTC D08 DO4 fs NTC Negative ContrgHID FullRange 75 Profiler Plus v1X CE F HDD GS500 75 4 None 2008 04 09 18 05 1 im e 10 y NTC 08 Do6 fs NTC Negative ContrgHD FullRange 75 COfier v1X CE F HDD GS500 75 4 None 2008 04 03 20 25 2 11 PositiveControl Ol PositiveControl Positive Control HID Full Range 75 Profiler Plus v1X CE F HID GS500 75 4 None 2008 04 09 19 05 1 12 PositiveControl O PositiveControl Positive Control HID Full Range 75 COfiler_v1 x CE F HID GS500 75 4 None 2008 04 09 20 25 2 m e Note When making changes to the Panel column a separate window opens instead of a drop down list Open the folder and select the appropriate panel 2 Click the Analyze icon on the toolbar 3 The Save Project dialog box is displayed Fill in the Save Project dialog box as shown below then click OK Save Project xi Name Pro_co Test Security Group GeneMapper ID X Security Group Y OK Cancel Help GeneMapper ID X Software Version 1 1 Getting Started Guide 101 Chapter 7 Analyze Merged Results Step 3 Analyze Samples The Analysis Summary dialog box is displayed Samples Analysis Summary Genotypes Analysis Summary Selec run folder to play Sample Status Total of Samples Unanalyzed g 0 00 Analyzed 12 U Analysis Setting Changed 0 Click a l
43. 28 0 1 Zj Reference 2 H4 Hz8 1 0 Reference 2 H4 H28 1 0 Hypotheses select one or more Hypothesis 1 Hp Mixture of Ci H4 H28 0 1 and C2 H4 H28 1 0 F Hp Mixture of C1 H4_H28_0_1 and C2 H4 H28 1 0 Ha Mixture of Ci H4 H28 O0 1 and one unknown unrelated person Hd Mixture of C1 H4 H28 0 1 and one unknown unrelated persor Database AB Identifiler UM Population African American jo He Mixture of C1 H4_H28_0_1 and C2 H4 H28 1 0 Theta 0 01 Hd Mixture of C2 H4_H28_1_0 and one unknown unrelated persor LR 1E0 2 1216E 5 4 7134E4 Hypothesis 2 Hp Mixture of C1 4 Hom 0 1 and C2 HACHOS 1 0 Hp Mixture of Ci H4 H28 0 1 and C2 H4 H28 1 0 Zi a a A T cdpoiuy Lis Hd Mixture of C2 H4 H28 1 0 and one unknown unrelated person Database AB Identifiler UM Population African American Theta 0 01 LR 1E0 1 0982kE 14 9 1056E13 I Hp Mixture of C1 H4 H28 0 1 and one unknown unrelated persor Hd Mixture of two unknown unrelated people Hypothesis 3 Hp Mixture of Ci H4 H28 O 1 and C2 H4 H28 1 0 Had Mixture of two unknown unrelated people 4 gt Database AB Tdentitiiet um Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel Back Next Finish cd Hp Mixture of C2 H4_H28_1_0 and one unknown unrelated persor Hd Mixture of two unknown unrelated people GeneMapper D X Sof
44. 4 Eds os n AR SampleName S808 SQ SSPK MIX OMR tGQ EAE 9 p3istss WA l1 piss 5 este 75 115 155 195 235 275 315 355 2 Select then right click on the peak label to assign a custom allele label to the peak Label the peak as 11 as shown in the following figure Enter a reason for change when prompted AAtS 3 Repeat the labeling of the off ladder D3S1358 allele for sample H4 H28 AAI8 1 1 2 4 When the review is complete exit the Samples Plot 34 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis vu Step 5 Export and View a Known Genotype Profile Step 5 Export and View a Known Genotype Profile Select Samples 1 Inthe Samples table select the Known Sample Export Table for Viewing Setting ch a Hi UN gt Table Setting Known Sample Export Samples Analysis Summary Genotypes Sample File Sample Name 2 AA19 D04 BD8 f 3 H4 H28 0 1 001 H4 H28 0 1 4 H4 H28 1 0 Diz H4 H28 1 0 5 H4 H28 1 1 DOz H4 H28 1 1 6 7 8 H4 H28 1 2 00t H4 H28 1 2 H4 H28 1 3 007 H4 H28 1 3 H4 H28 1 5 0t H4 H28 1 5 9 H4 H28 1 9 011 H4 H28 1 9 10 H4 H28 AA18 1 H4 H28 amp AA18 1 11 Ladder 012 FO8 Ladder 12 NTC 008 D G fs i NTC 13 PositiveControl QI PositiveControl The Samples table should now contain only the Sample File and Sample Name columns as shown next Samples Filtered
45. AA18 AMEL x Y 17 AA19 D04 BO8 fsa AAIS DSS1178 13 15 18 AA19 004 BO8 fsa AA19 pasi 31 19 AA19 004 BOB8 fsa AA19 D18551 17 20 AA19 004 BOB8 fsa AA18 D9S433 14 15 21 AA19 004 BO8 fsa AA18 THO1 8 22 AA18 004 BO8 fsa AA19 FGA 24 25 IMPORTANT Be sure that no off ladder OL only allele labels are present OL alleles are not incorporated into known filtering Allele labels containing OL are acceptable if OL is followed by another character for example OL lt 6 Select the Samples tab select single source sample H4_H28_0_1 then click the display plots icon toolbar to display the Samples Plot in the GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis Step 5 Export and View a Known Genotype Profile 4 Select the Data Interpretation Plot Setting to display the Genotypes table together with the electropherogram s SGM TEST Samples Plot File Edit View Plots Tools Alleles Help amp A Plot Setting pata Interpretation Panes 2 x ma An aaa AMEE ie li 1448 lis ms n AR Sample File Sample Name ses a ser mix oMR cea H4 H28 0 1 001 A07fsa H28 0 Mark Sample for Deletion a H4_H28_0_1_001_AD7 fsa H4_H28_0_1 m ms A B m T Mark Sampie far Deletion 75 115 155 195 235 275 315 355 395 435 Sample File Sample Name Marker H4_H28_0_1_001_A07 fsa H4_H28_01 D351358 15 16 H4 H28
46. African American D251338 F F 1 0000 1 0000 6 AB Identifiler UM African American D851179 10 13 0 0111 0 0111 AB Identifiler UM African American D195433 FF 1 0000 1 0000 GeneMapper ID X Software Version 1 1 Getting Started Guide AB Identifiler UM African American AB Identifiler UM African American THO1 FF 1 0000 0 4314 1 0000 0 4314 3 Click the CPI CPE Statistics tab to review the results of the calculations 4 Review the CPI CPE results for sample H4_H28_1_5 In some instances the software calculates that the possibility of allele dropout at a particular marker or markers is viable For such markers the software assigns the marker inclusion frequency a value of 1 0 based on the possibility that alleles may be present below the mixture interpretation threshold Because the software includes all these potential alleles in the calculations the marker is uninformative 73 a Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results Step 6 Calculate and Review Likelihood Ratio Results Calculate the Likelihood Ratio Based on Contributors to the Mixture 74 Note If you are unfamiliar with Likelihood Ratio calculations review Appendix A Statistical Analysis and Algorithms before proceeding with this step To calculate the Likelihood Ratio you must set up your alternate hypotheses by sel
47. Calculate and review Likelihood Ratio LR results N Oo Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Assign known genotypes 2 Extract individual genotypes of the two possible contributors to a two person mixture where 1 contributor is known 3 Determine which genotype combinations to include in the statistical calculations 4 Calculate Random Match Probabilities RMP for each individual contributor 5 Calculate and review Likelihood Ratio LR results Chapter 7 Analyze Merged Results 1 Create a project containing the same sample analyzed with both the AmpF STR Profiler Plus and COfiler kits Add samples to the project Analyze the samples Prepare for mixture analysis Segregate and review individual profiles oa fF OQ Nm Merge the data to create a composite profile using the 13 genetic markers detectable from both kits 7 Calculate statistics and review results from replicate amplifications of the same sample GeneMapper D X Software Version 1 1 Getting Started Guide 7 Chapter 1 Getting Started Using this Guide for Mixture Analysis For More Information IMPORTANT Some steps performed in this Getting Started Guide are meant only to demonstrate the use of certain features in the GeneMapper D X Software v1 1 and may not be a part of your routine analysis workflow Refer to your own lab procedures when using the GeneMapper D
48. D Full Range 75 4 Click OK in the Choose Security Group dialog box to confirm the GeneMapper D X Security Group then click Done 28 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis Fu Step 3 Analyze Data Using Appropriate Settings Step 3 Analyze Data Using Appropriate Settings 1 Define each sample from left to right as shown in the Samples table below a Assign the Sample Type to each sample b Select the Analysis method HID_Full Range_75 c Select the Panel SGM_Plus_v1X d Select the Size Standard CE_F_HID_GS500 75 450 To make your selections click in each cell and select from the drop down list To change an entire column click in the first cell make your selection then click in the column header and press Ctrl D to populate fill down the column View Tools Admin Help cl mosua Be Table setting 31xx Data Analysis m ei amp ace Samples Soni l y Status Sample File Sample Name Custom Control Run Date amp Time sE ARNm SOS sa 1 Aa18_010_E08 tsa aag mm HDS Perea 75 MPS vix Ceternm 75 4 None 2008 04 08 21 05 24 eo 2 l AA19_004_B08 fsa AA19 Sample HD FulRenge 75 SGM Plus vIX CE F HD GS500 75 4 None 2008 04 09 21 05 24 9 3 l H4 H28 0 1 000 A07 fsa H4 H28 0 1 Sample HD FulRange 7 SGM Plus vIX CE F HDD GS500 75 4 None 2008 04 09 21 05 24 e 4 H4 H28 1 0 013 GO7
49. FGA 24 2 w D195433 24 3 D75820 E T D351358 I D851179 25 2 D18551 26 p CSF1PO D251338 B net een Allele not observed or below minimum allele Frequency U S Hispanic Minimum allele frequency will be used For analysis Native American Minimum allele frequency 5 2n 0 0070 Help 44 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples wm Step 3 Create a New Mixture Analysis Method Step 3 Create a New Mixture Analysis Method Create a Mixture Analysis Method using the Mixture Analysis Manager 1 In the Mixture Analysis Manager select the Mixture Analysis Methods tab then click New to open the New Mixture Analysis Method dialog box Review the existing parameters Mixture Analysis Method Name Note The following symbols are not allowed in mixture analysis method file names W 2 V Optional Method Description Heterozygote PHR Settings Mixture Interpretation Threshold IMPORTANT The default entries in the Heterozygote Peak Height Ratio PHR Settings table below are for demonstration purposes only Use an internal validation study to determine the appropriate settings to use for your interpretation then use the following procedure to create new settings for your analysis To change existing PHR settings refer to Editing Heterozygote Peak Height Ratio Settings in the GeneMapper ID X Software Help GeneMa
50. For these markers the software incorporates a value of 1 0 into the statistical calculation as shown in the example below RMP Statistics Details Contributor 2 Minor Database Population Marker AB Identifiler UM African American Alleles Genotype Frequency 1 0000 Combined Frequency 1 0000 AB Identifiler UM African American D251338 AB Identifiler UM African American D851179 AB Identifiler UM African American D165539 AB Identifiler UM African American D165539 9 10 0 0416 AB Identifiler UM African American D165539 9 12 0 0715 0 1510 AB Identifiler LIM African American D21511 33 2 F 0 0756 0 0756 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 5 Review the Results of Random Match Probability and Combined Probability of Inclusion Exclusion Calculations For markers D3S1358 D21S11 and FGA the software attributes a single allele to the minor contributor For those markers the software calculates a genotype frequency of 2p based on the detected allele frequency and this is incorporated into the statistical calculation RMP Statistics Details Contributor 2 Minor AB Identifiler LIM African American AB Identifiler UM African American D18551 0 0756 Database Population Marker Alleles Genotype Frequency Combined Frequency 5 AB Identifiler UM
51. Mapper ID X Software Version 1 1 Getting Started Guide Selected Genotype Combinations Marker D351358 D351358 YWA VWA VWA VWA vWA VWA ejaj xj ejaj ejoj ny YWA C1 Major Inconclusixy C2 Minor Inconclusisy Known Genotype ADBI Mx 15 16 15 16 15 18 15 18 15 18 15 18 15 18 15 18 15 18 Tj nmm mmn m mm O 16 17 17 17 15 18 15 F1 18 F1 FLF2 15 15 18 18 FLF1 JA m mpm mnn nm Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 2 Review the Results of the Extraction Review the data automatically assigned to the Selected Genotype Combinations table for sample H4 H28 1 3 Note All selected genotype combinations show a green IQ flag Additional columns display the following 0 236 0 003 0 113 0 019 N A 0 000 0 089 0 006 0 087 0 008 0 088 0 009 N A 0 014 Inja 0 019 0 046 0 027 0 920 0 920 E 0 703 NJA 0 975 0 975 ij 0 934 0 934 E 0 890 0 890 i 0 975 N A INJA INJA N A NJA 10 975 N A Residual PHR1 PHR2 Residual Status PHR Status IQ Sort Unselect Missing Markers The Mixture Proportion Mx value for each genotype combination Where calculation of the Mx value is not possible N A is displayed The residual value for each genotype combination The peak height ratio for the C1 Major contributor PHR1 and for the C2 Minor contributor PHR2 Where calculation of the peak height ratio is not possi
52. More Contributors Extraction Status Review Status Run Folder Sample File Sample Mame Mixture Analysis Methog Known 1 MA SGM F4 H28 1 1 003 B07 fsa H4 H28 1 1 MA Test Method None 2 amp MA_SGM H4 H28 1 2 005 C07 fsa H4 H28 12 MA Test Method None 3 1 MA SGM F4 H28 1 3 007 D07 fsa H4 H28 1 3 MA Test Method None 4 1 MA SGM H4 H28 1 5 009 E07 fsa H4_H28_1_5 MA Test Method None 5 amp MA SGM H4 H28 1 9 01 1 F07 fsa H4_H28_1_9 MA Test Method None 0 Export Table Mixture Analysis Manager Cancel Back Next gt Finish 52 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples VA Step 4 Segregate the Samples 3 Review the 1 Contributor tab 4 samples were determined to originate from a single contributor sf Mixture Analysis Sample Segregation by Minimum Number of Contributors GeneMapper ID X Project Mame en resr 2 Contributors 1 Contributor 3 or More Contributors Run Folder Sample File Sample Name Mixture Analysis Method 1 AA18_010_E08 fsa AALS MA Test Method 2 MA_SGM 4A19_004_B08 Fsa AA19 MA Test Method 3 MA SGM H4 H28 0 1 001 A07 fsa H4 H28 0 1 MA Test Method 4 MA SGM H4 H28 1 0 013 G07 fsa H4 H28 1 0 MA Test Method Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish GeneMapper ID X Software Version 1 1 Getti
53. Reference 1 H4 H28 1 0 Reference 1 H4 H28 1 0 Reference 2 None x Hypotheses select one or more Reference 2 None Please select Reference to display available hypotheses Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next gt Finish o 2 Select the known H4 H28 0 1 as Reference 2 Only one hypothesis is available H H4 H28 1 3 originates from a mixture of H4 and H28 94 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor wu Step 3 Calculate the Likelihood Ratio for 2 Contributor Mixtures Extracted with a Known Contributor e H H4 H28 l1 3 originates from a mixture of H4 and one unknown unrelated person The observed profile is 91 trillion times more likely to occur if it originated from a mixture of H4 and H28 than from a mixture of H4 and one unknown unrelated person s Mixture Analysis Results Viewer Minimum Number of Contributors 2 BETES Sample File H4 H28 1 3 007 D07 fsa Panel SGM Plus vix Run Folder MA SGM Sample Name H4 H28 1 3 Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major RIP Statistics CZ ino CPI CPE Statistics LR Statistics p Likelihood Ratio LR Calculation LR Statistics Summary LR Pr E Hp Pr EI Hd where Pre probability E evidence pipeba
54. Sample s select one or more iss Se aaa od eference v Use C1 Major Only Hypothesis 1 Reference 1 H4 H28 0 1 giu C1 H4 H28 0 1 Reference 2 None Hd Ci unknown unrelated person Database AB Identifiler UM Population African American Theta 0 01 LR 1E0 1 0982E 14 9 1056E13 Hypotheses select one or more Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel Back Next gt Finish 27 The software calculates the Likelihood Ratio based on the following alternate hypotheses H Reference H28 is the source of the major contributor DNA H An unknown contributor is the source of the major contributor DNA In this example the observed profile is 9 1056E13 or 91 trillion times more likely to occur if it originated from reference H28 than from an unknown unrelated African American individual Note The Likelihood Ratio Summary displays only a brief description of the LR calculations To view detailed LR calculations select Export then LR Statistics Save the exported report as a comma separated values file csv The exported report contains the details for each population calculated using the likelihood ratio 82 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns m Step 6 Calculate and Review Likelihood Ratio Results Refer to the GeneMapper ID X Software Help for ad
55. Sample segregation and statistical calculations e Population databases Example data Analysis Chapter 3 Prepare for Mixture 1 Create a GeneMapper ID X Software project add samples and select table settings 2 Import an analysis method 3 Analyze data using appropriate analysis settings 4 Review the analysis results Analysis Requirements Summary Analysis Summary 5 Export and view a known genotype for later use GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started m Using this Guide for Mixture Analysis Chapter Description Chapter 4 Segregate Samples Launch the Mixture Analysis Tool Import a population database Create a new mixture analysis method BRO N Segregate the samples into one of the three classification groups Chapter 5 Analyze 2 Contributor 1 Extract individual genotypes of the two possible Mixtures with Two Unknowns contributors to a two person mixture where both contributors are unknown 2 Use the GeneMapper D X Mixture Analysis Quality Value system to review the results of the extraction 3 Determine which genotype combinations to include in the statistical calculations 4 Calculate Random Match Probabilities RMP for each individual contributor 5 Calculate Combined Probability of Inclusion Exclusion CPI CPE for the mixed sample Review the results of the RMP and CPI CPE calculations
56. What s New in the GeneMapper D X Software The Mixture Analysis TOO seanoir teed Meis tok het Robien ket E a a ee EXT cnt deni 2 GeneMapper D X Software Mixture Analysis Workflows 4 Using this Guide for Mixture Analysis 0 0000 6 OvervleW ccce rsin sakneni TR Yeas eX Xem E OY ede ee as 6 For More Information 00 0c cece eee eee eee 8 Glossary of Terms 0 eee 9 Chapter 2 Understanding the Software 19 OVERVIEW s 2 2 ac es pepe ERA Baler e ne wm Semele ee eed Ras 20 About the Software 0 ees 20 In This Chapter 00000 ees 20 Mixture Analysis Methods 0 0 e eee eee eee 20 Sample Segregation and Statistical Calculations 21 Population Databases 0 0000 eee 22 Example Data aoir a a a eee 22 OverVieW 2520 ced oe kes Eee dU RA ee ee a i 22 How to Access the Example Data Files 23 GeneMapper D X Software Version 1 1 Getting Started Guide iii Chapter 3 Prepare for Mixture Analysis 25 OVOIVIGW s pium ree WEE Ce REN d CE eese 26 Mixture Analysis Preparation 002 00sec eee 26 In This Chapter 2 2 0 0 00000 c eee ee 26 Step 1 Create a GeneMapper D X Software Project 27 Open and Create a New GeneMapper ID X Projects ac caja ec Ae eee eet Caged Re e p Reda 27 Add Samples to the Project 00000 eee 27 Step 2 Import an Analysis Met
57. X Software Mixture Analysis tool features and their use GeneMapper ID X Software Version 1 0 1 1 Installation Guide Replaces the version 1 0 Installation Guide and provides instructions for installing the GeneMapper D X Software v1 0 or v1 1 as a full installation a client only installation or a co installation GeneMapper ID X Software Version 1 0 Getting Started Guide Provides a workflow and tutorial that guides the user through the new ID X features GeneMapper ID X Software Version 1 0 Administrator s Guide Provides procedures for creating user accounts user groups and security groups configuring the audit trail and E signature tools and maintaining version 1 0 of the GeneMapper ID X Software GeneMapper ID X Software Version 1 0 Quick Reference Guide Provides abbreviated procedures for analyzing viewing and interpreting data using GeneMapper JD X Software GeneMapper ID X Software Version 1 0 Reference Guide Describes peak detection sizing and genotyping algorithms and the GeneMapper D X Software quality value system GeneMapper ID X Software Help Contains context sensitive help for all screens and procedures and background information needed to use the software GeneMapper D X Software Version 1 1 Getting Started Guide ix Preface How to Obtain More Information Obtaining Information from the Help System Send Us Your Comments Portable document format PDF version
58. X Software for forensic analysis This guide contains basic procedures It does not describe all the features and parameters in the GeneMapper D X Software v1 1 For detailed information on topics presented in this guide see the GeneMapper ID X Software Help Note Before using any of the procedures in this guide you must have successfully installed and registered the GeneMapper D X Software v1 1 For additional information see the GeneMapper ID X Software v1 0 1 1 Installation Guide Proceed to Chapter 2 Understanding the Software for an overview of the software functions and to learn how to access the example data files for use with the Mixture Analysis Tool tutorial GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started Glossary of Terms Glossary of Terms Term Definition ADBI Above Detection Below A column in the Mixture Analysis Results Viewer Genotype Interpretation Combinations table Also a quality flag that indicates whether any allele peak height within a marker genotype combination falls above the minimum peak amplitude threshold set in the GeneMapper D X Software and above or below the Mixture Interpretation Threshold MIT set in the mixture analysis method Allele Frequency The relative occurrence of a particular allele in a given population In the Mixture Analysis tool the allele frequencies associated with an individual population datab
59. ase stored in the Mixture Analysis Manager are used to calculate the genotype frequencies for a particular DNA profile Note Each marker within a population is associated with a sample size n used to determine the minimum allele frequency calculated as 5 2n The minimum allele frequency is automatically assigned to any allele in each marker when an allele frequency is either not observed or below the calculated minimum allele frequency designated by C1 Major The DNA profile within a 2 contributor mixture sample representing the greater proportion of DNA corresponding to greater peak heights at each marker within the sample mixture In general for mixtures of 1 3 or higher ratios the allele peak heights from the major contributor are clearly higher than the allele peak heights from the minor contributor In situations where mixtures approaching 1 1 are analyzed the major and minor contributors may become indistinguishable C2 Minor In a 2 contributor mixture sample the DNA profile representing the minority proportion of DNA corresponding to lower peak heights at each marker within the sample mixture In general for mixtures of 1 3 or higher ratios the allele peak heights from the minor contributor are clearly lower than the allele peak heights from the major contributor and in some cases alleles or markers may drop out In situations where mixtures approaching 1 1 are analyzed the major and minor contributors may
60. ation Results 99 E Step 1 Create a New Project and Add Samples 99 E Step 2 Import an Analysis Method 100 Understanding the E Step 3 Analyze Samples 0 0 0 0 cece eee 100 Software E Step 4 Prepare for Mixture Analysis 103 E Step 5 Segregate Samples and Review Profiles 104 E Step 6 View Merged Results 000000 c eee 105 Prepare for Mixture Analysis W Step 7 Calculate and Analyze the Results 106 Segregate Samples Analyze 2 Contributor Mixtures with Two Unknowns J Analyze 2 Contributor Mixtures with One Known Contributor Chapter 7 Analyze Merged Results GeneMapper D X Software Version 1 1 Getting Started Guide 97 Chapter 7 Analyze Merged Results Overview Overview 98 This chapter provides guidelines for analyzing merged results You will learn how to Create a project containing the same sample analyzed with both the AmpF STR Profiler Plus and COfiler kits Add samples to the project Import an analysis method Analyze the samples Prepare for mixture analysis Segregate and review individual profiles Merge the data to create a composite profile containing the 13 genetic markers detectable from both kits Calculate statistics and review results from replicate amplifications of the same sample For additional information on replicate amplifications see t
61. become indistinguishable GeneMapper D X Software Version 1 1 Getting Started Guide 9 Chapter 1 Getting Started Glossary of Terms Term Definition Combined Frequency The sum of all possible genotype frequencies at a given marker when multiple possible genotypes exist In the Mixture Analysis Results Viewer RMP Statistics Details table the column showing the combined genotype frequency for a given marker Contributor An individual whose DNA profile is present in a mixture sample For 2 person mixture samples in the Mixture Analysis tool contributor 1 major contributor C1 Major and contributor 2 minor contributor C2 Minor CPE Combined Probability of Exclusion The probability that a random person would be excluded as a possible contributor to the observed DNA mixture Note A CPE may be calculated in instances involving 2 or more contributors to a mixture This calculation is not available for single source samples CPI Combined Probability of Inclusion The probability that a random person would be included as a possible contributor to the observed DNA mixture Note A CPI may be calculated in instances involving 2 or more contributors to a mixture This calculation is not available for single source samples Extraction The process of separating a 2 person mixture sample into individual contributor profiles and identifying the most likely genotype combinations
62. binations that meet the criteria for inclusion in the statistical calculations You can review the results of the extraction and select genotype combinations for statistical analysis For a discussion of mixture analysis methods refer to Gill et al 1998 see Bibliography For additional information on 2 contributor samples refer to the GeneMapper ID X Software Help In this chapter you will learn to Extract individual genotypes from possible contributors of a two person mixture where both contributors are unknown e Use the GeneMapper ID X Mixture Analysis Quality Value system to review the results of the extraction Determine which genotype combinations to include in the statistical calculations Calculate Random Match Probabilities RMP for each individual contributor to the mixture Calculate the Combined Probability of Inclusion Exclusion CPI CPE for the mixed sample GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns NH Step 1 Extract Individual Genotypes Review the results of the RMP and CPI CPE calculations Calculate and review Likelihood Ratios LR results Step 1 Extract Individual Genotypes 1 Select the 2 Contributors tab in the Mixture Analysis Sample Segregation dialog box Five samples are displayed as shown below lo x s Mixture Analysis Sample Segregation by Minimum Number of Contributors GeneMappe
63. ble for a homozygous genotype N A is displayed The Residual Status which displays a green IQ value if the calculated residual is below the residual threshold The PHR Status which displays a green IQ value if all calculated peak height ratios exceed the thresholds set in the Mixture Analysis Method Note The ADBI Above Detection Below Interpretation column in the table displays a yellow d flag when any allele peak height within a marker genotype combination falls above the minimum peak amplitude threshold set in the GeneMapper ID X Software and below the Mixture Interpretation Threshold MIT set in the mixture analysis method GeneMapper ID X Software Version 1 1 Getting Started Guide 61 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 2 Review the Results of the Extraction 3 Select the Missing Markers button The following message is displayed Mixture Analysis J All Markers are present in Selected Genotype Table This message indicates that at least one genotype combination was selected for each of the markers detected for the sample 4 Click OK For instances where a detected marker does not have any combinations in the Selected Genotype Combinations table a dialog box similar to the one below is displayed Click Close s Missing Markers x The following markers are not present in the Selected Genotype Combinations table 1 Missing Markers in S
64. cluded 0 99975 100 99 98 Likelihood Ratio Based on available information the software allows the user to specify a set of hypotheses to calculate Likelihood Ratios for two person mixtures using the formula LR Pr E HyPr E Hy where LR Likelihood Ratio Pr probability E evidence given H Prosecution hypothesis the explanation put forward by the prosecution for the constituents of the mixture H Defense hypothesis the explanation put forward by the defense for the constituents of the mixture GeneMapper ID X Software v1 1 Getting Started Guide 115 uw Appendix A Statistical Analysis and Algorithms m Statistical Approaches Note H and Hg must be mutually exclusive explanations of the mixture evidence For example consider the following mixture scenario originating from an intimate body swab at locus M1 a b c d Assuming a two person mixture with a suspect of type c d and a victim of type a b the following hypotheses apply H The evidence originates from a mixture of the victim and the suspect H The evidence originates from a mixture of the victim and an unknown person In this instance H Ha 2pcpa LR 1 2p pq The Mixture Analysis Tool provides the following Likelihood Ratio functionality The user may elect to calculate the Likelihood Ratio based on a clear major contributor to the mixture effectively a single source Likelihood Ratio calculation The user may s
65. contain the known contributor GeneMapper ID X Software Version 1 1 Getting Started Guide 11 mm Chapter 1 Getting Started Glossary of Terms Term Definition Known Match An exact match of the known genotype to one of the contributors extracted from a 2 person mixture sample In the Mixture Analysis tool statistical analysis can only be performed on the unknown contributor when there is a complete 100 match of the known genotype to a single contributor either C1 Major or C2 Minor as displayed in the Selected Genotype Combinations table of the Mixture Analysis Results Viewer Known Matching The process whereby a known genotype profile is compared to both of the contributor profiles extracted from a 2 person mixture sample to determine which contributor displays the best match to the known LR Likelihood Ratio A ratio of the probabilities of two hypotheses that offer different explanations for the existence of the DNA profile evidence e g possible contributors to the mixture sample Note In the Mixture Analysis tool LR statistical calculations are only performed on 1 contributor and 2 contributor samples Major Contributor See C1 Major Marker Inclusion Frequency In the Mixture Analysis Results Viewer CPI CPE Statistics Details table the column showing the probability that a random person would be included as a possible contributor to the observed DNA mixture at a
66. contributor 53 2 contributors 21 52 104 3 or more contributors 54 statistical options 1 contributor 21 2 contributors 21 3 or more contributors 21 T Technical Support contacting xi text conventions vii training information on xi 124 GeneMapper D X Software Version 1 0 Getting Started Guide Index U unknown contributors sample analysis 56 Unselected Genotype Combinations table 17 60 user attention words described viii V viewing known genotypes 35 merged results 105 GeneMapper ID X Software Version 1 0 Getting Started Guide 125 Index 126 GeneMapper ID X Software Version 1 0 Getting Started Guide www appliedbiosystems com Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches 150 countries on six continents For sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com Applera is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 9 2008 Applied Bibsystems Part Number 43967783 Rev A
67. culations Random Match Probability RMP for each of the extracted contributor genotypes Combined Probability of Inclusion Exclusion CPI CPE and Likelihood Ratio Refer to Appendix A Statistical Analysis and Algorithms and the GeneMapper ID X Software Help for additional information GeneMapper ID X Software Version 1 1 Getting Started Guide 71 Calculations Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 5 Review the Results of Random Match Probability and Combined Probability of Inclusion Exclusion 2 In the Population Database Selection dialog box select the African American population from the Applied Biosystems Identifiler User Manual click the Apply to all samples radio buton then click OK to view the results of the RMP and CPI CPE statistical calculations for each sample The RMP Statistics C1 Major tab opens by default Data for the second contributor is found under the RMP Statistics C2 Minor tab Continue to Step 5 to review the results Step 5 Review the Results of Random Match Probability and Combined Probability of Inclusion Exclusion Calculations 1 Review the RMP data for the major contributor to sample H4 H28 1 5 Only one possible genotype per marker was selected for the major contributor Review the RMP data for the minor contributor for sample H4 H28 1 5 For markers vWA D2S1338 D18S51 D19S433 and THO1 marker dropout is represented by the F F combination
68. d Genotype Combinations table for inclusion in statistical calculations GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns E Step 2 Review the Results of the Extraction The Mixture Analysis Results Viewer is shown in the following figure Mixture Analysis Results Viewer Minimum Number of Contributors 2 Bl x Sample File H4 H28 1 1 003 B07 fsa Panel SGM Plus v1X Next Sample gt gt cs l LR St BBS Average mx 0 456 Residual Threshold 0 040 Filter by Marker fal x Known None Sample Review Complete Run Folder MA SGM Sample Name 2580 Mixture Analysis Results iP Statistics Cl sor RMP Stal aA nap CPI ERE SES Selected Genotype Combinations Marker C1 Majory Incondlusiw C2 Minor Inconclusivg Known Genotype ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 parse pisse r 1617 E 0 466 0 000 0 979 0 979 m I n i LI 2 D351358 15 17 i 16 16 Oo m 0 495 0 003 0 874 N A IL in 3 D351358 16 17 r 15 16 oO 0 534 0 003 0 979 0 979 iy im Sort 4 D351358 16 16 r 15 17 r I 0 505 0 004 N A 0 874 I e LL m Unsel 5 vWA 15 15 r 18 18 oO im 0 476 0 001 N A NJA B 6 vWA 15 18 r 15 18 n I N A 0 001 0 908 0 908 j L Missing Markers
69. d features of the Mixture Analysis Tool Mixture Analysis Methods A mixture analysis method contains Peak Height Ratio and Mixture Interpretation Threshold information The software uses this information to Segregate samples according to their contributor categories 1 2 or 3 or more contributors Determine the most likely genotypes of the individual contributors to a 2 person mixture during the extraction process You will learn how to create a mixture analysis method in Chapter 4 Segregate Samples Note Applied Biosystems recommends creating a set of mixture analysis methods that corresponds to the interpretation criteria developed by your laboratory based on internal validation studies Different mixture analysis parameters may be appropriate for data generated using different AmpFZSTR kits instrument platforms or for particular sample types 20 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 2 Understanding the Software wu Sample Segregation and Statistical Calculations Sample Segregation and Statistical Calculations The software segregates samples on the basis of the minimum number of contributors according to the following rules 1 Contributor single source Samples that Do not contain markers that fail the peak height ratio thresholds specified in the mixture analysis method and Contain a maximum of 1 marker with three called alleles are categorized as originating
70. ditional information on segregating samples and extracting individuals from 2 contributor mixtures GeneMapper ID X Software Version 1 1 Getting Started Guide 83 min Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results 84 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor This chapter covers B Overview iousess so E bn dat OO OE OR EU S 86 Getting Started E Step 1 Assign Known Genotypes 02 05 86 E Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor 92 Understanding the E Step 3 Calculate the Likelihood Ratio for 2 Contributor Software Mixtures Extracted with a Known Contributor 94 l Prepare for Mixture Analysis Segregate Samples J Analyze 2 Contributor Mixtures with Two Unknowns Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Analyze Merged Results GeneMapper ID X Software Version 1 1 Getting Started Guide 85 Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor a Overview Overview About Analysis of 2 Contributor Samples Where 1 contributor is Known In This Chapter In this chapter you will repeat the workflow described in Chapter 5 Analyze 2 Contribut
71. e 516 E 17 m BE 0 466 0 000 0 979 0 979 m m 2 D351358 15 17 r 16 16 r B 0 495 0 003 0 874 NjA gg m m s pasisse 1617 ri 15 16 r gi 0 534 0 003 0 979 0 979 a B BH Sort f t r fja 0351358 16 16 r 15 17 r Em 505 0 004 Na 0 874 ag m m e s pwa sis r 18 18 r Ip 0 476 0 001 na wa m m umee g vwa 15 18 r 15 18 m im N A 0 001 0 908 0 908 i B B Missing Markers 7 vwa 18 18 r 15 15 oO BE 0 524 0 009 nja w fs D165539 p10 r 12 12 r im 0 441 2 000 0 994 N A im B fg p165s39 10 12 r 9 12 l m lo 502 0 006 10 789 0 789 mE m m Unselected Genotype Combinations Fiter nQ WOAS Fiter on Known Match il Marker C1 Major Inconclusiys C2 Minor Inconclusiy Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ n Perse 5 16 r 17 F1 r im 0 272 0 072 0 545 0 213 e 2 D35138 16 17 n 15 F1 E L 0 304 0 075 0 476 0 186 le e d 3 D351358 t617 r 1515 r im Nja 0 085 10 476 NIA e e Em Is D351358 16 F1 r 15 17 r im 0 481 0 091 0 101 0 874 e zm s pss1s88 157 r 16 F1 r BI 0 519 0 094 0 874 0 101 e Select fe D351358 15 16 r 17 17 r M a 0 098 oss NIA e e 7 0351358 15 16 r 1517 im NIA 0 103 10 369 0 369 9 e Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Mext Frish 60 Gene
72. e Analysis you can perform sample segregation You will create a new mixture analysis method in which you will define the peak height ratio settings that are applied to different peak height ranges and the Mixture Interpretation Threshold You can then proceed with sample segregation using the mixture analysis method you have defined Note Applied Biosystems recommends creating a set of mixture analysis methods that correspond to the interpretation criteria developed by your laboratory based on internal validation studies Different mixture analysis parameters may be appropriate for data generated using different AmpF STR kits instrument platforms or for particular sample types In this chapter you will learn to Launch the Mixture Analysis Tool Import a population database Create a new mixture analysis method Segregate the samples into one of the three classification groups 1 contributor single source 2 contributors or 3 or more contributors GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples wu Step 1 Launch the Mixture Analysis Tool Step 1 Launch the Mixture Analysis Tool 1 Unless already open launch the GeneMapper D X Software Version 1 1 v1 1 Navigate to lt drive gt AppliedBiosystems GeneMapper ID X Example Data Mixture Analysis and select MA SGM 2 Select Tools gt Mixture Analysis Manager from the toolbar to open the Mixture Analysis Manager
73. e Combinations Unmerged select one panel to add per marker Filter by Marker all Run Folder Sample File Panel Marker C1 Major Inconclusiw C2 Minor Inconclusiv f f C Add Marker Notes Calculate Statistics Export Mixture Anal Samples Plot Cancel lt Back Next gt Finish Q When you are finished calculate statistics as shown in the following section Step 7 Calculate and Analyze the Results 106 1 Click Calculate Statistics 2 Inthe Population Database Selection dialog box select the African American population for the Applied Biosystems Identifiler User Manual database apply it to the current sample then click OK 3 Review and analyze the statistics for the composite profile GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results ea Step 7 Calculate and Analyze the Results 4 Click lt Back to return to the Mixture Analysis Results Viewer displaying the COfiler kit results 5 Deselect Sample Review Complete 6 Highlight the result for D3S1358 in Row 1 ofthe Selected Genotype Combinations table then click Unselect to move the genotype combination to the Unselected Genotype Combinations table as shown below Mixture Analysis Results Viewer Minimum Number of Contributors 2 nix Sample File H4 H28 1 3 007 DO5 fsa Panel COfiler v1X RunFolder MA CO Sample Name H4 H28 1 3 Previou
74. ecked Sample Review Complete where no known contributor was used but then went back and selected a known contributor to include during extraction 3 Click Yes GeneMapper ID X Software Version 1 1 Getting Started Guide 87 nn Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Step 1 Assign Known Genotypes 4 The sample is displayed in the Known column of the Mixture Analysis Sample Segregation by Minimum Number of Contributors table as shown s Mixture Analysis Sample Segregation by Minimum Number of Contributors Ioj x GeneMapper ID X Project Mame en resr 2 Contributors 1 Contributor 3 or More Contributors Extraction Status Review Status Run Folder Sample File Sample Name Mixture Analysis Methog Known n amp MA SGM H4 H28 1 1 003 B07 fsa H4 H28 1 1 MA Test Method H4_H28_1_0 f2 v MA SGM H4 H28 1 2 005 CO7 fsa H4 H28 1 2 MA Test Method None g Z MA SGM H4 H28 1 3 007 D07 fsa H4 H28 1 3 MA Test Method None 4 MA SGM H4 H28 1 5 009 E07 fsa H4 H28 1 5 MA Test Method None g Z MA SGM H4 H28 1 9 011 F07 fsa H4 H28 1 9 MA Test Method None 0 Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish Q Note A green I arrow appears in the Extraction Status column for sample H4 H28 1 1 indicating a change to the mixture analysis criteria Previous results will be lost unless you click No before proceeding with known genotype s
75. ecting the reference sample which under the prosecution s hypothesis H cannot be excluded as the contributor of the evidence profile Click the LR Statistics tab In this tab you can Define the hypotheses for calculating the Likelihood Ratio based on the extracted mixture results selected genotype combinations of both contributors to the mixture Calculate a Likelihood Ratio based on a major contributor only This approach can be used only when the minor contributor is uninterpretable and when the major component can be interpreted unambiguously Note Refer to Appendix A Statistical Analysis and Algorithms and the GeneMapper ID X Software Help for detailed statistics information The Use C1 Major Only check box is deselected by default When this box is unselected the software calculates Likelihood Ratios based on alternate hypotheses using both contributors to the mixture The hypotheses available are based on whether one or two references are incorporated into the prosecution s hypothesis GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns m Step 6 Calculate and Review Likelihood Ratio Results To calculate the Likelihood Ratio 1 Select a single reference by choosing Import from the Reference 1 drop down menu and navigating to the Known H28 txt file you saved earlier in Chapter 3 Step 5 Export and View a Known Genotype Profile o
76. elect one or a multiple set of hypotheses which are applicable to the two person mixture data 116 GeneMapper ID X Software v1 1 Getting Started Guide Appendix A Statistical Analysis and Algorithms m s Statistical Approaches mn The Likelihood Ratios are calculated based on the extracted data results that is only those genotype combinations included in the Selected Genotypes Combinations table will be used in the Likelihood Ratio calculation GeneMapper ID X Software v1 1 Getting Started Guide 117 ww Appendix A Statistical Analysis and Algorithms mH Statistical Approaches 118 GeneMapper ID X Software v1 1 Getting Started Guide Bibliography Gill P et al Interpreting simple STR mixtures using allele peak areas Forensic Sci Int 1998 91 1 41 53 GeneMapper ID X Software v1 1 Getting Started Guide 119 Bibliography 120 GeneMapper ID X Software v1 1 Getting Started Guide Symbols 15 A ADBI definition 9 adding samples to projects 27 99 allele frequency definition 9 amplification results combining different results 99 analysis method importing 28 100 analysis samples reviewing 33 saving 33 segregating 51 analysis summaries reviewing 31 analyzing data 29 analyzing merged results 101 106 Applied Biosystems contacting xi customer feedback on documentation x Information Development department x Technical Support xi assigning genotypes 86 assumptions for using this guide vii
77. elected Genotype Combinations Table D163539 Close Help 62 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns m Step 3 Determine Genotype Combinations to Include in Statistical Calculations 5 Review the data contained in the Unselected Genotype Combinations table All possible genotype combinations show either a yellow or a red re IQ flag These combinations were not automatically selected by the software because they failed to meet one or more criteria Note You can also filter both tables according to IQ status by clicking a Filter on IQ icon Fiter n E Step 3 Determine Genotype Combinations to Include in Statistical Calculations Review First 1 Select sample H4 H28 1 3 from the drop down menu Sample 2 Click the Samples Plot button then OK in the popup dialog box that explains the editing functions to view the electropherogram for mixture sample H4 H28 1 3 The editing functions are disabled for the Mixture Analysis Tool Sample Plot however other functions such as the Plot Setting Editor tables and viewing functions are enabled 3 Select the following icon on the Samples Plot to display the Mixture Analysis Selected Genotype Combinations table below the Sample Plot k A 9 Mixture Analysis Selected Genotype Combinations Table 4 Select 2 in the Panes drop down list to simultaneously view the electropherogram infor
78. election 5 Select the Known column header to highlight the column press Ctrl D to apply fill down the known to all samples then click Yes when the Review status message is displayed for each sample 6 Click Next gt to proceed with extraction of the mixtures with consideration of the selected known contributor The Mixture Analysis Results Viewer displays sample H4 H28 1 1 88 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor v Step 1 Assign Known Genotypes Review Extraction 1 Review the Selected Genotype Combinations table The bright Results green highlighting indicates that the known genotype profile exactly matches across all markers the extracted genotype combinations of 1 contributor to the mixture The bright yellow highlighting indicates the extracted genotype combinations of the unknown contributor to the mixture The software uses the known genotypes to further filter the table and only displays combinations that have passing IQ status and contain the known genotype Mixture Analysis Results Viewer Minimum Number of Contributors 2 nl x Sample File H4 H28 1 1 003 B07 fsa Panel SGM Plus vix Run Folder MA sGM Sample Name lt lt Previous Sample Next Sample gt gt BeBe Average mx 0 456 Residual Threshold 0 040 Filter by Marker All v Known H4 H28 1 0 Known Match C1 Major Sample Review Com
79. es The Mixture Analysis Results Viewer contains two data tables to aid in the review of the extraction results Information Found in Tables The data appearing automatically in each table are determined by the GeneMapper ID X Mixture Analysis Quality Value System The system assists with review and interpretation of the data produced through the genotype extraction process The system assesses each possible genotype combination to determine whether the following thresholds are met The peak height ratio PHR thresholds set in the Mixture Analysis Method The peak height ratio settings were described in Chapter 3 Prepare for Mixture Analysis when the mixture analysis method was created and The residual threshold specified by the software The residual is a measure of how close the minor contributor proportion for a particular genotype combination is to the expected minor contributor proportion for a particular profile The combination of the above measures determines the inclusion quality IQ value assigned to the genotype combination The PQV results of these quality assessment tools are displayed using the same color coded flags B A amp as employed by the GeneMapper ID X Software during data analysis The color of the flag depends on software specified thresholds or user defined thresholds set in the mixture analysis method Genotype combinations with a passing green IQ are automatically assigned to the Selecte
80. for each contributor profile F Allele An allele designation used to indicate the potential for allelic dropout In the Mixture Analysis tool an F allele is included in a genotype combination if detected peaks are sufficiently low that a potential heterozygous partner to one of the detected peaks could exist below the Mixture Interpretation Threshold MIT within the constraints of the Peak Height Ratio PHR settings Filtering The process of identifying eligible samples in the GeneMapper D X Software project to prevent ineligible samples from being imported into the Mixture Analysis tool Genotype Combination A pair of genotypes that could represent the two individual contributors to a 2 person mixture sample Genotype Frequency A column in the Mixture Analysis Results Viewer RMP Statistics Details table Also the relative occurrence of a particular genotype in a given population 10 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started ia Glossary of Terms Term Definition Genotype Profile Allele designations for all markers of a single source sample or an individual contributor to a mixture sample Heterozygote Individual with two different alleles at a particular marker locus Homozygote Individual with one allele at a particular marker locus Hypothesis See Likelihood Ratio Inconclusive A designation given to a marker f
81. from a single source 2 Contributors Samples that contain lor more 2 peak markers failing peak height ratio thresholds 3or more alleles at 2 or more markers with the maximum number of alleles not exceeding 4 are categorized as originating from a minimum of 2 contributors 3or more Contributors Samples that contain 1 or more markers with more than 4 alleles are categorized as originating from a minimum of 3 contributors The following table details the statistical options available for each of the three categories of samples 1 Contributor Single source 2 Contributors 3 or More Contributors Random Match Probability X X RMP Combined Probability of X X Inclusion Exclusion CPI CPE Likelihood Ratio LR X X For additional information refer to Appendix A Statistical Analysis and Algorithms and to the GeneMapper ID X Software Help GeneMapper D X Software Version 1 1 Getting Started Guide wu Chapter 2 Understanding the Software Population Databases Population Databases For the software to perform statistical calculations it requires population databases that contain the appropriate allele frequency information Three ready to use population databases are provided by Applied Biosystems to use with the Mixture Analysis Tool You can import these databases and or create and import custom databases based on your own allele frequency data Refer to Chapter
82. given marker Minimum Allele Frequency Value used in statistical analysis of DNA profiles representing either alleles not present in the population database or alleles that have an observed allele frequency below the calculated minimum allele frequency Calculated using the following formula Minimum allele frequency 5 2n where n number of samples for each marker in the ethnic population Minor Contributor See C2 Minor Missing Markers Markers that are present in the mixture sample but are not represented in the Selected Genotype Combinations table or the known genotype profile MIT Mixture Interpretation Threshold A user defined setting in the mixture analysis method Also the minimum peak height threshold used for mixture analysis 12 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started Glossary of Terms Term Definition Mixture Sample containing DNA from two or more contributors Mixture Analysis The process of identifying the minimum number of possible contributors to a mixture sample from data produced using a single AmpFZSTR panel extracting the potential genotypes of the contributors 2 person mixtures only and performing statistical analysis Mixture Analysis Merged Results The process of identifying the minimum number of possible contributors to a mixture sample from data produced using one or more AmpF STR
83. he GeneMapper ID X Software Help GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results Em Combine Different Amplification Results Combine Different Amplification Results To combine results from different amplifications of the same sample you must create a new project containing the sample files for each amplification of the same sample IMPORTANT Different amplifications of the same sample MUST have the same sample name in order to use the merge function The following procedures are based on the sample data provided See Using this Guide for Mixture Analysis on page 6 for additional information Step 1 Create a New Project and Add Samples T If a project is currently opened select File New Project to open a blank project If prompted to save changes to an existing project save any necessary changes or click No In the Project window select Edit Add Samples to Project Ctrl K Navigate to lt drive gt Example Data Mixture Analysis Samples select the MA_PP folder then click Add to List in the lower left hand side of the window to add the sample files to the project Add the sample files in the MA_CO folder using the same process then click Add when you are finished adding samples to the project list From the Table Setting drop down list in the Project window select 31XX Data Analysis Cy BG amp treble setting J fS6QA De i
84. hod 222055 28 Step 3 Analyze Data Using Appropriate Settings 29 Step 4 Review Analysis Results lllelselesess 31 Review Analysis Summaries 0 00 0 eee ee ees 31 Review and Save Samples 200000 eee eee 33 Step 5 Export and View a Known Genotype Profile 35 Select Samples for Viewing 00 eee eee ees 35 Export the Table 0 0 000 cece ee 38 Chapter 4 Segregate SamplesS 000 cece eee eee eee 41 OVERVIEW 1 a ns RENE Ln a Aa dec ane E 42 About Sample Segregation 00 e eee eee 42 In Fis Chapter mir Einte Eug Ue px Ebor nim 42 Step 1 Launch the Mixture Analysis Tool 43 Step 2 Import a Population Database 43 Step 3 Create a New Mixture Analysis Method 45 Create a Mixture Analysis Method using the Mixture Analysis Manager cec oe tee nea ge ie EUG E E NEEE UP 45 Apply a Mixture Analysis Method to Samples 49 Create an MA Method using the Column Drop Down Method Alternate Method lssllllleeleeelllleen 50 Step 4 Segregate the Samples 000002 eee eee 51 iv GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns eeeeeeles 55 OVervIe W oet obe ep PEN ES CY RR URDU ae EROR VUE RU NUES 56 About Analysis of 2 Contributor Samples Where Both Contributor
85. i GeneMapper ID X Software Version 1 1 Getting Started Guide 99 E Chapter 7 Analyze Merged Results Step 2 Import an Analysis Method Step 2 Import an Analysis Method Analysis methods define the peak detection sizing genotyping and quality assessment parameters applied during analysis of sample data In this step you will import the analysis method configured specifically for use with the GeneMapper D X Software example data provided using the procedures outlined in this guide IMPORTANT The values used in this guide may not be suitable for analyzing data generated in your laboratory You must optimize and validate these values as part of an internal validation study In the GeneMapper D X Project window 1 2 Select Tools gt GeneMapper ID X Manager In the Analysis Methods tab select Import Navigate to lt drive gt AppliedBiosystems GeneMapper ID X Example Data Mixture Analysis GSG Analysis Method and select HID Full Range 75 Click OK in the Choose Security Group dialog box to confirm the GeneMapper D X Security Group then click Done Step 3 Analyze Samples 1 100 Define each sample from left to right as shown in the Samples table below a Assign the Sample Type to each sample b Select the Analysis method HID Full Range 75 c Select the Panel Profiler Plus v1X or COfiler v1X d Select the Size Standard CE_F_HID_GS500 75 450 GeneMapper D X Software Version 1
86. ical analysis Genotype combinations are assigned to this table automatically if they were not assigned a passing ig Inclusion Quality IQ during extraction of contributors GeneMapper ID X Software Version 1 1 Getting Started Guide 17 Chapter 1 Getting Started Glossary of Terms 18 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 2 Understanding the Software This chapter covers B Overview seeseesee RR 20 Getting Started E Sample Segregation and Statistical Calculations 21 E Population Databases 0 eens 22 Chapter 2 B Example Data 2 0 cece ene 22 Understanding the Software Prepare for Mixture Analysis Segregate Samples i Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Contributor Mixtures with One Known Contributor i Analyze Merged Results GeneMapper D X Software Version 1 1 Getting Started Guide 19 wu Chapter 2 Understanding the Software Overview Overview About the The software performs a number of functions that require setup by Software the user This chapter describes these functions In This Chapter In this chapter you will learn how the software Uses mixture analysis methods Segregates samples and calculates statistics Uses population databases for statistical calculations Usesexample data to demonstrate the functionality an
87. ink below to display a filtered Samples Table containing only the samples selected Allelic Ladder Quality per run folder based on SQ and CGQ only MA PP I o o Control Quality per project based on sample PQVs SOS SSPK MIX OMR SQ CGQ Control Type Total of Samples All thresholds met One or more thresholds not met Negative Control Total Imo Hem oj ojojo Sample Quality per project based on sample PQVs SOS SSPK MIX OMR SQ CGQ Hound Total of Samples BB All thresholds met One or more thresholds not met Samples 6 3 3 4 Inthe Analysis Summary under Sample Quality per project select the 6 samples from the Total of Samples column to display a filtered samples table that enables edit and review of all the samples 5 Highlight all sample rows in the table then click the Display Plots icon in the tool bar to review the data and verify that there are no off ladder OL only allele labels 6 Close the Samples Plot 102 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results E Step 4 Prepare for Mixture Analysis Step 4 Prepare for Mixture Analysis 1 In the samples table select Tools Mixture Analysis 2 In the Mixture Analysis Method column select MA Test Method for all samples and click Select All Mixture Analysis Sample Selection Select Samples and Mixture Analysis Methods
88. is Workflows The GeneMapper ID X Software flowchart summarizes the steps for performing a typical data analysis workflow using the GeneMapper ID X Software To the left are the steps the user performs when analyzing samples and interpreting results To the right are the software operations that occur automatically during analysis The Mixture Analysis flowchart that follows summarizes the steps for performing mixture analysis using the GeneMapper ID X Software GeneMapper ID X Software Workflow Set up the software one time 1 Create an analysis method 2 Set Project Options CE 0 Create a project 1 Add samples 2 Apply analysis settings 3 Start analysis Review analysis workflow summaries Optional Analysis Requirements Summary Optional Allelic Ladder Analysis Summary Analysis Summary Review and edit required samples Optional Perform secondary analysis Usethe profile comparison tool Export known genotypes for use in mixture analysis Use the Mixture Analysis tool next pg Optional Report results 1 Generate a custom report 2 Export reports and tables 3 Print During analysis the software performs Analysis requirements check Peak detection and sizing Allelic ladder quality assessment Genotyping Sample quality assessment Analysis summary generation Based on your lab protocol
89. jay d d 4 VWA 0 088 0 009 0 975 N E B d 5 VWA 0 046 0 027 0 975 NJA EE B 5 Check the Sample Review Complete box to indicate that this sample is ready for statistical analysis The Sample Workflow Completion dialog box is displayed Sample Workflow Completion x The statistical results for the selected sample are calculated based on the current genotype combination and population database selections and are not saved once you exit the Mixture Analysis Results Viewer Do you want to export the statistical results for the selected sample now w 6 Click No Note You will calculate statistics in Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor 7 Select Next Sample gt gt to review the next sample extracted with the known Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor 1 Click Calculate Statistics 2 Inthe Population Database dialog box select the African American population for the Applied Biosystems Identifiler User Manual database apply it to the current sample then click OK 92 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor wu Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor 3 Verify and note that the RMP statistic is only
90. ll amp zm 4 D351358 16 17 r 15 15 r B us 0 140 0 251 N A e amp 5 D351358 15 17 r 16 16 O Bb ia 0179 oja e Select 6 D351358 16 17 r rA r E 0 424 0 179 0 251 1218 e 7 D351358 16 17 D 15 16 r B 0 767 0 182 0 926 0 9268 Bm Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next gt Finish 7 Mark Sample Review Complete and select Next gt 8 Click No in the Sample Workflow Completion dialog box then select Next gt GeneMapper ID X Software Version 1 1 Getting Started Guide 107 Chapter 7 Analyze Merged Results Step 7 Calculate and Analyze the Results 9 View the Mixture Analysis Merged Results Viewer as shown next The Merged Results Viewer now displays the discordant results obtained for D3S1358 using the COfiler and Profiler Plus kits Mixture Analysis Merged Results Viewer zjali Sample Name Mixture Analysis Results En Statistics CT Major Rire Statisuics Ge minor GANGFE aie meaig l Bee Known None Selected Genotype Combinations Merged includes markers automatically added from one or more panels Run Folder Sample File Panel Marker C1 Major Inconclusi C2 Minor Inconclusiys Ifi Multiple lt Multiple gt AMEL EN r XN r 2 MA CO H4 H28 1 3 007 COfiler vix CSFIPO 1112 r 9 11 r 3 MA PP H4 H28 1 3 007 Profler Plus vIX D135317 8 9 ri 11 11 O 4
91. llleee ellen 86 In This Chapter ai ana aa a es 86 Step 1 Assign Known Genotypes 00 02s eee eee 86 Select Known Contributors 02 00000 eee eee 86 Review Extraction Results 0000002e eee eeee 89 GeneMapper ID X Software Version 1 1 Getting Started Guide V Chapter 7 Appendix A vi Step 2 Calculate the Random Match Probability for 2 Contributor Mixtures Extracted with a Known Contributor 92 Step 3 Calculate the Likelihood Ratio for 2 Contributor Mixtures Extracted with a Known Contributor 94 Analyze Merged Results L 97 OVEIVICW x uui iso rude fe Pte Dew DE PT Rite 98 Combine Different Amplification Results 99 Step 1 Create a New Project and Add Samples 99 Step 2 Import an Analysis Method 2 45 100 Step 3 Analyze Samples 000 00 eee eee 100 Step 4 Prepare for Mixture Analysis llle lll 103 Step 5 Segregate Samples and Review Profiles 104 Step 6 View Merged Results 00 eee 105 Step 7 Calculate and Analyze the Results 106 Statistical Analysis and Algorithms 111 OVOLVIGW Cauet uis ears Pad sint ue Eee sd die e qu Ree 112 Statistical Approaches 000 cee selle 113 Random Match Probability 000 eae 113 Combined Probability of Inclusion Exclusion 114 Likelihood Ratio
92. llow sizing quality SQ flags and no off ladder OL only allele labels are eligible for mixture analysis Unanalyzed samples controls allelic ladders and samples that fail sizing or have no allele labels are not eligble Categorizes and segregates eligible samples by the minimum number of contributors contained in each sample 1 2 or 3 or more contributors 2 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started a What s New in the GeneMapper ID X Software The Mixture Analysis Tool Extracts and separates contributor profiles into individual major and minor genotype combinations for all markers present 2 contributors only Filters known profiles from selected sample profiles 2 contributors only Calculates statistics using population databases stored in the Mixture Analysis Manager Displays a ranked set of possible genotype combinations to facilitate interpretation Refer to Chapter 2 Understanding the Software for an overview of the software functions and to learn how to access the example data files for use with the Mixture Analysis Tool tutorial For more detailed information refer to Appendix A Statistical Analysis and Algorithms and to the GeneMapper ID X Software Help GeneMapper D X Software Version 1 1 Getting Started Guide 3 m Chapter 1 Getting Started GeneMapper ID X Software Mixture Analysis Workflows GeneMapper ID X Software Mixture Analys
93. lus Kit example data 22 sample files 22 project creating 27 99 Q quality value system mixture analysis 58 R Random Match Probability calculating 71 92 calculating 2 contributor mixtures 92 calculating known contributor 92 heterozygous genotype frequencies 113 homozygous genotype frequencies 113 reviewing 71 reviewing calculation results 72 statistical approach 113 residual status definition 15 residual threshold definition 15 RMP definition 15 tules of sample segregation 4 S sample analysis unknown contributors 56 sample analysis merged samples 101 sample files COfiler Kit 22 how to use 22 Profiler Plus Kit 22 SGM Plus Kit 22 sample segregation 1 contributor 53 2 contributors 52 104 3 or more contributors 54 definition 15 tules 4 segregating analysis samples 51 Selected Genotype Combinations table 15 59 reviewing extraction results 89 selecting genotypes 68 SGM Plus Kit example data 22 sample files 22 software calculating statistics 20 features 2 locating example data 20 mixture analysis workflow 5 segregating samples 20 using example data 20 using mixture analysis methods 20 using population datases 20 what s new 2 statistical analysis 2 contributor mixtures 56 86 known contributors 86 unknown contributors 56 statistical approaches Combined Probability of Inclusion and Exclusion 114 Likelihood Ratio 115 Random Match Probability 113 statistical calculations 1
94. lyzed 0 Analyzed 13 X Ur Analysis Setting Changed 0 Click a link below to display a filtered Samples Table containing only the samples selected Allelic Ladder Quality per run folder based on SQ and CGO only Control Quality per project based on sample PQVs SOS SSPK MIX OMR SQ CGQ Control Type Total of Samples i All thresholds met e 9 One or more remote not met Positive Control Custom Control Negative Control Total o I p ope Im op ojo Sample Quality per project based on sample PQVs SOS SSPK MIX OMR SQ CGQ PY Total of Samples All thresholds met e One or more thresholds not met Samples 10 2 8 Note If you did not set up the Samples tab in the GeneMapper ID X Project window correctly the Analysis Requirements Summary may display first Review the reason s why the analysis requirements are not met and correct them to proceed with the analysis For additional information refer to the GeneMapper ID X Software Help GeneMapper ID X Software Version 1 1 Getting Started Guide 31 Fu Chapter 3 Prepare for Mixture Analysis Step 4 Review Analysis Results View Tools Admin Help To review the data 1 In the Analysis Summary under Sample Quality per project select the 10 from the Total of Samples column shown above to display a filtered Samples Table that allows access to all the samples for editing and review
95. mation and the table GeneMapper ID X Software Version 1 1 Getting Started Guide 63 V Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 3 Determine Genotype Combinations to Include in Statistical Calculations 5 Select Filter by Marker D3S1358 to the right of the Selected Genotype Combinations table to filter the results as shown Note You can also highlight the genotype combinations corresponding to a particular marker without filtering the table by clicking on the marker header bar for that marker sf SGM_TEST Samples Plot F 1o x File Edit View Plots Tools Alleles Help amp Plot Setting Data Interpretation Panes 2 s Baran Guu mm E Gi HR o mS A RA Sample File Sample Name SOS SQ SSPK mix ome cea H4_H28_1_3_007_DO7fsa UT 22 9 i12 17 512 1885 1237 830 273 10 1623 H4 H28 1 3 007 D07 fsa H4 H28 1 3 ry e 75 115 155 135 235 275 315 355 395 435 2000 1000 o 4 m 4 4 re x 10 t3 ho 33 2 12 fis 2541 353 420 2624 352 411 1487 Y 14 13 351 2023 1050 lie is Ir Resi Marker __ C1 Major InconciusiwiC2 Minor Inconclusiy Known Senotymg aDe Mx
96. mple Selection r Select Samples and Mixture Analysis Methods Selected Mixture Analysis Status Run Folder Sample File Sample Name Mixture Analysis Method 1 Vv MA SGM AA18 010 EO8 fsa aars 2 Vv t MA SGM AA19 004 BO8 fsa AA19 3 v MA SGM H4 H28 0 1 001 AQ7 fs H4 H28 0 1 4 v amp MA_SGM H4 H28 1 0 013 G07 fs H4 H28 1 0 5 Vv amp MA SGM FM H28 1 1 003 B07 fe H4 H28 1 1 6 Iv amp MA SGM H4 H28 1 2 005 CO7 fs H4 H28 1 2 7 Iv amp MA_SGM H4 H28 1 3 D07 DO7 fs H4 H28 1 3 8 Iv amp MA_SGM H4_H28_1 5 009 E07 fe H4 H28 1 5 9 Vv amp MA_SGM H4 H28 1 9 01 1 F07 fs H4 H28 1 9 10 Vv MA SGM FM H28 AA18 1 1 2 OQ H4 H28 AAI8 1 12 Select All Select All Analyzed Samples Select All Unanalyzed Samples Clear All 10 out of 10 samples analyzed in Genemapper ID X loaded successfully sample Details Cancel S Back Next gt Finish 9 1 Click Next gt then click each of the contributor tabs to review the results of the sample segregation process as follows GeneMapper ID X Software Version 1 1 Getting Started Guide 51 Chapter 4 Segregate Samples Step 4 Segregate the Samples 2 Review the 2 Contributors tab results 5 samples were segregated as mixtures with a minimum of 2 contributors s Mixture Analysis Sample Segregation by Minimum Number of Contributors GeneMapper ID X Project Mame en esr 2 Contributors 1 Contributor 3 or
97. mples Plot Cancel Back Next gt Finish 4 Select the CPI CPE Statistics tab to display the Combined Probability of Inclusion Exclusion This statistic incorporates the entire complement of alleles present and does not change when you use a known contributor in the extraction process GeneMapper ID X Software Version 1 1 Getting Started Guide 93 nam Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Step 3 Calculate the Likelihood Ratio for 2 Contributor Mixtures Extracted with a Known Contributor Step 3 Calculate the Likelihood Ratio for 2 Contributor Mixtures Extracted with a Known Contributor 1 Select the LR Statistics tab Note that the known reference that you used in the extraction is already selected as Reference 1 s Mixture Analysis Results Viewer Minimum Number of Contributors 2 P Inl x Sample File H4 H28 1 3 007 D07 fsa Panel SGM Plus vix RunFolder MA saM Sample Name Ha poo 3 X Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major FP Statistics C2 Minor CPIJCPE Statistics LR Statistics is kelihood Ratio LR Calculation LR Statistics Summary LR Pr E Hp Pr E Hd where Pr probability E evidence pipebar given Hp prosecution hypothesis Hd defense hypothesis LR Analysis Summary sample H4 H28 1 3 analyst gmidx Reference Sample s select one or more
98. n 1 1 Getting Started Guide Appendix A yu otatistical Analysis and m Algorithms This appendix covers B Overview elssslese I eens 112 B Statistical Approaches 00 0 lesen 113 111 GeneMapper D X Software v1 1 Getting Started Guide we Appendix A Statistical Analysis and Algorithms Overview Overview This appendix provides supplemental information on Random Match Probability Combined Probability of Inclusion Exclusion Likelihood Ratio Refer to the GeneMapper ID X Sofiware Help for more detailed information regarding the statistical calculations performed in the software 112 GeneMapper D X Software v1 1 Getting Started Guide Appendix A Statistical Analysis and Algorithms ww Statistical Approaches m Statistical Approaches A The software incorporates three different statistical calculations into the Mixture Analysis Tool Random Match Probability Combined Probability of Inclusion Exclusion and Likelihood Ratio All rely on allele frequency data obtained from user selectable population databases that reside within the software Analysts can make use of the default population databases supplied with GeneMapper JD X Software v1 1 or they can import their own population database information to create new selections Random Match The software calculates Random Match Probabilities for those Probability samples categorized as single source and for the individual contributors res
99. n page 35 Note When you select the reference it does not display the exported file name Instead it displays the original sample name taken from the sample file IMPORTANT If you import a new known genotype containing the same name as one that currently exists in the Mixture Analysis tool and there are marker conflicts same name different alleles no markers from the new known genotype profile are imported the existing known genotype profile remains unchanged If there are no marker conflicts same name same alleles then all markers from the new known genotype profile that do not occur in the existing known genotype profile are added to that profile 2 In the Known Genotypes dialog box click OK When you select a single reference one hypothesis is displayed 3 Check the box to the left of the hypothesis to display the Likelihood Ratio Statistics Summary as shown next GeneMapper ID X Software Version 1 1 Getting Started Guide 75 E Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results s Mixture Analysis Results Viewer Minimum Number of Contributors 2 Bl xl Sample File H4 H28 1 5 009 EO7 fsa Panel SGM Plus v1X Run Folder MA SGM Sample Name H4 H28 1 5 lt lt Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major RMP Statistics C2 Minor CPI CPE Statistics LR Statistics
100. ng Started Guide 53 wu Chapter 4 Segregate Samples Step 4 Segregate the Samples 4 Review the 3 or More Contributors tab 1 sample was identified by the software as containing 3 or more contributors s Mixture Analysis Sample Segregation by Minimum Number of Contributors ioj x GeneMapper ID X Project Mame peer 2 Contributors 1 Contributor 3 or More Contributors Run Folder Sample File Sample Name Mixture Analysis Method 1 IA SGM H4 H28 AA18 1 1 2 002 AO8 fsa H4 H28 AAI8 1 1 MA Test Method Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish IMPORTANT Saved sample segregation results are overwritten when you reanalyze a sample 5 Go back to the 2 Contributors tab and continue to Chapter 5 to extract 2 contributor mixtures Refer to the GeneMapper ID X Software Help for additional information on segregating samples 54 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 5 Getting Started Soft Understanding the ware Prepare or Mixture Analysis Segregate Samples Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Mixtures with One Known Contributor Contributor Analyze Merged Results Analyze 2 Contributor Mixtures with Two Unknowns This chapter covers OVerVIeW cies ges e x E Re IRI Ee 4 a Ex 56 Step 1 Extract Individual Genotypes
101. ns 8 Close the Samples Plot GeneMapper ID X Software Version 1 1 Getting Started Guide 39 wu Chapter 3 Prepare for Mixture Analysis Step 5 Export and View a Known Genotype Profile 40 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Getting Started Understanding the Software Prepare for Mixture Analysis Chapter 4 Segregate Samples Analyze 2 Contributor Mixtures with Two Unknowns Analyze 2 Contributor Mixtures with One Known Contributor i Analyze Merged Results oegregate Samples This chapter covers B Overview sssesleeee RI Ie 42 BW Step 1 Launch the Mixture Analysis Tool 43 E Step 2 Import a Population Database 43 E Step 3 Create a New Mixture Analysis Method 45 E Step 4 Segregate the Samples 0 0 0000 51 GeneMapper D X Software Version 1 1 Getting Started Guide 41 Chapter 4 Segregate Samples wu Overview Overview 42 About Sample Segregation In This Chapter This chapter describes how to select and launch the Mixture Analysis tool from the Tools menu select a population database select and segregate samples and define mixture analysis methods You will create a new mixture analysis method during this process Once you complete the preliminary preparation for Mixture Analysis described in Chapter 3 Prepare for Mixtur
102. on of contributors GeneMapper ID X Software Version 1 1 Getting Started Guide 15 mm Chapter 1 Getting Started Glossary of Terms Term Definition Single Source Sample In the Mixture Analysis tool samples originating from only 1 contributor Defined as samples that contain No markers that fail the peak height ratio PHR thresholds specified in the mixture analysis method and e Only one marker with three called alleles Random Match Probability and Likelihood Ratio calculations can be performed on single source samples following sample segregation Statistical Analysis The process of calculating statistics Random Match Probability Combined Probability of Inclusion Combined Probability of Exclusion Likelihood Ratio for a DNA profile Note The Mixture Analysis tool excludes the Amelogenin AMEL marker from all statistical analyses Statistical Analysis Options 1 Contributor Column in the Mixture Analysis Results Viewer Minimum Number of Contributors 1 1 Contributor Results tab Displays the genotype frequency calculation options available for use in Random Match Probability RMP statistical analysis of 1 contributor samples Note The Mixture Analysis tool excludes the Amelogenin AMEL marker from all statistical analyses RMP CPI CPE LR The following marker specific genotype frequency calculation options are available based on allele number One allele U
103. onclusive Minor box relating to any one of the D3S1358 possible genotype combinations in the Selected Genotype Combinations table Mixture Analysis Results Viewer Minimum Number of Contributors 2 ioj xi Sample File H4 H28 1 5 009 E07 fsa Panel SGM Plus vix Run Folder MA SGM Sample Name H H28 1 5 Previous Sample Next Sample gt gt Mixture Analysis Results irae Statistics Cl Major AMP statistic Tren eeepc roe EE BR BE average Mx 0 140 Residual Threshold 0 040 Filter by Marker x Known None Sample Review Complete Selected Genotype Combinations Marker C1 Major Inconclusiyg C2 Minor InconclusiwKnown Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 D351358 15 16 n 1217 Iv 0 103 0 002 0 994 N A L 2 D351358 15 16 Dn 16 17 I Bp 0 187 0 004 0 909 0 809 T 3 D351358 15 16 rH 1517 Vv 0 187 0 004 0 817 0 817 a ILI Sort 4 VWA 15 18 r 15 18 D BE wa joo 0 912 0 912 L m E Ly S5 wA si 5A Fr HB 0 102 jo 001 0 985 0 985 m BH NI 6 wwa 518 m FLF2 m 0 098 0 003 0 912 NjA m B Missing Markers 7 VWA 15 18 r 15 15 r BE wA oo wa wA i B 8 wa ms r per m Bp 0 094 0 007 0 826 0 626 I L m 3 YWA 15 18 L FLFL L EH 0051 0013 0 912 N A E pr m Unselected Genotype Combinations Fiter on 1Q NH EX Fiter on Known Match i
104. ontributors to the mixture are known 76 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns E Step 6 Calculate and Review Likelihood Ratio Results 4 Select a second reference In the Reference 2 drop down field click Import navigate to the location where you saved the Known H4 txt file as shown in Chapter 3 Step 5 Export and View a Known Genotype Profile on page 35 then select Import 5 In the Known Genotypes dialog box click OK When you select two references multiple hypotheses are displayed 6 Check the boxes to the left of the hypotheses to display the Likelihood Ratio Statistics Summary as shown next s Mixture Analysis Results Viewer Minimum Number of Contributors 2 Sample File H4 H28 1 5 009 E07 fsa Panel SGM Plus vix Run Folder MA SGM Sample Name H4 H28 1 5 X lt lt Previous Sample Next Sample gt gt Mixture Analysis Results l RMP Statistics C1 Major l RMP Statistics C2 Minor CPI CPE Statistics LR Statistics likelihood Ratio LR Calculation LR Statistics Summary LR Pr E Hp Pr E Hd where Pr probability E evidence pipebar given Hp prosecution hypothesis LR Analysis Summary Hd defense hypothesis sample H4 H28 1 5 analyst gmidx Reference Sample s select one or more Use C1 Major Only Reference 1 H4 H28 0 1 Reference 1 H4 H
105. or Mixtures with Two Unknowns but this time a known reference will be used to further refine the selected genotype combinations You can use this method when one known contributor to an evidence sample can be reasonably assumed to be present For example from an intimate vaginal sample it is reasonable to assume that the DNA taken from the female is present on the swab In such cases the known contributor is subtracted from the selected genotype combinations following extraction leaving the possible profiles for the unknown contributor In this chapter you will learn to Assign known genotypes Extract individual genotypes of two possible contributors of a two person mixture where 1 contributor is known Determine which genotype combinations to include in the statistical calculations Calculate Random Match Probability RMP for the unknown contributor Calculate and review Likelihood Ratio results Step 1 Assign Known Genotypes 86 Select Known Contributors 1 Select the 2 Contributors tab in the Mixture Analysis Sample Segregation dialog box After conducting the review processes in Chapter 5 Step 2 Review the Results of the Extraction on page 58 the Review Status column should indicate that all samples were reviewed 2 Click in the Known column adjacent to sample H4 H28 1 1 and select H4 H28 1 0 from the drop down list This sample was previously imported in Chapter 5 Step 6 Calculate and
106. or which the genotype cannot be determined with certainty In the Mixture Analysis tool inconclusive markers are not included in statistical analysis IQ Inclusion Quality A column in the Mixture Analysis Results Viewer Genotype Combinations tables Also a composite quality flag that indicates the Peak Height Ratio PHR Status and the Residual Status for genotype combinations Known Filtering The process whereby a known genotype is used to reduce filter the list of genotype combinations extracted from a 2 person mixture sample to display only those combinations that also match the known genotype profile In the Mixture Analysis tool the genotype combinations of the contributor with the best match to the known contributor are displayed in the Genotype Combinations tables of the Mixture Analysis Results Viewer Where a known genotype is used during the extraction process only the Selected Genotype Combinations associated with the unknown contributor to the mixture sample are included in statistical analysis Known Genotype Profile Genotype of a reference sample used for comparison to a mixture sample where a known genotype is inferred for example an intimate body swab sample In the Mixture Analysis tool the known genotype profile is matched to one of the contributor profiles extracted from a 2 person mixture sample and is used to filter the genotype combinations tables to display only those combinations that
107. plete Mixture Analysis Results ir lt Heer cT Major l RMESE AeA n GPICPE Statistics URISE r Selected Genotype Combinations Marker ct Majori Inconclusiyg C2 Minor Inconclusis Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status 1Q 1 r r Bp 0534 o 003 0 979 0 979 I di B 2 VWA r r BE wA 0001 0 908 0 908 I B B 3 D165539 O r 0 498 0 006 0 789 0 789 iB Sort 4 D251338 r r 0 538 0 005 0 866 0 866 I di B eum 5 AMEL r r BE wA ooo mwa Na NN B _ e 6 D851179 O r in 0 477 0 004 0 715 N A in i Missing Markers 7 pasm r r BE w joo mwa Na Nj B 8 D18551 r n 0 488 0 001 0 917 0 917 i i i 9 D195433 Im m EH N A 10 000 inja inja Ni Ir Unselected Genotype Combinations Fiter on 1Q WAE Fiter on Known Match B Marker C1 Major Inconclusiw C2 Minor Inconclusis Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ r 0 466 0 000 0 979 0 979 1616 16 17 0 495 0 003 0 874 N A D351358 16 16 15 17 16 17 D351358 351358 351358 351358 0 505 0 004 N A 0 874 0 272 0 072 0 545 0 213 0 304 0 075 0 476 0 186 N A 0 085 0 476 NjA 0 481 0 091 0 101 0 874 ss oO al a oO n
108. pper ID X Software Version 1 1 Getting Started Guide 45 wu Chapter 4 Segregate Samples Step 3 Create a New Mixture Analysis Method New Mixture Analysis Method x Mixture Analysis Method Name Method Description Heterozygote Peak Height Ratio PHR Settings Min Peak Height RFU Max Peak Height RFU PHR Threshold 150 0 4000 300 0 5400 1000 0 6300 99999 0 7500 New Delete Mixture Interpretation Threshold Minimum Peak Height RFU 150 Factory Defaults Save Cancel Help 3 In the Mixture Analysis Method Name field of the New Mixture Analysis Method dialog box shown above enter the name MA Test Method 4 In the Mixture Interpretation Threshold Minimum Peak Height RFU field enter 150 5 In the Heterozygote Peak Height Ratio PHR Settings area of the dialog box highlight all four rows as shown then click Delete to remove all of the default settings 6 Click New to launch the Heterozygote PHR Settings dialog box then enter the following a In the Minimum Peak Height RFU field enter 150 b In the Maximum Peak Height RFU field enter 300 c In the PHR Threshold between 0 and 1 field enter 0 54 as shown in the next dialog box 46 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 4 Segregate Samples wu Step 3 Create a New Mixture Analysis Method s Heterozygote PHR Settings x Minimum Peak Height RFU 150 Maximum
109. r given Hp prosecution hypothesis Hd defense hypothesis LR Analysis Summary sample H4 H28 1 3 analyst gmidx Reference Sample s select one or more Reference 1 H4 H28 1 0 Reference 1 H4 H28 1 0 Reference 2 H4 H28 0 1 Reference 2 H4 H28 0 1 X Hypothesis 1 Hp Mixture of C2 H4 H28 1 0 and C1 H4 H28 0 1 7 Mixture of C2 H4 H28 1 0 and one unknown unrelated person Hypotheses select one or more Database B Identifiler UM Population African American Theta 0 01 LR 1 E0 1 0982E 14 9 1056E13 Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next Finish o 3 Click Finish then Yes to exit the Mixture Analysis tool and return to the GeneMapper ID X Project window Refer to the GeneMapper ID X Software Help for additional information on segregating samples extracting individuals from 2 contributor mixtures and known matches GeneMapper ID X Software Version 1 1 Getting Started Guide 95 wa Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Step 3 Calculate the Likelihood Ratio for 2 Contributor Mixtures Extracted with a Known Contributor 96 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 7 Analyze Merged Results This chapter covers B Overview ssssseslesen RR III 98 Getting Started B Combine Different Amplific
110. r ID X Project Mame sn esr 2 Contributors 1 Contributor 3 or More Contributors Extraction Status Review Status Run Folder Sample File Sample Name Mixture Analysis Methog Known 1 m MA SGM H4 H28 1 1 D03 B07 fsa H4 H28 1 1 MA Test Method None 2 1 MA SGM H4 H28 1 2 005 C07 fsa H4 H28 1 2 MA Test Method None 3 1 MA 5GM H4 H28 1 3 007 D07 fsa H4 H28 1 3 MA Test Method None 4 amp MA SGM H4 H28 1 5 009 EQ7 fsa H4 H28 1 5 MA Test Method None 5 E MA SGM H4 H28 1 9 011 F07 fsa H4 H28 1 9 MA Test Method None 0 Export Table Mixture Analysis Manager Cancel lt Back Next gt Finish The dialog box buttons specific to the 2 contributor mixture workflow are Export Table Exports the table of samples characterized as minimum 2 contributor mixtures Next Performs new extraction Performs extraction of the mixture to identify the individual genotypes of the 2 contributors present in the mixture Back Returns to the previous dialog box GeneMapper ID X Software Version 1 1 Getting Started Guide 57 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 2 Review the Results of the Extraction Finish Returns to the GeneMapper ID X Samples table 2 Click Next gt to display the Mixture Analysis Results Viewer Step 2 Review the Results of the Extraction About Mixture Analysis Results 58 Viewer Tabl
111. r the selected sample are calculated based on the current genotype combination and population database selections and are not saved once you exit the Mixture Analysis Results Viewer Do you want to export the statistical results for the selected sample now 10 Click No Note You will calculate statistics in Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion Review Second _ 1 Select Next Sample gt gt to review sample H4_H28_1_5 Sample Click the Samples Plot button then click OK in the popup dialog box that explains the editing functions 3 Review the Selected Genotype Combinations table GeneMapper ID X Software Version 1 1 Getting Started Guide 65 wu Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 3 Determine Genotype Combinations to Include in Statistical Calculations Selected Genotype Combinations Marker D351358 1 2 D351358 3 D351358 4 D351358 66 4 Select Filter by Marker D3S1358 The following combinations are selected for D381358 C1 Major Inconclusiw C2 Minor Inconclusiv Known Genotypsg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 15 16 15 16 15 16 15 16 r ajaja 17 F1 r g 0 5 0 001 0 994 0 542 lg a a 17 17 r a 0 103 0 002 0 994 N A ul a 16 17 oO i 0 187 0 004 0 809 0 809 gg a a 15 17 rn a 0 187 0 004 0 817 0 817 ul a Note The combination in row 1 contains a minor
112. raction definition 10 F frequency allele definition 9 combined definition 10 genotype definition 10 marker inclusion definition 12 minimum allele definition 12 full installation 23 G genotype combination definition 10 genotype combinations definition 10 selected 15 59 table 15 17 59 60 unselected 17 60 122 genotype frequency definition 10 genotype profile definition 11 genotypes assigning 86 determining for calculation 63 exporting knowns 35 extracting 57 frequency definition 10 selecting 68 viewing knowns 35 Getting Started Guide chapter overviews 6 locating example files 23 using example data 22 using this guide 6 glossary of terms 9 H Help system accessing x heterozygote definition 11 homozygote definition 11 importing population databases 43 inconclusive marker definition 11 Information Development department contacting x installation client 23 full 23 installation configurations client 23 full 23 IQ definition 11 italic text when to use vii GeneMapper D X Software Version 1 0 Getting Started Guide K known contributors selecting 86 known genotypes exporting 35 viewing 35 L license disclaimer ii Likelihood Ratio calculating 74 94 calculating known contributor 94 calculating two contributor mixtures 94 definition 12 major contributor 74 81 minor contributor 74 reviewing calculation results 74 statistical approach 115 LR definition 12
113. re Analysis tool Residual Threshold As defined in the Mixture Analysis tool the value 0 04 above which genotype combinations are not automatically considered as possible contributors to the mixture sample Note The residual threshold set internally within the Mixture Analysis tool based on extensive testing of DNA mixtures cannot be adjusted by the user RMP Random Match Probability The probability that an individual chosen at random from the population has a DNA profile that matches the profile being compared In the Mixture Analysis tool RMP statistical calculations are only performed on 1 contributor and 2 contributor samples Sample Segregation The process by which samples transferred into the Mixture Analysis tool from a GeneMapper D X Software project are identified as containing a minimum of 1 2 or 3 or more contributors and separated into the appropriate mixture analysis workflow for each contributor category Sample Selection The process by which potential mixture samples transferred into the Mixture Analysis tool from a GeneMapper ID X Software project are selected and mixture analysis methods applied in order to proceed with sample segregation Selected Genotype Combinations Table containing genotype combinations that are included in Table statistical analysis Genotype combinations are assigned to this table automatically if they are assigned a passing gl Inclusion Quality IQ during extracti
114. re analysis analyze and edit the data in a GeneMapper D X Software project then process the data using the Mixture Analysis Tool IMPORTANT The settings used for this Getting Started Guide are for demonstration purposes only and require customization and optimization for data generated in your laboratory Note Before using the procedures in this chapter you must successfully install and register GeneMapper D X Software v1 1 For additional information see the GeneMapper ID X Software v1 0 1 1 Installation Guide In this chapter you will learn how to e Create a GeneMapper JD X Software project add samples and select table settings Import an analysis method Analyze data using appropriate analysis settings Review the analysis results Analysis Requirements Summary Analysis Summary Export and view a known genotype profile This profile will be used later in the analysis of mixed samples in which 1 contributor is known for example from an intimate body swab GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis Step 1 Create a GeneMapper ID X Software Project iu Step 1 Create a GeneMapper D X Software Project Open and Create Ifa project is already open in the Project window go to File New aNew Project or click New Project to open a blank Project window GeneMapper ID X Project Note If you have a previous project open you may be
115. ributor profiles extracted from a 2 person mixture sample as part of mixture interpretation Profile Frequency An entry in the Mixture Analysis Results Viewer RMP Statistics Summary section The estimated frequency of occurrence of a particular profile based on values from a given population database Reference Profile In the Profile Comparison tool the profile against which another profile is compared to determine the Match The software performs pairwise comparisons to determine the direction of comparison that yields the higher 96 Match then reports only the direction of comparison with the higher 96 Match In the Mixture Analysis tool one or two reference profiles known genotypes can be assigned to a mixture sample when calculating Likelihood Ratio LR statistics 14 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started w Glossary of Terms Term Definition Residual A measure of how close the observed contributor proportions for a particular genotype combination are to the expected contributor proportions for a particular 2 person mixture sample as described by Gill et a 1998 see Bibliography Residual Status A column in the Mixture Analysis Results Viewer Genotype Combinations tables It indicates whether the calculated residual value for a genotype combination falls above or below the residual threshold of 0 04 supplied with the Mixtu
116. rted Guide Chapter 3 Prepare for Mixture Analysis vu Step 4 Review Analysis Results 3 Select the Data Interpretation Plot Setting Note the spike in the D3S1358 analysis range SGM_TEST Samples Plot File Edit View Plots Tools Alleles Help amp amp Plot Setting Data Interpretation Panes 2 x BEAN SEX MERE E E 114 lids ys am AK Sample File Sample Name sos so SSPK MIX OMR caa H4 H28 0 1 001 A07 sa 4 Highlight the Spike label and right click to view the Peak Raw Data then confirm that the peak is a spike Note Peaks with magenta artifact labels such as Spike peaks will not be interpreted by the Mixture Analysis Tool 5 Close the Samples Plot 6 Highlight all sample rows and click the Display Plots icon in the tool bar Review and Save _ 1 Review all samples to ensure that no off ladder OL only calls Samples are present Select the Traditional Genotype Plot Setting for review Note Samples containing OL only allele calls cannot be processed by the Mixture Analysis Tool GeneMapper ID X Software Version 1 1 Getting Started Guide 33 Chapter 3 Prepare for Mixture Analysis Step 4 Review Analysis Results Sample AA18 contains a true D3S1358 peak that is labeled as an OL allele SGM Test Samples Plot File Edit view Plots Tools Alleles Help amp h amp Plot Setting Traditional Genotype Plot Panes 4 mug mn Eha ll Ch 14
117. s Term Definition PHR Status A column in the Mixture Analysis Results Viewer Genotype Combinations tables Also a mixture analysis quality flag that indicates whether the calculated Peak Height Ratio PHR for a given genotype combination falls above or below the Peak Height Ratio PHR thresholds set per peak height range in the mixture analysis method Note The PHR thresholds defined in a mixture analysis method and applied to samples in the Mixture Analysis tool differ from the minimum peak height ratio threshold defined in an analysis method and applied to samples in a GeneMapper ID X Software project Population Database A collection of the alleles and allele frequencies obtained from a random group of unrelated individuals from one or more ethnic groups In the Mixture Analysis tool these allele frequencies are used to calculate genotype frequencies for a DNA profile Note Each marker within a population is associated with a sample size n used to determine the minimum allele frequency calculated as 5 2n The minimum allele frequency is automatically assigned to any allele in each marker when an allele frequency is either not observed or below the calculated minimum allele frequency designated by Profile Sample The genotype allele designations of a sample In the Mixture Analysis tool you can import known profiles into a mixture analysis project to compare against each of the cont
118. s Results cie Statistics nena l apea Panel SGM Plus v1X Previous Sample Next Sample gt gt Ses nA CPIICPESE IRS SEE Average Mx 0 181 Residual Threshold 0 040 Filter by Marker all Known H4_H28_1_0 Sample Review Complete Selected Genotype Combinations Marker C1 Major Inconclusiy C2 Minor Inconclusiw Known Genotypg ADBI Residual PHR1 PHR2 Residual Status PHR Status IQ 10351358 0 003 0 920 0 920 1 r r a a m E 2 wa Dn r 0 000 0 975 0 975 a 3 wa D r i 0 006 0 934 0 934 a i Sort 4 WA r r d 0 008 0 890 0 890 BH BH Unselect S WA D D B 0 009 0 975 N A B B 6 VWA r r B 0 027 0 975 NA BH BH Missing Markers 7 pi6s539 r r d 0 002 0 883 0 885 mH BH 8 D251338 r r r 0 005 0 892 0 892 i BH d 9 AMEL r r BH 0 002 NA Na Unselected Genotype Combinations Fiter on Q WOAS Fiter on Known Match B Marker C1 Major Inconclusiyg C2 Minor Inconclusiy Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 0381358 1516 m Dr BE 0 53 0014 0 703 0 414 o9 a 2 D351358 15 16 n 17 17 Dn 16 17 E 0 15 o0 19 o 703 w mn 3 p35iss8 15 16 r 15 17 n 16 17 Bp wa 0 031 0 578 o 578 I o9 a 4 pssisse r ists Ir Bp we
119. s Sample Next Sample gt gt Mixture Analysis Results R sniene l RIMP EESHSECETCZYIIROD l CPIJCPESteHsHcs mecie l E B BE Average Mx 0 175 Residual Threshold 0 040 Filter by Marker fan z Known None Sample Review Complete r Selected Genotype Combinations Marker C1 Majora Inconclusis C2 Minor Inconclusiy Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 D351358 15 16 r 17 17 Oo i 0 121 0 008 0 829 N A a 2 p1es539 10 12 9 9 D BE 01530 00 0 983 n A EN k 3 press m z m 9 12 r Bp 0267 o010 0 746 0 746 i B BH 4 D165539 10 12 n 9 10 r E 0263 0 01 0 724 0 724 E B B 5 AMEL ux nr XY r BE wA 0 001 Mia NA i e mi 593 m 7 9 r E o207 0 003 0 868 0 868 l n C 7 TPOX p n 8 8 O Bp ma ooo wa wa Hi d 8 TPOX 8 11 D 8 F1 Oo i 0 121 0 008 0 751 0 751 m a 9 CsFIPO 11 12 L 9 11 r HH 10 219 0 005 10 844 0 844 IEI L Unselected Genotype Combinations Filter on IQ HOAE Filter on Known Match Marker C1 Major Inconclusiv C2 Minor Inconclusiy Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ 1 0351358 m E E EJ f 2 p351358 15 16 r 17 F1 r BE 9 158 0 006 0 829 0 370 a amp 3 D351358 15 16 r 15 17 r B ua 0 016 0 663 0 663 f
120. s are Unknown 22000 cee eee eee 56 In This Chapter wi asen pa aeia a e E E ees 56 Step 1 Extract Individual Genotypes 225 57 Step 2 Review the Results of the Extraction 58 About Mixture Analysis Results Viewer Tables 58 Review Extraction Results lille lille 60 Step 3 Determine Genotype Combinations to Include in Statistical Calculations ov sene RR eget Shaves EBay RR XU RAS URS 63 Review First Sample 2000 0c eee eee eee 63 Review Second Sample 000000e eee eeeees 65 Select Genotypes for Second Sample 68 Review Remaining Samples 000 eee eee 70 Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion llle 71 Step 5 Review the Results of Random Match Probability and Combined Probability of Inclusion Exclusion Calculations 72 Step 6 Calculate and Review Likelihood Ratio Results 74 Calculate the Likelihood Ratio Based on Contributors to the MIXtUIe uide ee ade ee ben es Se alas 74 Calculate the Likelihood Ratio Based on the Major Contributor Only zs scat ch etoie e eter ae vene ner Aog sp bos qu M an 81 Chapter 6 Analyze 2 Contributor Mixtures with One Known COMMPIDULOF x 6 eT re km diode eene are e ci 85 OVOrVIeW stes csbarmimiauteusrsemoy6a Gema dubi be state nd 86 About Analysis of 2 Contributor Samples Where 1 contributor is Known lslll
121. s of this guide and the other documents listed above are also available on the GeneMapper ID X Software Version 1 1 Documentation CD Note To open the user documentation included on the GeneMapper ID X Software Version 1 1 Documentation CD use the Adobe Acrobat Reader software available from www adobe com Note For additional documentation see How to Obtain Support on page xi The GeneMapper D X Software has a Help system that describes how to use each feature of the user interface Access the Help system by doing one of the following e Click in the toolbar of the Project window Select Help gt Contents and Index Press F1 You can use the Help system to find topics of interest by Reviewing the table of contents Searching for a specific topic Searching an alphabetized index You can also access PDF versions of all documents in the GeneMapper ID X Software document set from the Help system Applied Biosystems welcomes your comments and suggestions for improving its user documents You can e mail your comments to techpubs appliedbiosystems com IMPORTANT The e mail address above is only for submitting comments and suggestions relating to documentation To order documents download PDF files or for help with a technical question go to http www appliedbiosystems com then click the link for Support See How to Obtain Support on page xi GeneMapper D X Software Version 1 1 Getting
122. sample plot viewer Repeat for all remaining 2 contributor samples and remember to check Sample Review Complete following evaluation of each sample Note You may observe during analysis of your own data that some samples do not produce any results following extraction This is expected with samples containing a very low level minor contribution where there are only 2 peak markers and no 3 peak or 4 peak markers GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns NH Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion Step 4 Calculate Random Match Probabilities and Combined Probability of Inclusion Exclusion 1 In the Mixture Analysis Results Viewer select Sample Name H4 H28 1 5 and click Calculate Statistics to display the Population Database Selection dialog box s Population Database Selection l x r Population Databases Select Database Name Population Theta Iz AB Identifiler UM African American 0 01 r AB Identifiler UM Native American 0 03 r1 AB Identifiler UM U S Caucasian 0 01 O AB Identifiler UM LI S Hispanic 0 01 Calculate Statistics Options Apply to all samples Apply to current sample Reset Theta OK Cancel Help Note For samples containing 2 contributors the software performs the following statistical cal
123. se Alleles Default Use 2p Inconclusive Two alleles Use Alleles Default Inconclusive Three alleles Min Genotype Freq Default Inconclusive Where Use Alleles Calculate the genotype frequency from the allele frequencies use heterozygous equation 2pq or homozygous equation p p 1 p 0 e Use 2p Calculate the genotype frequency from the allele frequency assuming possible allelic drop out use conservative frequency equation 2p e nconclusive Do not calculate a genotype frequency for the marker consider marker as uninformative Min Genotype Freq Calculate the genotype frequency from the minimum genotype frequency for a tri allelic marker use 3 n where n number of samples for each marker in the ethnic population as specified in the selected population database 16 GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 1 Getting Started m Glossary of Terms Term Definition Theta A correction factor applied to the homozygous genotype frequency calculation that compensates for possible population substructure that may lead to an underestimate of the genotype frequency for the marker In the Mixture Analysis tool a user defined setting Population Database Selection dialog box for each ethnic group within a population database designated by the symbol O Unselected Genotype Contains genotype combinations that will not be included in Combinations Table statist
124. select one or more Please select Reference1 to display available hypotheses Notes Calculate Statistics Export Mixture Analysis Parameters Samples Plot Cancel lt Back Next Finish 7 2 Inthe Reference 1 drop down field click Import navigate to the location where you saved the Known H26 txt file shown in Chapter 3 Step 5 Export and View a Known Genotype Profile on page 35 then select Import 3 In the Known Genotypes dialog box click OK One hypothesis is displayed 4 Check the box to the left of the hypothesis to display the Likelihood Ratio Statistics Summary as shown next GeneMapper ID X Software Version 1 1 Getting Started Guide 81 V Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results pixi s Mixture Analysis Results Viewer Minimum Number of Contributors 2 Sample File H4 H28 1 5 009 EO7 fsa Panel SGM Plus vix Run Folder MA sGM Sample Name ps H28 1 5 zl lt lt Previous Sample Next Sample gt gt Mixture Analysis Results RMP Statistics C1 Major RMP Statistics C2 Minor CPI CPE Statistics LR Statistics f Likelihood Ratio LR Calculation LR Statistics Summary LR Pr E Hp Pr E Hd where Pr probability E evidence pipebar given Hp prosecution hypothesis sample H4 H28 1 5 Hd defense hypothesis analyst gmidx LR Analysis Summary Reference
125. the Mixture Analysis tool Note When you make changes to the Panel column a separate window opens with a folder displayed instead of a drop down list Open the folder and select the appropriate panel GeneMapper ID X Software Version 1 1 Getting Started Guide 29 Chapter 3 Prepare for Mixture Analysis Step 3 Analyze Data Using Appropriate Settings s Select a Panel x Mone AmpFLSTR Panels viX H Green I vix c4 Profiler v1x v4 Blue v1X 4 COfiler v1X 4 Profiler Plus v1x SGM Plus vix Identifiler v1X e SEfiler v1X Cofilr CODIS vix Profiler Plus CODIS v1X Identifiler CODIS v1X 4 MiniFiler GS500 v1X 4 Yfiler vix amp PP16 Panels vix cma em 2 Click the Analyze icon on the toolbar The Save Project dialog box is displayed 3 Fill in the Save Project dialog box as shown below and click OK Save Project X Name saw TEST Security Group GeneMapper ID Security Group Y OK Cancel Help The Analysis Summary dialog box appears after analysis is completed 30 GeneMapper ID X Software Version 1 1 Getting Started Guide Chapter 3 Prepare for Mixture Analysis Fu Step 4 Review Analysis Results Step 4 Review Analysis Results Review Analysis The Analysis Summary dialog box appears as shown below Summaries Samples Analysis Summary Genotypes Analysis Summary Select run folder to display 5G k Unana
126. ts The software automatically merges individual results when identical results are obtained for markers that are common to both amplifications and for instances where only one kit contains a result for a particular marker as shown in the following figure This data can be exported to facilitate review GeneMapper D X Software Version 1 1 Getting Started Guide 105 Chapter 7 Analyze Merged Results Step 7 Calculate and Analyze the Results Mixture Analysis Merged Results Viewer Zio Sample Name Mixture Analysis Results E AP iStatisticsy renmed Next Sample gt gt RIP iStatisticsy co minor GN GPE Statistics IR Statistics EBE Known None Selected Genotype Combinations Merged includes markers automatically added from one or more panels Run Folder Sample File Panel Marker C1 Major Inconclusivs C2 Minor Inconclusivs 1 Multiple Multiple AMEL XX r X Y ri 2 MA CO H4 H28 1 3 007 COfiler vix CSFIPO 11 12 ni 9 11 r g MA PP H4 H28 1 3 007 Profiler Plus v1X D135317 8 9 rn 11 11 mil 4 MA PP H4 H28 1 3 007 Profler Plus vIX D135317 8 9 r 9 11 r Remove Marker 5 MA PP H4 H28 1 3007 Profiler Plus v1X D135317 8 9 r 11 F1 oO 6 MA CO H4 H28 1 3 00 COfiler v1X D165539 10 12 rH 9 9 r 7 MA CO H4 H28 1 3 007 COfiler vix D165539 10 12 r 9 10 r 8 MA CO H4 H28 1 3007 COfiler_v1x D165539 10 12 r 9 12 oO q MA PP H4 H2R 1 3 NNF Profiler Plis vix DIRSS1 13 15 m 12 12 m r Selected Genotyp
127. tsa H4 H2810 Sample HD FulRange 75 SGM Plus vIX CE_F_HD_G5500 75 4 None 2008 04 09 21 05 24 e 5 H4 H28 1 1003 B07 tsa H4 H28 1 1 Sample HD FulRenge 75 SGM Plus vIX CE F HD 65500 75 4 None 2008 04 08 21 05 24 e9 6 H4 28 1 2 005 CO tsa Ha H28 1 2 Sampie HD FulRenge 75 SGM Plus IX CE F HD 65500 75 4 None 2008 04 09 21 05 24 e 7 Q H4 H26 1 3 007 D07 tsa H4 H28 1 3 Sample HD FulRange 7 SGM Plus vIX CE F HD GS500 75 4 None 2008 04 09 21 05 24 e 8 y H4 H28 1 5 009 E07 fsa H4 H28 1 5 Sample HD FulRange 7 SGM Plus vIX CE F HDD GS500 75 4 None 2008 04 09 21 05 24 e 8 l H4H28 19 0f FO7 fsa H4 H28 1 9 Sample HD FulRenge 75 SGM Plus vIX CE F HD 65500 75 4 None 2008 04 08 21 05 24 e 10 ug H4 H28 AA18 1 1 2 002_A08 fsa H4 H28 AA18 1 Sample HD_Ful Range 75 SGM Plus v1X CEJ F_HID_GS500 75 4 None 2008 04 09 21 05 24 i 41 Ladder 012 FO8 fsa Ladder Allelic Ladder HD FulRange 75 SGM_Plus_v1X CE_F_HID_GS500 75 4 None 2008 04 09 21 05 24 e 42 l NTC 008 D08 fsa NTC Negative Control HD FulRange 7 SGM Plus vIX CE F HID GS500 75 4 None 2008 04 09 21 05 24 e 43 PositiveControl 006 C08 fsa PositiveControl Positive Control HID_FullRange_75 SGM Plus v1X CE F HID GS500 75 4 None 2008 04 09 21 05 24 Note The green e arrow in the status column indicates that these samples have never been analyzed Unanalyzed samples will not be imported into
128. tware Version 1 1 Getting Started Guide 77 78 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 6 Calculate and Review Likelihood Ratio Results The software calculates the Likelihood Ratio based on the following alternate hypotheses Hypothesis 1 Hp H4_H28_1_5 originates from a mixture of H28 and H4 H H4 H28 1 5 originates from a mixture of H28 and one unknown unrelated person The observed profile is 4 7134E4 or 47000 times more likely to occur if it originated from a mixture of H28 and H24 than from a mixture of H28 and one unknown unrelated person Hypothesis 2 H H4 H28 1 5 originates from a mixture of H28 and H24 H H4 H28 1 5 originates from a mixture of H4 and one unknown unrelated person The observed profile is 9 1056E13 or 9 trillion times more likely to occur if it originated from a mixture of H28 and H24 than from a mixture of H4 and one unknown unrelated person Hypothesis 3 Hp H4_H28_1_5 originates from a mixture of H28 and H24 H H4 H28 1 5 originates from a mixture of two unknown unrelated people The observed profile is 4 2918E18 or 4 3 quintillion times more likely to occur if it originated from mixture of H28 and H24 than from a mixture of two unknown unrelated people GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns m Step 6 Calculate and Review Likelihood Ratio Results Hypothesis 4
129. ty the known selection always displays the match to the C1 Major contributor Fikeron1Q WAE Fiter on Known Match B Marker C1 Major Inconclusiw C2 Minor Inconclusis Known Genotype ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ D351358 D351358 D351358 D351358 D351358 D351358 D351358 D351358 ofj w gt of om e ofl N e 0 466 0 000 0 979 0 979 EE 0 495 0 003 10 874 N A a 0 505 0 004 N A 0 874 j 0 272 0 072 0 545 0 213 e 9 0 304 0 075 0 476 0 186 amp N A 0 085 0 476 N A 0 481 0 091 0 101 0 874 eo 0 519 0 094 0 874 0 101 eo 16 17 90 Note In instances where markers are missing from the Selected Genotype Combinations table and the entire genotype cannot be attributed solely to 1 contributor the highlighting is light yellow and light green In such cases click the Missing Markers button then review the Unselected Genotype Combinations table to display the missing markers GeneMapper D X Software Version 1 1 Getting Started Guide Chapter 6 Analyze 2 Contributor Mixtures with One Known Contributor Step 1 Assign Known Genotypes V3 3 In this example review sample H4 H28 1 3 The known contributor matches the C2 Minor contributor completely s Mixture Analysis Results Viewer Minimum Number of Contributors 2 B nl xl SampleFile H4 H28 1 3 007 D07 fsa RunFolder MA SGM Sample Name afar Mixture Analysi
130. type combinations from the statistical calculations highlight the genotype combination s and click the Unselect button to the right of the table GeneMapper ID X Software Version 1 1 Getting Started Guide 59 5 Chapter 5 Analyze 2 Contributor Mixtures with Two Unknowns Step 2 Review the Results of the Extraction Unselected Genotype Combinations Table The Unselected Genotype Combinations table shows the list of possible genotype combinations deducible from the mixture which failed to pass the criteria for automatic inclusion in the Selected Genotype Combinations table To include these genotype combinations in statistical calculations highlight the required genotype combination and click the Select button to the right of the table This action moves the combinations from the Unselected Genotypes Combinations table to the Selected Genotypes Combinations table Review Extraction To review the results of the extraction Results 1 Select sample H4 H28 1 3 from the drop down menu s Mixture Analysis Results Viewer Minimum Number of Contributors 2 Bl xl Sample File H4 H28 1 1 003 B07 fsa Panel SGM Plus vix Run Folder MA SGM Sample Name H4_H28_1_1 zi Previous ample Next Sample gt gt Sample Review Complete Marker C1 Majorp Inconclusiy C2 Minor Inconclusiy Known Genotypg ADBI Mx Residual PHR1 PHR2 Residual Status PHR Status IQ E 1 ics nna I diia d n Pers
131. ulting from two person mixture extraction The software computes a minimum allele frequency of 5 2n where n sample number and uses this minimum allele frequency when the actual allele frequency does not exist in the population database or when the allele frequency is less than the minimum allele frequency Homozygous Genotype Frequencies Homozygous genotype frequencies are calculated as pl pl pl 1 0 p1 0 where pl allele 1 frequency 0 theta correction factor can be set by the user on a per population basis Heterozygous Genotype Frequencies Heterozygous genotype frequencies are calculated as 2 0 pl p2 where pl allele 1 frequency p2 allele 2 frequency In instances of possible allele dropout the genotype frequency is calculated as 2p GeneMapper ID X Software v1 1 Getting Started Guide 113 uw Appendix A Statistical Analysis and Algorithms m Statistical Approaches Combined Probability of Inclusion Exclusion 114 In instances of marker dropout partial profile or if the marker is deemed inconclusive the software renders the marker uninformative and substitutes a value of 1 0 for the genotype frequency In instances where multiple genotypes are included as possible contributors the software sums the genotype frequencies at a given marker resulting in a combined genotype frequency for the marker It multiplies the combined genotype frequencies to calculate the Random Match Probability
132. zing always prepare fresh matrix GeneMapper ID X Software Version 1 1 Getting Started Guide vii Preface How to Use This Guide A right arrow symbol gt separates successive commands you select from a drop down or shortcut menu For example Select File Open gt Spot Set Right click the sample row then select View Filter gt View All Runs User Attention Two user attention words appear in Applied Biosystems user Words 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 or software operation accurate chemistry kit use or safe use of a chemical Examples of the user attention words appear below Note Each registered user has his or her own set of preferences When you set these options if affects only the user currently logged in IMPORTANT To verify your client connection to the database you need a valid user ID and password viii GeneMapper D X Software Version 1 1 Getting Started Guide Preface How to Obtain More Information How to Obtain More Information Related The following related documents are shipped with the system Documentation GeneMapper ID X Software Version 1 1 Quick Reference Guide Provides a quick look at the new GeneMapper JD

GeneMapper® ID-X Software Version 1.1 (Mixture Analysis Tool

Contents

Download Pdf Manuals

Related Search

Related Contents

GeneMapper&reg; ID-X Software Version 1.1 (Mixture Analysis Tool

Contents

Download Pdf Manuals

Related Search

Related Contents

GeneMapper® ID-X Software Version 1.1 (Mixture Analysis Tool