GeneMapper® Software Version 4.0 LOH 解析 ユーザーガイド
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1 GeneMapper v4.0 LOH Getting Started Guide LOH (Loss of Heterozygosity) LOH (Loss of Heterozygosity)
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3 GeneMapper v4.0 LOH Getting Started Guide LOH (Loss of Heterozygosity) LOH (Loss of Heterozygosity)
4 2005 Applied Biosystems Japan Ltd. All rights reserved. Applied Biosystems Applied Biosystems : Applera Corporation GeneMapper HID GeneMapper HID : ABI Prism Applied Biosystems GeneMapper GeneScan SNaPshot AB Design Applera GeneMapper GeneScan SNPlex ZipChute Applera Corporation Apache Software Foundation ( Copyright The Apache Software Foundation.All rights reserved. ExoLab Project ( exolab.org/) Copyright 2000 Intalio Inc. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., AFLP Keygene N.V Microsoft Windows Microsoft Corporation Oracle Oracle Corporation Applera Corporation is committed to providing the world s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. Part Number Rev. B 06/2005 ii GeneMapper Software v4.0 LOH Getting Started Guide
5 v v vi vii 1 1 LOH LOH GeneMapper Software GeneMapper v LOH (Loss of Heterozygosity) Kit Panel Marker Table Settings Auto Bin Bin Set Bin Analysis Method LOH (Loss of Heterozygosity) LOH LOH LOH Report Setting GeneMapper Software v4.0 LOH Getting Started Guide iii
6 iv GeneMapper Software v4.0 LOH Getting Started Guide
7 GeneMapper Software v4.0 LOH Getting Started Guide Applied Biosystems Data Collection LOH GeneMapper Software GeneMapper Software GeneMapper Software v4.0 Quick Installation and Administration Guide (PN ) GeneMapper Software v4.0 Microsoft Winows XP 0 [Enter] FileOpenSpot Set View FilterView All Runs Applied Biosystems Getting Started Guide 2 GeneMapper Software v4.0 LOH Getting Started Guide v
8 Control Console Oracle ID Sample Entry GeneMapper Software v4.0 Installation and Administration Guide (PN ) GeneMapper Software v4.0 Installation and Administration Guide (PN ) GeneMapper Software 4.0 Installation and Administration Guide (PN ) GeneMapper Software v4.0 Installation and Administration Guide GeneMapper Software v4.0 GeneMapper Software v4.0 Getting Started Guide GeneMapper Software 5 Applied Biosystems Data Collection LOH AFLP SNaPshot SNPlex GeneMapper Software GeneMapper Software v4.0 Online Help GeneMapper Software [F1] HelpContents and IndexGeneMapper 3 GeneMapper Software v4.0 Quick Reference Guide GeneMapper Software GeneMapper Software v4.0 Reference and Troubleshooting Guide vi GeneMapper Software v4.0 LOH Getting Started Guide
9 PDF GeneMapper Software v4.0 Documentation CD vii GeneMapper Software [F1] HelpContents and IndexGeneMapper 3 Applied Biosystems jptechsupport@appliedbiosystems.com Customer Support FAQ Applied Biosystems MSDSCertification of Analysis PDF Applied Biosystems GeneMapper Software v4.0 LOH Getting Started Guide vii
10 viii GeneMapper Software v4.0 LOH Getting Started Guide
11 1 LOH (Loss of Heterozygosity) LOH LOH GeneMapper Software GeneMapper v LOH (Loss of Heterozygosity) GeneMapper Software v4.0 LOH Getting Started Guide 1
12 1 LOH LOH LOH LOH STR DNA PCR PCR GeneMapper TSGtwo-hit TSG 2 TSG LOH Loss of Heterozygosity; TSG 1 LOH LOH LOH TSG DNA LOH LOH 2 LOH DNA GeneMapper Report Manager Peak Height Ratio Peak-Height Ratio LOH DNA Applied Biosystems Applied Biosystems Web 2 GeneMapper Software v4.0 LOH Getting Started Guide
13 1 LOH Applied Biosystems GeneMapper Software v4.0 Quick Reference Guide (PN ) GeneMapper LOH Default Report Setting : 1_Healthy.fsa, 1_Tumor.fsa, 2_Healthy.fsa, 2_Tumor.fsa LOH LOH Default Report Setting LOH GeneMapper LOH 45 LOH Report Setting Report Setting : Healthy_1.fsa, Healthy_2.fsa,,Tumor_2.fsa, Tumor_1.fsa 4.fsa <drive>:\appliedbiosystems\genemapper\example Data\LOH GeneMapper D PCR GeneScan 500LIZ ABI PRISM bp R5 Blue R26 Blue R14 Blue R21 Yellow R24 Yellow R2 Green LOH (Loss of Heterozygosity) Panel Marker GeneMapper Software v4.0 LOH Getting Started Guide 3
14 1 LOH LOH GeneMapper LOH LOH (Loss of Heterozygosity) ( 2 ) 1. Kit Panel Marker Table Settings Bin Set Bin Auto Bin ( 3 ) 1. Analysis Method Bin Set LOH (Loss of Heterozygosity) ( 4 ) 1. Genotypes LOH 2. LOH 3. LOH Report Setting ( 5 ) GeneMapper Software v4.0 LOH Getting Started Guide
15 1 GeneMapper Software GeneMapper Software Bin Bin Set Marker Panel Kit Analysis Method Size Standard Panel GeneMapper Marker bpbin Marker Bin ) Bin Set bp Marker GeneMapper Panel Bin Set Marker Bin Panel GeneMapper 1. StartAll ProgramsApplied BiosystemsGeneMapper GeneMapper Login to GeneMapper a. b. OK LOH GeneMapper Software Online Help GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 LOH GeneMapper Software v4.0 LOH Getting Started Guide 5
16 1 GeneMapper LOH GeneMapper LOH 2 LOH (Loss of Heterozygosity) LOH GeneMapper Data Collection LOH GeneMapper Software v4.0 Quick Installation and Administration Guide (PN ) GeneMapper 2 LOH (Loss of Heterozygosity) LOH GeneMapper GeneMapper Software v4.0 Quick Installation and Administration Guide (PN ) 6 GeneMapper Software v4.0 LOH Getting Started Guide
17 2 LOH (Loss of Heterozygosity) Kit Panel Marker Table Settings LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin LOH (Loss of Heterozygosity) GeneMapper Software v4.0 LOH Getting Started Guide 7
18 2 LOH (Loss of Heterozygosity) Kit Panel Marker Display Settings AutoBin Bin Set Bin GeneMapper GeneMapper Software Online Help Creating a New Kit Kit Creating a Custom Panel Creating Markers Marker Creating a Project Adding Samples Applying Analysis Settings Analysis Settings Starting Analysis Creating a New Bin Set Bin Set Using the Auto Bin Function Auto Bin Help [F1] 8 GeneMapper Software v4.0 LOH Getting Started Guide
19 2 LOH (Loss of Heterozygosity) Kit Panel Marker Kit Panel Marker Panel Manager Kit Panel Panel Marker Marker bp Panel Marker Marker Panel Applied Biosystems Linkage Mapping Set GeneMapper Panel Panel GeneMapper Software Online Help Kit Panel Marker Kit Panel Marker 1. Panel Manager ToolsPanel Manager 2. Panel Manager FileNew Kit GeneMapper Software v4.0 LOH Getting Started Guide 9
20 2 LOH (Loss of Heterozygosity) Kit Panel Marker 3. New Kit Kit Name LOH Kit Kit Type Microsatellite OK LOH Kit 4. LOH Kit FileNew Panel 5. Panel Manager New Panel Panel Name LOH Panel [Enter] LOH Kit LOH Panel 6. LOH Panel FileNew Marker 10 GeneMapper Software v4.0 LOH Getting Started Guide
21 2 LOH (Loss of Heterozygosity) Kit Panel Marker 7. Panel Manager Marker Marker Marker Dye Color Minimum Size (bp) Maximum Size (bp) Marker Repeat R26 Blue R14 Blue R21 Yellow R24 Yellow R2 Green Panel Manager OK 12.fsa GeneMapper Software v4.0 LOH Getting Started Guide 11
22 2 LOH (Loss of Heterozygosity) GeneMapper Project Project 1. FileNew Project 2. New Project Microsatellite OK GeneMapper v GeneMapper FileAdd Samples to Project 4. Add Samples to Project Files <drive>:\appliedbiosystems\genemapper\exampledata GeneMapper D 12 GeneMapper Software v4.0 LOH Getting Started Guide
23 2 LOH (Loss of Heterozygosity) 5. LOH Add to ListAdd LOH 2 [Ctrl] Add To List LOH Data 4 Applied Biosystems Data Collection Samples 14 GeneMapper Software v4.0 LOH Getting Started Guide 13
24 2 LOH (Loss of Heterozygosity) Table Settings Table Settings GeneMapper Analysis Method Bin Set Panel Marker ) Size Standard GeneMapper Table Settings Plot Settings 1. GeneMapperSamples 2. Analysis Method New Analysis Method GeneMapper Manager Analysis Method 3. New Analysis Method Analysis Type Microsatellite OK 14 GeneMapper Software v4.0 LOH Getting Started Guide
25 2 LOH (Loss of Heterozygosity) Table Settings 4. Analysis Method Editor 5 General Name LOH Analysis Method Allele Bin Set None GeneMapper Software v4.0 LOH Getting Started Guide 15
26 2 LOH (Loss of Heterozygosity) Table Settings Peak Detector Peak Detection Algorithm Basic Peak Quality Process Quality Values PQV (Pass) (Check) Max peak width (basepairs) GeneMapper Software v4.0 LOH Getting Started Guide
27 2 LOH (Loss of Heterozygosity) Table Settings Quality Flags Process Quality Values (PQV) Genotype Quality (GQ) PQV Sizing Quality SQ GQ Pass Check Low Quality SQ GQ 1 PQV 1 SQ GQ Analysis Method GeneMapper Software Online Help 5. OK Analysis Method Analysis Method Editor GeneMapper Software v4.0 LOH Getting Started Guide 17
28 2 LOH (Loss of Heterozygosity) Table Settings 6. Panel Select a Panel LOH Kit LOH Panel 9 LOH Kit 7. Size Standard GS500LIZ_3130 GeneMapper GeneScan 500 LIZ GS500LIZ GeneScan 500 LIZ GS500(-250)LIZ 250-bp GS500LIZ_ bp GS500LIZ_ bp 1 35-bp 250-bp 340-bp GeneMapper Software Online Help 8. Samples a. Analysis Method Panel Size Standard 3 b. EditFill Down[Ctrl] [D] 18 GeneMapper Software v4.0 LOH Getting Started Guide
29 2 LOH (Loss of Heterozygosity) Table Settings Table Settings GeneMapperTable Settings Microsatellite Default Table Settings SamplesGenotypes Microsatellite Default GeneMapper Table Settings 1 GeneMapper Manager Table Settings GeneMapper Software Online Help 1. FileSave Project 2. Save Project LOH Project OK GeneMapper LOH Project 20 GeneMapper Software v4.0 LOH Getting Started Guide 19
30 2 LOH (Loss of Heterozygosity) Panel GeneMapper Analysis Method Bin Set Genotype Quality (GQ) SQ PQV Raw Data AnalysisAnalyze GeneMapper GeneMapper SQ PQV Size Quality (SQ) Process Quality Value PQV 1. GeneMapper Analysis Completed 2. Samples SQ SQ SQ (Pass) SQ SFNF MNF SNF OS PQV 20 GeneMapper Software v4.0 LOH Getting Started Guide
31 2 LOH (Loss of Heterozygosity) SQ SQ (Check) (Low Quality) PQV SFNF MNF SNF OS 21 SQ Samples SQ 1. EditSelect AllSamples 2. Size Match Editor AnalysisSize Match Editor Size Quality (SQ) 2-1 Size Match Editor Size Matches 3. Size Matches Size Quality (SQ) 4. Sizing Quality 2-1 SQ (Pass) (Check) (Low Quality) Sizing Quality > 0.75 SQ (Pass) Sizing Quality SQ (Check) (Low Quality) GeneMapper Software v4.0 LOH Getting Started Guide 21
32 2 LOH (Loss of Heterozygosity) 6. Size Calling Curve 7. Size Match Editor OKSize Match Editor 2-1 Sizing Quality SQ (Check) (Low Quality) Size MatchesOverride SQ Sizing Quality 2-1 Sizing Quality 1.0 Size Matches Apply GeneMapper Software Online Help GeneMapper Software Online Help GeneMapper Software Reference and Troubleshooting Guide Raw Data InfoRaw Data Raw Data 22 GeneMapper Software v4.0 LOH Getting Started Guide
![2 LOH (Loss of Heterozygosity) Sample Plot 1. ViewSamplesSamples 2. Samples[Shift] [Ctrl] Edit Select All 3. AnalysisDisplay Plots Samples Plot Plot Setting Microsatellite Default X - 4.](/docs-images/92/110410879/images/33-0.jpg "Plot Setting Microsatellite Default Plot Settings Samples Plot Microsatellite Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 5.")
33 2 LOH (Loss of Heterozygosity) Sample Plot 1. ViewSamplesSamples 2. Samples[Shift] [Ctrl] Edit Select All 3. AnalysisDisplay Plots Samples Plot Plot Setting Microsatellite Default X - 4. Plot Setting Microsatellite Default Plot Settings Samples Plot Microsatellite Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 5. Samples Plot X Y X X [Shift] Zoom To OK Y Y Zoom To Apply to all electropherogramsok X Y X Y Full View GeneMapper Software v4.0 LOH Getting Started Guide 23
![2 LOH (Loss of Heterozygosity) Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing 24 2-2 [F1] GeneMapper Software Online Help Samples Plot 25](/docs-images/92/110410879/images/34-0.jpg "Auto Bin Bin Set Bin Sizing Sizing [Ctrl] [Shift] Sizing : Sizing [Ctrl] [G] Sizing 2-2 Samples Plot 24 GeneMapper Software v4.")
34 2 LOH (Loss of Heterozygosity) Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing [F1] GeneMapper Software Online Help Samples Plot 25 Auto Bin Bin Set Bin Sizing Sizing [Ctrl] [Shift] Sizing : Sizing [Ctrl] [G] Sizing 2-2 Samples Plot 24 GeneMapper Software v4.0 LOH Getting Started Guide
35 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin Auto Bin Bin Set Bin Panel Manager Bin Set Bin Bin Set Kit Kit Kit Panel Bin Set Bin Panel Bin Set Panel Bin Panel Bin Panel Marker Bin Set Auto Bin Bin Bin Bin Set Bin Bin Set Bin GeneMapper Software Online Help Bin Set Bin Set 1. Panel Manager ToolsPanel Manager 2. 9 LOH Kit 3. BinsNew Bin Set 4. New Bin Set Bin Set Name LOH Bin Set OK Panel Manager Bin Set LOH Bin Set LOH Bin Set LOH Panel LOH Kit Panel Panel Bin Set LOH Panel LOH Bin Set 1. Bin Set LOH Bin Set GeneMapper Software v4.0 LOH Getting Started Guide 25
36 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin 2. LOH Kit 9 LOH Panel Marker Panel Manager BinsAdd Reference Data Add Microsatellite Reference Data LOH Project Panel 4. Add Microsatellite Reference Data a. LOH Project b. LOH c. [Ctrl] d. Add to List e. Add LOH Project LOH Data 2 Add To ListAdd LOH Panel Panel Manager GeneMapper Software v4.0 LOH Getting Started Guide
37 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin 2-3 Panel Marker Panel Manager Auto Bin Bin Auto Bin Bin 1. LOH Panel Bin Set LOH Bin Set Bins Auto Bin 2. Auto Bin Minimum quality value 0.1 Allele Naming Scheme Rounded basepair Auto Bin Options Auto Bin (clear existing bins) 3. OK 4. Autobinning completedok GeneMapper Software v4.0 LOH Getting Started Guide 27
38 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin Marker Bin Marker Bin 1. LOH Panel Marker 2-4 Marker ) Marker Bin Bin + 2. Marker 2-5 Applied Biosystems Marker Marker Bin Bin GeneMapper Software Reference and Troubleshooting Guide Bin bp bp Marker Marker bp 2-4 Marker Marker 2-5 Marker 28 GeneMapper Software v4.0 LOH Getting Started Guide
39 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin Bin Set Bin Set Panel Manager OK Bin Marker Bin Marker Panel Manager LOH Kit LOH Panel Bin Marker PanelManager CancelOKApply Marker Bin 1. Marker Bins Add Bin 2. Bin 3. Add Bin Bin Name Location Offsets OK Bin 1. Bin 2. BinsEdit Bin Bin Edit Bin 3. Edit Bin Bin Name Location Offsets OK Bin 1. BinBin Bin 3. Bin EditUndo Bin Bin 2-6 Bin GeneMapper Software v4.0 LOH Getting Started Guide 29
40 2 LOH (Loss of Heterozygosity) Auto Bin Bin Set Bin Bin Bin Marker Bin BinsDelete Bin Bin Bin Delete Bin Marker 1. Marker Marker EditUndo Marker 2-7 Marker Panel Marker 1. Marker 2. EditClear Marker 3 LOH 30 GeneMapper Software v4.0 LOH Getting Started Guide
41 3 Analysis Method LOH (Loss of Heterozygosity) LOH (Loss of Heterozygosity) GeneMapper Software v4.0 LOH Getting Started Guide 31
42 3 Analysis Method Analysis Method Analysis Method 14 LOH Analysis Method Bin Set Bin Set Analysis Method Bin Set Bin Set GeneMapper LOH Analysis Method 1. GeneMapper Manager ToolsGeneMapper Manager 2. Analysis Methods 3. LOH Analysis Method Open 32 GeneMapper Software v4.0 LOH Getting Started Guide
43 3 Analysis Method 4. Analysis Method Editor AlleleBin Set LOH Bin Set OK 5. Done GeneMapper Manager GeneMapperSamplesAnalysis Method Analysis Method Editor GeneMapper Software v4.0 LOH Getting Started Guide 33
44 3 Analysis Method Bin Set GeneMapper GeneMapperSamples Status Samples LOH Analysis Method REF Bin Set Bin Set AnalysisAnalyze GeneMapper GeneMapper SQ PQV Size Standard GQ PQV Genotype Plot 36 Genotypes Plot37 37 GQ PQV Genotype Quality (GQ) Genotypes Genotypes GQ GQ 34 GeneMapper Software v4.0 LOH Getting Started Guide
45 3 GQ (Pass) GQ Process Quality Values (PQV) AN BD BIN LPH OBA OS PHR SHP SP SPA SPU XTLK PHR (Peak Height Ratio) PHR LOH LOH PHR Analysis Method Peak QualityHeterozygote BalanceMinimum Peak Height Ratio 16 GQ GQ (Check) (Low Quality) GQ PQV AN BD BIN LPH OBA OS PHR SHP SP SPA SPU XTLK Marker Bin GeneMapper Software Reference and Troubleshooting Guide GQ Genotypes GQ Marker Genotypes Allele 1 Allele 2 Marker GeneMapper Software v4.0 LOH Getting Started Guide 35
![3 Genotype Plot Genotypes Plot 1. Genotypes Marker Marker [Shift] [Ctrl] Marker EditSelect All 2. AnalysisDisplay Plots Genotypes Plot Marker Plot Setting Microsatellite Default X - 3.](/docs-images/92/110410879/images/46-0.jpg "Plot Setting Microsatellite Default Plot Settings Genotypes Plot Microsatellite Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 4.")
46 3 Genotype Plot Genotypes Plot 1. Genotypes Marker Marker [Shift] [Ctrl] Marker EditSelect All 2. AnalysisDisplay Plots Genotypes Plot Marker Plot Setting Microsatellite Default X - 3. Plot Setting Microsatellite Default Plot Settings Genotypes Plot Microsatellite Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 4. Genotypes Plot X Y X X Zoom To OK Y Y Zoom To Apply to all electropherogramsok X Y X Y Full View 36 GeneMapper Software v4.0 LOH Getting Started Guide
47 3 Genotypes Plot Genotypes Plot X ) Y Marker Bin [F1] GeneMapper Software Online Help Genotypes Plot Marker 1. Panel Manager ToolsPanel Manager 2. LOH Kit LOH Panel Marker 3. BinsShow Project Alleles Y Marker GQ GeneMapper Software v4.0 LOH Getting Started Guide 37
48 3 38 GeneMapper Software v4.0 LOH Getting Started Guide
49 4 LOH (Loss of Heterozygosity) LOH LOH LOH Report Setting LOH (Loss of Heterozygosity) LOH (Loss of Heterozygosity) GeneMapper Software v4.0 LOH Getting Started Guide 39
50 4 LOH (Loss of Heterozygosity) LOH 2 LOH 2 1 DNA GeneMapper Report Manager LOH Default Report Setting PHR (Peak Height Ratio) 4-1Report Manager Peak-Height Ratio LOH DNA GeneMapper Software v4.0 LOH Getting Started Guide
51 4 LOH (Loss of Heterozygosity) LOH Default Report Setting LOH 1. Marker 2 Allele Ratio Peak Height of Allele 1 Allele Ratio = Peak Height of Allele 2 2. Marker Allele Ratio Allelic Imbalance Allele Imbalance = Allele Ratio of Healthy Sample Allele Ratio of Diseased Sample 3. Marker Allelic Imbalance Allelic Imbalance > 1.35 LOH Candidate Allelic Imbalance < 0.67 LOH Candidate 4-2 LOH Default Report Setting LOH Default Report Setting Report Setting (45 GeneMapper Software v4.0 LOH Getting Started Guide 41
52 4 LOH (Loss of Heterozygosity) LOH LOH LOH Default Report Setting LOH Marker LOH 1. GeneMapperGenotypes 2. [Shift] Sample File 1_Healthy Marker 1_Tumor [Shift] Sample File GeneMapper Software v4.0 LOH Getting Started Guide
53 4 LOH (Loss of Heterozygosity) LOH 3. [Shift] Marker Marker Marker [Shift] Marker 4-4 Marker 44 LOH GeneMapper Software v4.0 LOH Getting Started Guide 43
54 4 LOH (Loss of Heterozygosity) LOH LOH LOH (Loss of Heterozygosity) EditSelect AllGenotypes 3. AnalysisReport Manager 4. Report Manager Report Setting LOH Default LOH Default LOH Default Report Setting LOH Project Allele Ratio Allelic Imbalance LOH Assessment 5. File Samples SQ Low Quality SQ Low Quality Marker Genotypes Report Setting 44 GeneMapper Software v4.0 LOH Getting Started Guide
55 4 LOH (Loss of Heterozygosity) LOH Report Setting LOH Report Setting GeneMapper LOH Default Report Setting Allelic Imbalance 2 Allelic Imbalance Peak Height Ratio Report Setting Genotypes 2 Marker Marker LOH Assessment Thresholds LOH > 1.35 < 0.67 LOH Default Report Setting Allelic Imbalance Marker 4-5 1_Healthy.fsa 1_Tumor.fsa 2_Healthy.fsa 2_Tumor.fsa 3_Healthy.fsa 3_Tumor.fsa... n_healthy.fsa n_tumor.fsa Healthy_1.fsa Healthy_2.fsa Healthy_3.fsa... Healthy_n.fsa Tumor_1.fsa Tumor_2.fsa Tumor_3.fsa... Tumor_n.fsa 4-5 Marker LOH Default Report Setting Allelic Imbalance 1. GeneMapper Manager ToolsGeneMapper Manager 2. Report Settings 4-6 GeneMapper Software v4.0 LOH Getting Started Guide 45
56 4 LOH (Loss of Heterozygosity) LOH Report Setting 3. LOH Default Report Setting Open LOH Default Report Setting Open 4-6 GeneMapper Manager Report Settings 4. Report Settings Editor 4-7 Calculation a. Calculation b. Selected Columns Allelic Imbalance c. Allelic Imbalance Calculation Allelic Imbalance 4-7 Report Settings Editor 5. CalculationAllelic Imbalance Edit 46 GeneMapper Software v4.0 LOH Getting Started Guide
57 4 LOH (Loss of Heterozygosity) LOH Report Setting 6. Edit Calculation n + 1 n m 2 n Edit Calculation 7. OKEdit Calculation 8. Report Settings Editor 4-7 Calculation Allelic Imbalance Selected Columns 9. Report Settings Editor 4-7 a. Analysis b. Selected Columns LOH Assessment c. LOH Assessment Analysis 10. Analysis LOH Assessment Edit GeneMapper Software v4.0 LOH Getting Started Guide 47
58 4 LOH (Loss of Heterozygosity) LOH Report Setting 11. Edit Analysis AnalysisFor every group of n + 1 n For every row 2 n Edit Analysis 12. OKEdit Analysis 13. Report Settings Editor Analysis LOH Assessment Selected Columns 14. OKReport Settings Editor Done GeneMapper Manager LOH Assessment Thresholds DNA LOH Assessment Thresholds 40 LOH Default Report Setting LOH Assessment Thresholds 1. GeneMapper Manager ToolsGeneMapper Manager 2. Report Settings LOH Default Report Setting Open 4. Report Settings Editor a. Analysis b. Selected Columns LOH Assessment c. LOH Assessment Analysis 48 GeneMapper Software v4.0 LOH Getting Started Guide
59 4 LOH (Loss of Heterozygosity) LOH Report Setting 5. Analysis LOH Assessment Edit 6. Edit Analysis Value OKEdit Analysis 8. Report Settings Editor 4-7 Analysis LOH Assessment Selected Columns 9. OKReport Settings Editor Done GeneMapper Manager GeneMapper Software v4.0 LOH Getting Started Guide 49
60 4 LOH (Loss of Heterozygosity) LOH Report Setting 50 GeneMapper Software v4.0 LOH Getting Started Guide
61 LOH (Loss of Heterozygosity) LOH (Loss of Heterozygosity) GeneMapper Software v4.0 LOH Getting Started Guide 51
62 5 FilePrint / GeneMapper Samples GeneMapper Genotypes GeneMapper Info GeneMapper Raw Data GeneMapper EPT Data Samples Plot Genotypes Plot Report Manager GeneMapper Project ViewSamples ViewGenotypes ViewSample Info ViewRaw Data ViewEPT Data Samples AnalysisDisplay Plots Genotypes AnalysisDisplay Plots AnalysisReport Manager Report Settings GeneMapper Software Online Help 52 GeneMapper Software v4.0 LOH Getting Started Guide
63 5 Samples Genotypes GeneMapperSamplesGenotypes 1. a. GeneMapper Table Setting Table Setting b. Edit Sort SamplesGenotypes[Shift] AnalysisLow Quality on TopGQ Table Settings GeneMapper Software Online Help 2. 1 FileExport Table FileExport Combined Table Samples Kit Panel Manager Kit 1. Panel Manager ToolsPanel Manager 2. FileExport All Kits Panel Kit Panel 1. Panel Manager ToolsPanel Manager 2. Kit 3. FileExport Panels Bin Set Bin Set 1. Panel Manager ToolsPanel Manager 2. Bin Set 3. Bin Set Bin Set 4. FileExport Bin Set GeneMapper Software v4.0 LOH Getting Started Guide 53
64 5 Project Settings Size Standard Project Analysis Method Table Settings Plot Settings Reports Settings Size Standard 1. GeneMapper Manager ToolsGeneMapper Manager 2. 1 Projects Analysis Methods Table Settings Plot Settings Report Settings Size Standards 3. [Shift] [Ctrl] 4. Export Report Settings GeneMapper Software Online Help 54 GeneMapper Software v4.0 LOH Getting Started Guide
65 A Advanced 16 Allele Ratio 41 Allelic Imbalance 41, 45 Analysis Method Bin Set 15, Analysis Method Editor Allele 33, 15 General 15 Peak Detector 16 Peak Quality 16 Quality Flags 17 Applied Biosystems vii vii Auto Bin 27 B Bin 27 Auto Bin Bin 27 Marker , Bin Set Analysis Method 15, , 25 F Fill Down 18 G Genotype Quality GQ Genotypes Plot vii Genotypes 34 Genotypes 24 GQ GeneMapper Software v4.0 LOH Getting Started Guide 55 K Kit L , 9 LOH 2, LOH Assessment Thresholds 41, 45, 48 LOH Default Report Setting 41, 45 LOH LOH , M Marker 28 Bin 29 Panel , 5, 9 3, MSDS P vii Panel 9
66 , 9 25 Panel Manager 9 Plot Setting 23, 36, 54 Plot Genotypes Plot Samples Plot R Report LOH 44 44, 52 44, Report Manager 44 Report Setting LOH Default 41, Report Settings Editor 46 S Sample Plot 23, 36 23, 36 Samples Plot Samples 14 Size Match Editor 21 Size Quality (SQ) SQ Size Standard Sizing 24 SQ T Table Settings 14, 19, 54 X X 23, 36 24, 37 Y Y 23, 36 24, Genotypes Plot 52 Report 44, 52 Samples Plot Bin Set 25 Panel 9 Analysis Method 54 Bin Set 53 Genotypes Plot 53 Kit 53 Panel 53 Plot Settings 54 Project 54 Report 44, 54 Report Settings 54 Samples Plot 53 Size Standard 54 Table Settings vi, vii LOH 56 GeneMapper Software v4.0 LOH Getting Started Guide
67 7 14 5, 14 23, 36 Genotypes Plot 36 Samples Plot 23 X 23, 36 Y 23, 36 2 vi 24, v Bin 30 Marker Analysis Method 14 Bin 27 Bin Set 25 Kit 9 LOH 44 Marker 9 Panel 9 Project 12 Report 54 Report Setting 54 LOH 42 23, 36 21, 35 23, , 35, , 36 3, 45 LOH Assessment Thresholds 23, LOH 3 3 LOH 42 21, Marker Bin Size Standard , 11 vii 16 v v! v v v v v vii v GeneMapper Software v4.0 LOH Getting Started Guide 57
68 v Table Settings , , 34 Sample Plot ii Panel Allele Ratio 41 Allelic Imbalance 41, 45 LOH Assessment 41, 45, 48 vi, vii Allelic Imbalance 45 Analysis Method 32 Bin 29 LOH Assessment Thresholds 48 Marker 30 Report Setting Analysis Method LOH v Analysis Method v v vii 58 GeneMapper Software v4.0 LOH Getting Started Guide
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