GeneMapperR Software Version 4.0 マイクロサテライト解析 Getting Started Guide
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1 GeneMapper v4.0 Getting Started Guide
2
3 GeneMapper v4.0 Getting Started Guide
4 Copyright 2005, Applied Biosystems.All rights reserved. Applied Biosystems Applied Biosystems : Applera Corporation GeneMapper HID GeneMapper HID : ABI PRISM, Applied Biosystems, GeneMapper, GeneScan, LIZ and SNaPshot are registered trademarks and AB(Design), Applera GeneMapper, GeneScan and SNPlex are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. This product includes software developed by the Apache Software Foundation ( Copyright The Apache Software Foundation. All rights reserved. This product includes software developed by the ExoLab Project ( exolab.org/). Copyright 2000 Intalio Inc. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., Oracle is a registered trademark of Oracle Corporation. All other trademarks are the sole property of their respective owners. Applera Corporation is committed to providing the world s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. ii GeneMapper Software Version 4.0 Getting Started Guide
5 v v vi vii GeneMapper GeneMapper v Kit Panel Marker Table Settings Auto Bin Bin Set Bin Analysis Method GeneMapper Software Version 4.0 Getting Started Guide iii
6 iv GeneMapper Software Version 4.0 Getting Started Guide
7 GeneMapper Software Version 4.0 Getting Started Guide Applied Biosystems Data Collection GeneMapper GeneMapper GeneMapper Software Version 4.0 Installation and Administration Guide (PN ) GeneMapper v4.0 Microsoft Winows XP 0 [Enter] File Open Spot Set View Filter View All Runs Applied Biosystems 2 Control Console GeneMapper Software Version 4.0 Getting Started Guide v
8 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 v4.0 GeneMapper Software v4.0 Getting Started Guide GeneMapper 5 Applied Biosystems Data Collection LOH AFLP SNaPshot SNPlex GeneMapper GeneMapper Software v4.0 Online Help GeneMapper [F1] Help Contents and Index GeneMapper 3 GeneMapper Software v4.0 Quick Reference Guide GeneMapper GeneMapper Software v4.0 Reference and Troubleshooting Guide PDF GeneMapper Software v4.0 Documentation CD vii GeneMapper [F1] Help Contents and Index GeneMapper 3 vi GeneMapper Software Version 4.0 Getting Started Guide
9 Applied Biosystems Customer Support FAQ Applied Biosystems MSDS Certification of Analysis PDF Applied Biosystems GeneMapper Software Version 4.0 Getting Started Guide vii
10 viii GeneMapper Software Version 4.0 Getting Started Guide
11 GeneMapper GeneMapper v GeneMapper Software Version 4.0 Getting Started Guide 1
12 1 STR DNA PCR PCR GeneMapper Applied Biosystems PCR Applied Biosystems Web Applied Biosystems GeneMapper Software Version 4.0 Quick Reference Guide (PN ) 2 GeneMapper Software Version 4.0 Getting Started Guide
13 1 3.fsa <drive>:\appliedbiosystems\genemapper\example Data\Microsatellite GeneMapper D PCR GeneScan 500 LIZ ABI PRISM bp D6S264 Blue D6S1574 Blue D6S276 Blue D5S408 Blue D6S308 Blue D6S287 Green D6S292 Green D6S434 Green D5S426 Green D5S1981 Yellow D6S257 Yellow D6S446 Yellow D5S641 Yellow D5S433 Red D5S406 Red D5S400 Red D6S309 Red Panel Marker GeneMapper Software Version 4.0 Getting Started Guide 3
14 1 GeneMapper ( 2 ) 1. Kit Panel Marker Table Settings Bin Set Bin Auto Bin ( 3 ) 1. Analysis Method Bin Set ( 4 ) GeneMapper Bin Bin Set Marker Panel Kit Analysis Method Size Standard Panel GeneMapper Marker bp Bin Marker Bin ) Bin Set bp Marker GeneMapper Panel Bin Set Marker Bin Panel 4 GeneMapper Software Version 4.0 Getting Started Guide
15 1 GeneMapper 1. Start All Program Applied Biosystems GeneMapper GeneMapper Login to GeneMapper a. b. OK GeneMapper Software Online Help GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 GeneMapper Software Version 4.0 Getting Started Guide 5
16 1 GeneMapper GeneMapper 2 GeneMapper Data Collection GeneMapper Version 4.0 Installation and Administration Guide (PN ) GeneMapper 2 GeneMapper GeneMapper Version 4.0 Installation and Administration Guide (PN ) 6 GeneMapper Software Version 4.0 Getting Started Guide
17 Kit Panel Marker Table Settings Auto Bin Bin Set Bin GeneMapper Software Version 4.0 Getting Started Guide 7
18 2 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 Version 4.0 Getting Started Guide
19 2 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 Tools Panel Manager 2. Panel Manager File New Kit 3. New Kit Kit Name Microsatellite Kit Kit Type Microsatellite OK GeneMapper Software Version 4.0 Getting Started Guide 9
20 2 Kit Panel Marker Microsatellite Kit 4. Microsatellite Kit File New Panel 5. Panel Manager New Panel Panel Name Microsatellite Panel Enter Microsatellite Kit Microsatellite Panel 6. Microsatellite Panel File New Marker 7. Panel Manager Marker 10 GeneMapper Software Version 4.0 Getting Started Guide
21 2 Kit Panel Marker Marker Marker Dye Color Minimum Size (bp) Maximum Size (bp) Marker Repeat D6S1574 Blue D6S276 Blue D5S408 Blue D6S308 Blue D6S287 Green D6S292 Green D6S434 Green D5S426 Green D5S1981 Yellow D6S257 Yellow D6S446 Yellow D5S641 Yellow D5S433 Red D5S406 Red D5S400 Red D6S309 Red Panel Manager OK 12.fsa GeneMapper Software Version 4.0 Getting Started Guide 11
22 2 GeneMapper Project Project 1. File New Project 2. New Project Microsatellite OK 3. GeneMapper File Add Samples to Project 4. Add Samples to Project Files <drive>:\appliedbiosystems\genemapper\example Data GeneMapper D 5. Microsatellite Add to List Add Microsatellite 3 2 [Ctrl] Add To List 12 GeneMapper Software Version 4.0 Getting Started Guide
23 2 Microsatellite 3 Applied Biosystems Data Collection Samples 14 GeneMapper Software Version 4.0 Getting Started Guide 13
24 2 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 Version 4.0 Getting Started Guide
25 2 Table Settings 4. Analysis Method Editor 5 General Name Microsatellite Analysis Method Allele Bin Set None GeneMapper Software Version 4.0 Getting Started Guide 15
26 2 Table Settings Peak Detector Peak Detection Algorithm Basic Peak Quality Process Quality Values PQV (Pass) (Check) Homozygous min peak height Heterozygous min peak height 85.0 Min peak height ratio GeneMapper Software Version 4.0 Getting Started Guide
27 2 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 Version 4.0 Getting Started Guide 17
28 2 Table Settings 6. Panel Select a Panel Microsatellite Kit Microsatellite Panel 9 Microsatellite Kit 7. Size Standard GS500 (-250)LIZ 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. Edit Fill Down[Ctrl] [D] 18 GeneMapper Software Version 4.0 Getting Started Guide
29 2 Table Settings Table Settings GeneMapper Table Settings Microsatellite Default Table Settings Samples Genotypes Microsatellite Default GeneMapper Table Settings 1 GeneMapper Manager Table Settings GeneMapper Software Online Help 1. File Save Project 2. Save Project Microsatellite Project OK GeneMapper Microsatellite Project 20 GeneMapper Software Version 4.0 Getting Started Guide 19
30 2 Panel GeneMapper Analysis Method Bin Set Genotype Quality (GQ) SQ PQV Raw Data Analysis Analyze 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 Version 4.0 Getting Started Guide
31 2 SQ SQ (Check) (Low Quality) PQV SFNF MNF SNF OS 21 SQ Samples SQ 1. Edit Select AllSamples 2. Size Match Editor Analysis Size 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 Version 4.0 Getting Started Guide 21
32 2 6. Size Calling Curve 7. Size Match Editor OK Size Match Editor 2-1 Sizing Quality SQ (Check) (Low Quality) Size Matches Override 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 Version 4.0 Getting Started Guide
![2 1. View Samples Samples 2. Samples [Shift] [Ctrl] Edit Select All 3. Analysis Display Plots Samples Plot Plot Setting Microsatellite Default X - 4.](/docs-images/92/110410850/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 1. View Samples Samples 2. Samples [Shift] [Ctrl] Edit Select All 3. Analysis Display 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 Version 4.0 Getting Started Guide 23
![2 Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing 24 2-2 [F1] GeneMapper Software Online Help Samples Plot 25 Auto Bin Bin Set](/docs-images/92/110410850/images/34-0.jpg "Bin Sizing [Ctrl] [Shift] Sizing Sizing : Sizing [Ctrl] [G] Sizing 2-2 Samples Plot 24 GeneMapper Software Version 4.")
34 2 Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing [F1] GeneMapper Software Online Help Samples Plot 25 Auto Bin Bin Set Bin Sizing [Ctrl] [Shift] Sizing Sizing : Sizing [Ctrl] [G] Sizing 2-2 Samples Plot 24 GeneMapper Software Version 4.0 Getting Started Guide
35 2 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 Tools Panel Manager 2. 9 Microsatellite Kit 3. Bins New Bin Set 4. New Bin Set Bin Set Name Microsatellite Bin Set OK Panel Manager Bin Set Microsatellite Bin Set Microsatellite Bin Set Microsatellite Panel Microsatellite Kit Panel GeneMapper Software Version 4.0 Getting Started Guide 25
36 2 Auto Bin Bin Set Bin Panel Bin Set Microsatellite Panel Microsatellite Bin Set 1. Bin Set Microsatellite Bin Set 2. Microsatellite Kit 9 Microsatellite Panel Marker Panel Manager Bins Add Reference Data Add Microsatellite Reference Data Microsatellite Project Panel 12 Microsatellite Project 26 GeneMapper Software Version 4.0 Getting Started Guide
37 2 Auto Bin Bin Set Bin 4. Microsatellite Project Microsatellite Add to List Add Microsatellite Project Microsatellite Panel Panel Manager Panel Marker Panel Manager Auto Bin Bin Auto Bin Bin 1. Microsatellite Panel Bin Set Microsatellite Bin Set Bins Auto Bin 2. Auto Bin Minimum quality value 0.1 Allele Naming Scheme Number Auto Bin Options Auto Bin (clear existing bins) 3. OK 4. Autobinning completedok 5. Panel Manager Apply GeneMapper Software Version 4.0 Getting Started Guide 27
38 2 Auto Bin Bin Set Bin Marker Bin Marker Bin 1. Microsatellite 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 28 GeneMapper Software Version 4.0 Getting Started Guide
39 2 Auto Bin Bin Set Bin Marker 2-5 Marker Bin Set Bin Set Panel Manager OK Bin Marker Bin Marker Panel Manager Microsatellite Kit Microsatellite Panel Bin Marker Panel Manager CancelOK Apply Marker Bin 1. Marker Bins Add Bin 2. Bin 3. Add Bin Bin Name Location Offsets OK Bin 1. Bin 2. Bins Edit Bin Bin Edit Bin 3. Edit Bin Bin Name Location Offsets OK GeneMapper Software Version 4.0 Getting Started Guide 29
40 2 Auto Bin Bin Set Bin Bin 1. BinBin Bin 3. Bin Edit Undo Bin Bin 2-6 Bin Bin Bin Marker Bin Bins Delete Bin Bin Bin Delete Bin Marker 1. Marker Marker Edit Undo Marker 2-7 Marker 30 GeneMapper Software Version 4.0 Getting Started Guide
41 2 Auto Bin Bin Set Bin Panel Marker 1. Marker 2. Edit Clear Marker 3 GeneMapper Software Version 4.0 Getting Started Guide 31
42 2 Auto Bin Bin Set Bin 32 GeneMapper Software Version 4.0 Getting Started Guide
43 3 Analysis Method GeneMapper Software Version 4.0 Getting Started Guide 33
44 3 Analysis Method Analysis Method Analysis Method 14 Microsatellite Analysis Method Bin Set Bin Set Analysis Method Bin Set Bin Set GeneMapper Microsatellite Analysis Method 1. GeneMapper Manager Tools GeneMapper Manager 2. Analysis Methods 3. Microsatellite Analysis Method Open 34 GeneMapper Software Version 4.0 Getting Started Guide
45 3 Analysis Method 4. Analysis Method Editor AlleleBin Set Microsatellite Bin Set OK 5. Done GeneMapper Manager GeneMapperSamples Analysis Method Analysis Method Editor GeneMapper Software Version 4.0 Getting Started Guide 35
46 3 Analysis Method Bin Set GeneMapper GeneMapperSamples Status Samples Microsatellite Analysis Method REF Bin Set Analysis Analyze GeneMapper GeneMapper 36 GeneMapper Software Version 4.0 Getting Started Guide
47 3 SQ PQV Size Standard GQ PQV Genotype Plot 38 Genotypes Plot GQ PQV Genotype Quality (GQ) Genotypes Genotypes GQ GQ (Pass) GQ Process Quality Values (PQV) AN BD BIN LPH OBA OS PHR SHP SP SPA SPU XTLK GQ GQ (Check) (Low Quality) GQ PQV AN BD BIN CC LPH OBA OS PHR SHP SP SPA SPU XTLK Marker Bin GeneMapper Software Reference and Troubleshooting Guide GQ Genotypes GQ GeneMapper Software Version 4.0 Getting Started Guide 37
48 3 Marker Genotypes Allele 1Allele 2 Marker Genotype Plot Genotypes Plot 1. Genotypes Marker Marker [Shift] [Ctrl] Marker Edit Select All 2. Analysis Display 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 38 GeneMapper Software Version 4.0 Getting Started Guide
49 3 4. Genotypes Plot X Y X X Zoom To OK Y Y Zoom To Apply to all electropherogramsok X Y X Y Full View Genotypes Plot Genotypes Plot X ) Y Marker Bin [F1] GeneMapper Software Online Help Genotypes Plot Marker 1. Panel Manager Tools Panel Manager 2. Microsatellite Kit Microsatellite Panel Marker 3. Bins Show Project Alleles Y Marker GQ GeneMapper Software Version 4.0 Getting Started Guide 39
50 3 40 GeneMapper Software Version 4.0 Getting Started Guide
51 GeneMapper Software Version 4.0 Getting Started Guide 41
52 4 File Print / GeneMapper Samples GeneMapper Genotypes GeneMapper Info GeneMapper Raw Data GeneMapper EPT Data Samples Plot Genotypes Plot Report Manager GeneMapper Project View Samples View Genotypes View Sample Info View Raw Data View EPT Data SamplesAnalysis Display Plots GenotypesAnalysis Display Plots Analysis Report Manager Report Settings GeneMapper Software Online Help 42 GeneMapper Software Version 4.0 Getting Started Guide
53 4 Samples Genotypes GeneMapperSamples Genotypes 1. a. GeneMapper Table Setting Table Setting b. Edit Sort Samples Genotypes [Shift] Analysis Low Quality on TopGQ Table Settings GeneMapper Software Online Help 2. 1 File Export Table File Export Combined Table Samples Kit Panel Manager Kit 1. Panel Manager Tools Panel Manager 2. File Export All Kits Panel Kit Panel 1. Panel Manager Tools Panel Manager 2. Kit 3. File Export Panels Bin Set Bin Set 1. Panel Manager Tools Panel Manager 2. Bin Set Kit 3. Bin Set Bin Set 4. File Export Bin Set GeneMapper Software Version 4.0 Getting Started Guide 43
54 4 Project Settings Size Standard Project Analysis Method Table Settings Plot Settings Reports Settings Size Standard 1. GeneMapper Manager Tools GeneMapper 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 44 GeneMapper Software Version 4.0 Getting Started Guide
55 A Advanced 16 Analysis Method , Analysis Method Editor Allele 15, 35 General 15 Peak Detector 16 Peak Quality 16 Quality Flags 17 Applied Biosystems vii vii vii Auto Bin 27 B Bin Auto Bin 27 Marker , Bin Set Analysis Method 15, , 25 G Genotype QualityGQ Genotypes Plot Genotypes 37 Genotypes 24 GQ H Heterozygous min peak height 16 Homozygous min peak height 16 K Kit M , 9 2 Marker Bin 29 Panel , 4, 9 3, Min peak height ratio 16 MSDS P vii Panel , 9 26 Panel Manager 9 Plot Setting 23, 38, 44 Plot Genotypes Plot GeneMapper Software Version 4.0 Getting Started Guide 45
56 R Samples Plot Report Report Settings 44 S Samples Plot Samples 14 Size Match Editor 21 Size Standard Size Quality (SQ) SQ Sizing 24 SQ T Table Settings 14, 19, 44 X X 23, 39 24, 39 Y Y 23, 39 24, Genotypes Plot 42 Report 42 Samples Plot Bin Set 25 Panel 9 Analysis Method 44 Bin Set 43 Genotypes Plot 43 Kit 43 Panel 43 Plot Settings 44 Project 44 Report 44 Report Settings 44 Samples Plot 43 Size Standard 44 Table Settings , 14 23, 39 Genotypes Plot 39 Samples Plot 23 X 23, 39 Y 23, 39 vi 24, vi 46 GeneMapper Software Version 4.0 Getting Started Guide
57 22 Bin 30 Marker Analysis Method 14 Bin 27 Bin Set 25 Kit 9 Marker 9 Panel 9 Project 12 Report 44 23, 39 21, 37 23, , , 38 23, 39 23, 38 23, v Marker Bin Size Standard , 11 vii 16 v v! v v v v v 30 vii 18 v 2 Table Settings , , 36 vi v GeneMapper Software Version 4.0 Getting Started Guide 47
58 Analysis Method 34 Bin 29, 30 Marker Analysis Method v Analysis Method v v vii ii Panel GeneMapper Software Version 4.0 Getting Started Guide
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