GeneMapper. Software Version 4.0 LOH Analysis Getting Started Guide (PN Rev. B)
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1 GeneMapper v4.0 SNaPshot Kit SNP Getting Started Guide Panel Bin Set Primer Focus Kit Panel Bin Set SNaPshot Kit
2
3 GeneMapper v4.0 SNaPshot Kit SNP Getting Started Guide Panel Bin Set Primer Focus Kit Panel Bin Set SNaPshot Kit
4 Copyright Copyright 2005, Applied Biosystems.All rights reserved. Applied Biosystems Applied Biosystems : Applera Corporation GeneMapper Software has not undergone specific developmental validation for human identification applications. Human identification laboratories analyzing single-source or parentage samples which choose to use GeneMapper Software for data analysis should perform their own developmental validation studies. : ABI PRISM, Applied Biosystems, GeneMapper, LIZ, Primer Focus, and SNaPshot are registered trademarks, and the AB Design, Applera, GeneMapper 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. Allrights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., AFLP is a registered trademark of Keygene N.V. Microsoft is registered trademark of Microsoft Corporation. Oracle is a registered trademark of Oracle Corporation. All other trademarks are the sole property of their respective owners. Applera Corporation is committed to providing the world's leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. Part Number Rev. B 06/2005 ii GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
5 v v vi vii 1 1 SNaPshot Kit SNaPshot Kit GeneMapper GeneMapper v Panel Bin Set Table Settings Kit Panel Marker Bin Set Bin Primer Focus Kit Panel Bin Set 31 Primer Focus Kit Table Settings Kit Panel Marker Bin Set Bin SNaPshot Kit Table Settings GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide iii
6 iv GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
7 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide Applied Biosystems Data Collection SNaPshot Kit GeneMapper GeneMapper GeneMapper Software v4.0 Quick 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 GeneMapper Software Version 4.0 SNaPshot Kit SNP 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 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 IndexGeneMapper 3 GeneMapper Software v4.0 Quick Reference Guide GeneMapper GeneMapper Software v4.0 Reference and Troubleshooting Guide PDF GeneMapper v4.0 Documentation CD vii vi GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
9 GeneMapper [F1] Help Contents and IndexGeneMapper 3 Applied Biosystems jptechsupport@appliedbiosystems.com Customer Support FAQ Applied Biosystems MSDS Certification of Analysis PDF Applied Biosystems GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide vii
10 viii GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
11 1 SNaPshot Kit SNaPshot Kit GeneMapper GeneMapper v GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 1
12 1 SNaPshot Kit SNaPshot Kit SNP SNP (Single Nucleotide Polymorphism) DNA 4...TCGTTGTAGCGCTTAGA......AGCAACATCGCTAATCT......TCGTTGTAACGCTTAGA......AGCAACATTGCTAATCT... G-C A-T SNP 2 SNaPshot Kit SNaPshot Muliplex Kit SNaPshot Multiplex Kit SNP PCR 10 SNP SNP ddntp 4 ddntp SNP GeneMapper ( 1-1 ) SNaPshot Multiplex Kit 10 SNP SNP GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
13 1 SNaPshot Kit 5 3 TCGTTGTA...NNNNNAGCAACATCGCTAANNNNN... SNP TCGTTGTAG...NNNNNAGCAACATCGCTAANNNNN... ddgtp ddctp ddutp ddatp TCGTTGTAG Applied Biosystems GR1770 GeneMapper = 1-1 SNaPshot Muliplex Kit A G C T C G 1-2 Primer Focus Kit Primer Focus Kit SNP 4 4 ddntp SNaPshot 3 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 3
14 1 SNaPshot Kit GeneMapper Primer Focus Kit SNP Auto Panel SNP Bin ddgtp ddctp ddutp ddatp G C SNP Primer Focus Kit 4 ddntp U A SNaPshot Kit Applied Biosystems Kit SNaPshot Multiplex Kit (PN: ) Primer Focus Kit (PN: ) SNaPshot Applied Biosystems GeneMapper Software v4.0 Quick Reference Guide (PN ) 4 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
15 1 3.fsa 6 Primer Focus Kit <drive>:\appliedbiosystems\genemapper\example Data\SNaPshot GeneMapper D SNaPshot Multiplex Kit GeneScan 120 LIZ ABI PRISM 3100 Primer Focus Kit GeneScan 120 LIZ ABI PRISM 3100 SNaPshot Kit 6 2 Marker Bin 3 GeneMapper Primer Focus Kit Auto Panel Marker Bin GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 5
16 1 SNaPshot Kit SNaPshot Kit GeneMapper SNaPshot Panel Bin Set ( 2 ) Table Settings Kit Panel Marker Bin Set Bin Primer Focus Kit Panel Bin Set ( 3 ) 1. Primer Focus Kit 2. Table Settings Kit Panel Marker Bin Set Bin SNaPshot Kit ( 4 ) Table Settings ( 5 ) ( 6 ) 6 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
17 1 GeneMapper GeneMapper Bin/ Bin Set/ Marker/ Panel/ Kit/ Analysis Method Size Standard Panel GeneMapper Marker bp Bin Marker Bin Bin Set SNP Marker bp Marker GeneMapper Panel Bin Set Marker Bin GeneMapper 1. Start All Program Applied Biosystems GeneMapper GeneMapper Login to GeneMapper a. b. OK SNaPshot Kit GeneMapper Software Online Help GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 SNaPshot Kit GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 7
18 1 GeneMapper SNaPshot Kit GeneMapper SNaPshot Kit SNaPshot Kit GeneMapper Data Collection SNaPshot Kit GeneMapper Software v4.0 Quick Installation and Administration Guide (PN ) GeneMapper SNaPshot Kit GeneMapper GeneMapper Software v4.0 Quick Installation and Administration Guide (PN ) 8 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
19 2 Panel Bin Set Table Settings Kit Panel Marker Bin Set Bin Marker Bin Primer Focus Kit Auto Panel Marker Bin 3 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 9
20 2 Panel Bin Set GeneMapper 1. File New Project 2. New Project SNaPshot OK GeneMapper v GeneMapper File Add Samples to Project 4. Add Samples to Project Files <drive>:\appliedbiosystems\genemapper\example Data\SNaPshot GeneMapper D 10 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
21 2 Panel Bin Set 5. SNaPshot Add to List Add SNaPshot [Ctrl] Add To List SNaPshot 3 Applied Biosystems Data Collection Samples 12 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 11
22 2 Panel Bin Set Table Settings Table Settings GeneMapper Analysis Method Bin Set Size Standard Panel Marker ) GeneMapper Table Settings Plot Settings 1. GeneMapperSamples 2. Analysis Method SNaPshot Default 3. Panel None Panel GeneMapper Panel Bin Set Panel 4. Size Standard GS120LIZ 5. Samples a. Analysis Method Panel Size Standard 3 b. Edit Fill Down[Ctrl] [D] 12 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
23 2 Panel Bin Set Table Settings Table Settings GeneMapper Table Settings SNaPshot Default Table Settings Samples Genotypes SNaPshot Default GeneMapper Table Settings 1 GeneMapper Manager Table Settings GeneMapper Software Online Help 1. File Save Project 2. Save Project SNaPshot Ref Data Project OK GeneMapper SNaPshot Ref Data Project 14 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 13
24 2 Panel Bin Set Bin 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 14 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
25 2 Panel Bin Set SQ SQ (Check) (Low Quality) PQV SFNF MNF SNF OS 15 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 SNaPshot Kit SNP Getting Started Guide 15
26 2 Panel Bin Set 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 2-1Sizing 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 16 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
27 2 Panel Bin Set 1. View Samples Samples 2. Samples [Shift] [Ctrl] Edit Select All 3. Analysis Display Plots Samples Plot Plot Setting SNaPshot Default X - 4. Plot Setting SNaPshot Default Plot Settings Samples Plot SNaPshot Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 5. Samples Plot X Y X X [Shift] X Zoom To OK Y Y Zoom To Apply to all electropherogramsok X Y X Y Full View GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 17
28 2 Panel Bin Set Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing [F1] GeneMapper Software Online Help Samples Plot Bin Kit 21 Marker Bin 24 Samples Plot 19 Kit Panel Marker Bin Set Bin Sizing Sizing [Ctrl] [Shift] Sizing : Sizing [Ctrl] [G] Sizing 2-2 Samples Plot 18 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
29 2 Panel Bin Set Kit Panel Marker Bin Set Bin Kit Panel Marker Bin Set Bin Panel Manager Kit Panel Panel Marker Marker bp Panel Marker Marker Panel Panel GeneMapper Software Online Help Panel Manager Bin Set Bin Bin bp Bin Set Kit SNP Kit Bin Set 1 Bin Set SNP Kit Panel Bin Panel Bin Set Bin Panel Marker Bin Set Bin Primer Focus Kit Auto Panel Bin Bin Bin Set Bin 3 Primer Focus Kit Panel Bin Set Bin Set GeneMapper Software Online Help Kit Panel Kit Panel 1. Panel Manager Tools Panel Manager 2. Panel Manager File New Kit GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 19
30 2 Panel Bin Set Kit Panel Marker Bin Set Bin 3. New Kit Kit Name SNaPshot Kit Kit TypeSNPOK SNaPshot Kit 4. SNaPshot Kit File New Panel 5. Panel Manager New Panel Panel Name SNaPshot 6plex Panel [Enter] SNaPshot Kit SNaPshot 6plex Panel 20 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
31 2 Panel Bin Set Kit Panel Marker Bin Set Bin Bin Set Bin Set SNaPshot Kit 2. Bins New Bin Set 3. New Bin Set Bin Set Name SNaPshot Bin Set OK Panel Manager Bin Set SNaPshot Bin Set SNaPshot Bin Set SNaPshot Panel SNaPshot Kit Panel Kit SNaPshot Kit SNaPshot Kit GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 21
32 2 Panel Bin Set Kit Panel Marker Bin Set Bin 2. Bins Add Reference Data Add SNP Reference Data Search SNaPshot Ref Data Project SNaPshot Add To List Add 3. Search GeneMapper 4. SNaPshot Ref Data Project SNaPshot Add to List Add SNaPshot Data 3 SNaPshot Kit Panel Manager 22 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
33 2 Panel Bin Set Kit Panel Marker Bin Set Bin Panel Kit Kit Panel SNaPshot 6plex Panel SNaPshot 6plex Panel 2. Bins Panel Reference Data 3. SNP Reference Data SNaPshot Kit [Shift] 3 4. SNaPshot Kit 3 SNaPshot 6plex Panel 5. OK GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 23
34 2 Panel Bin Set Kit Panel Marker Bin Set Bin Marker Bin 3 Marker Bin 1. Panel Manager Plot 2. a. SNaPshot 6plex Panel b. 5_E03_09.fsa 5_E03_09.fsa Plot Plot SNaPshot 6plex Panel 5_E03_09.fsa 3. ViewX Y X Y 4. X GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
35 2 Panel Bin Set Kit Panel Marker Bin Set Bin 5. File New SNP Marker 6. In the Add Marker a. Marker Name 25mer b. Green Allele Min 24.5Max 26.0 c. Name ddntp G A C T Primer Focus Kit Bin d. OK Marker Bin SNaPshot 6plex Panel Marker Bin Bin bp Marker bp 7. View Full View GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 25
36 2 Panel Bin Set Kit Panel Marker Bin Set Bin 8. SNP Marker Marker Bin SNaPshot 6plex Panel Bin GeneMapper Bin Marker 26 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
37 2 Panel Bin Set Kit Panel Marker Bin Set Bin 10. Bin 4 SNP 39mer 48mer 54mer 62mer Marker Bin Marker Name Allele Color Allele Name Min Max 39mer Blue G mer Red T mer Yellow C Red T mer Yellow C bp 11. SNaPshot 6plex Panel 2 2_B03_03.fsa 6_F03_11.fsa Plot 5_E03_09.fsa Bin Bin Bin 4 7 Bin GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 27
38 2 Panel Bin Set Kit Panel Marker Bin Set Bin Marker Bin Marker Bin 1. Panel Manager SNaPshot 6plex Panel Reference Samples Plot Panel X Marker X Bin 2. Panel Manager Table Marker Bin 3. Apply Marker Bin Bin Set Bin Set Panel Manager OK Bin Marker Marker Bin Panel Manager SNaPshot Kit SNaPshot 6plex Panel 29 SNaPshot 6plex Panel Marker Bin Panel Manager Cancel OK Apply 28 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
39 2 Panel Bin Set Kit Panel Marker Bin Set Bin Marker Bin 1. Plot X TableMarker 2. Bins Add Bin 3. Edit SNP Marker Bin Name Min Max OK Bin 1. Plot Bin X 2. Bins Edit Bin Bin Edit SNP Marker 3. Edit SNP Marker Bin Name Min Max OK 1. Table 2. Bin Name Bin Min Bin Max Bin 1. Plot Bin X 2. Bin 3. Bin Edit Undo Bin Bin GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 29
40 2 Panel Bin Set Kit Panel Marker Bin Set Bin Bin Bin Marker Plot Table Bin Bins Delete Bin Plot Bin X Bin Delete Bin Marker 1. Plot Marker X 2. Bins Edit SNP Marker Marker Edit SNP Marker 3. Edit SNP Marker Marker Name OK TableMarker Name Panel Marker Panel Marker Plot Marker X Marker Delete Marker 4 SNaPshot 30 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
41 3 Primer Focus Kit Panel Bin Set Primer Focus Kit Table Settings Kit Panel Marker Bin Set Bin Primer Focus Kit Marker Bin Marker Bin 2 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 31
42 3 Primer Focus Kit Panel Bin Set Primer Focus Kit Primer Focus Kit GeneMapper 1. File New Project 2. New Project SNaPshot OK GeneMapper v GeneMapper File Add Samples to Project 4. Add Samples to Project Files <drive>:\appliedbiosystems\genemapper\example Data\SNaPshot GeneMapper D 32 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
43 3 Primer Focus Kit Panel Bin Set Primer Focus Kit 5. Primer Focus Add to List Add Primer Focus [Ctrl] Add To List Primer Focus 6 Applied Biosystems Data Collection Samples 34 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 33
44 3 Primer Focus Kit Panel Bin Set Table Settings Table Settings GeneMapper Sample Type Analysis Method Bin Set Size Standard Panel Marker ) GeneMapper Table Settings Plot Settings 1. GeneMapperSamples 2. Sample Type Primer Focus 3. Analysis Method SNaPshot Default 4. Panel None Panel Panel GeneMapper Panel Bin Set Panel 5. Size Standard GS120LIZ 34 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
45 3 Primer Focus Kit Panel Bin Set Table Settings 6. Samples a. Analysis Method Panel Size Standard 3 b. Edit Fill Down[Ctrl] [D] Table Settings GeneMapper Table Settings SNaPshot Default Table Settings Samples Genotypes SNaPshot Default GeneMapper Table Settings 1 GeneMapper Manager Table Settings GeneMapper Software Online Help 1. File Save Project 2. Save Project SNaPshot Primer Focus Data Project OK GeneMapper SNaPshot Primer Focus Data Project 36 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 35
46 3 Primer Focus Kit Panel Bin Set Bin 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 36 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
47 3 Primer Focus Kit Panel Bin Set SQ SQ (Check) (Low Quality) PQV SFNF MNF SNF OS 37 SQ Samples SQ 1. Edit Select AllSamples 2. Size Match Editor Analysis Size Match Editor Size Quality (SQ) 3-1 Size Match Editor Size Matches 3. Size Matches Size Quality (SQ) 4. Sizing Quality 3-1 SQ (Pass) (Check) (Low Quality) Sizing Quality > 0.75 SQ (Pass) Sizing Quality SQ (Check) (Low Quality) GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 37
48 3 Primer Focus Kit Panel Bin Set 6. Size Calling Curve 7. Size Match Editor OK Size Match Editor Sizing Quality SQ (Check) (Low Quality) Size Matches Override SQ Sizing Quality 3-1 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 38 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
49 3 Primer Focus Kit Panel Bin Set 1. View Samples Samples 2. Samples [Shift] [Ctrl] Edit Select All 3. Analysis Display Plots Samples Plot Plot Setting SNaPshot Default X - 4. Plot Setting SNaPshot Default Plot Settings Samples Plot SNaPshot 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 electropherograms OK X Y X Y Full View GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 39
50 3 Primer Focus Kit Panel Bin Set Samples Plot Samples Plot X ) Y Sizing Genotypes Sizing [F1] GeneMapper Software Online Help Samples Plot 41 Kit Panel Marker Bin Set Bin Sizing Sizing [Ctrl] [Shift] Sizing : Sizing [Ctrl] [G] Sizing 3-2 Samples Plot 40 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
51 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin Kit Panel Marker Bin Set Bin Panel Manager Kit Panel Panel Marker Marker bp Panel Marker Marker Panel Panel GeneMapper Software Online Help Panel Manager Bin Set Bin Bin bp Bin Set Kit SNP Kit Bin Set 1 Bin Set SNP Kit Panel Bin Panel Bin Set Bin Panel Marker Bin Set Primer Focus Kit Auto Panel Bin Bin Bin Bin Set Bin 2 Panel Bin Set Bin Set Bin GeneMapper Software Online Help Kit Kit 1. Panel Manager Tools Panel Manager 2. Panel Manager File New Kit GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 41
52 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin 3. New Kit Kit Name Primer Focus Kit Kit TypeSNPOK Primer Focus Kit Bin Set Bin Set Primer Focus Kit 2. Bins New Bin Set 3. New Bin Set Bin Set Name Primer Focus Bin Set OK Panel Manager Bin Set Primer Focus Bin Set Primer Focus Bin Set Primer Focus Kit 42 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
53 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin Primer Focus Kit Kit Primer Focus Kit Primer Focus Kit Primer Focus Kit 2. Bins Add Reference Data Add SNP Reference Primer Focus Kit GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 43
54 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin 3. SNaPshot Primer Focus Data Project Primer Focus Add to List Add 32 SNaPshot Primer Focus Data Project Primer Focus SNaPshot Primer Focus Data Project 6 Primer Focus Kit Primer Focus Kit Panel Manager 44 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
55 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin Auto Panel Panel Marker Bin Auto Panel Panel Marker Bin Primer Focus Kit 2. Bins Add Panel 3. Auto Panel Allele Names ddntp G A C T Primer Focus Bin Marker Primer Focus Kit Marker Multiplex 5 20 Auto Panel Panel Marker Panel Names Primer Focus Panel Panel Marker Multiplex Panel Panel Primer Focus Panel_1 Primer Focus Panel_2 Marker Overlap Maximum Overlap Maximum Overlap Panel Marker Bin Save Existing Panels Panel Marker 4. Primer Focus Kit Auto Panel OK Marker Bin Auto Panel Panel 1. Primer Focus Kit 2. Primer Focus Panel-1 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 45
56 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin 3. Plot Panel X Marker X Bin Panel Primer Focus Kit 4. Table Marker Bin Panel Bin Set Panel Bin Set Panel Manager OK Bin Marker Marker Bin Panel Manager Primer Focus Kit Primer Focus Panel-1 Marker Bin Panel Manager CancelOK Apply Marker Bin 1. Plot X TableMarker 2. Bins Add Bin 3. Edit SNP Marker Bin Name Min Max OK 46 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
57 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin Bin 1. Plot Bin X 2. Bins Edit BinEdit SNP Marker 3. Edit SNP Marker Bin Name Min Max OK 1. Table 2. Bin Name Bin Min Bin Max Bin 1. Plot Bin X 2. Bin 3. Bin Edit Undo Bin Bin Bin Bin Marker Plot Table Bin Bins Delete Bin Plot Bin X Bin Delete Bin GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 47
58 3 Primer Focus Kit Panel Bin Set Kit Panel Marker Bin Set Bin Marker 1. Plot Marker X 2. Bins Edit SNP Marker Marker Edit SNP Marker 3. Edit SNP Marker Marker Name OK TableMarker Name Panel Marker Panel Marker Plot Marker X Marker Delete Marker 4 SNaPshot Kit 48 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
59 4 SNaPshot Kit Table Settings GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 49
60 4 SNaPshot Kit 1. File New Project 2. New Project SNaPshot OK GeneMapper v GeneMapper File Add Samples to Project 4. Add Samples to Project Files <drive>:\appliedbiosystems\genemapper\example Data\SNaPshot GeneMapper D 50 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
61 4 SNaPshot Kit 5. SNaPshot Add to List Add SNaPshot 3 2 [Ctrl] Add To List SNaPshot Data 3 Applied Biosystems Data Collection Samples 52 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 51
62 4 SNaPshot Kit 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 Analysis Method 3. New Analysis Method Analysis Type SNaPshot OK 52 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
63 4 SNaPshot Kit Table Settings 4. Analysis Method Editor 5 General Analysis method Name SNaPshot Analysis Method Allele Bin Set 1 SNaPshot Bin Set 2 SNaPshot Bin Set Primer Focus Bin Set 3 Primer Focus Kit Bin Set GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 53
64 4 SNaPshot Kit Table Settings Peak Detector Peak Detection Algorithm Basic Peak Quality Process Quality Values PQV (Pass) (Check) Min peak height ratio GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
65 4 SNaPshot Kit 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 6. Panel Select a Panel 1 SNaPshot Kit SNaPshot 6plex Panel 2 SNaPshot Panel Primer Focus Kit Primer Focus Panel-1 3 Primer Focus Kit Panel Kit Panel GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 55
66 4 SNaPshot Kit Table Settings 7. Size Standard GS120LIZ 8. Samples a. Analysis Method Panel Size Standard 3 b. Edit Fill Down[Ctrl] [D] Table Settings GeneMapper Table Settings SNaPshot Default Table Settings Samples Genotypes SNaPshot Default GeneMapper Table Settings 1 GeneMapper Manager Table Settings GeneMapper Software Online Help 1. File Save Project 2. Save Project SNaPshot Project OK GeneMapper SNaPshot Project 5 SNaPshot 56 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
67 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 57
68 5 Bin Set Panel Analysis Method GeneMapper GeneMapperSamples Status Samples Analysis Analyze GeneMapper GeneMapper 58 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
69 5 SQ PQV Size Standard GQ PQV Genotype Plot 60 Genotypes Plot 61 GQ PQV Genotype Quality (GQ) Genotypes Genotypes GQ GQ (Pass) GQ AN BD BIN DP LPH NB OS PHR SPU PQV GQ GQ (Check) (Low Quality) GQ PQV AN BD BIN DP LPH NB OS PHR SPU Marker Bin GeneMapper Software Reference and Troubleshooting Guide GQ Genotypes GQ GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 59
70 5 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 SNaPshot Default X - 3. Plot Setting SNaPshot Default Plot Settings Genotypes Plot SNaPshot Default GeneMapper Plot Settings 1 GeneMapper Manager Plot Settings GeneMapper Software Online Help 60 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
71 5 4. Genotypes Plot X Y X 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 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 61
72 5 62 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
73 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 63
74 6 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 64 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
75 6 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 SNaPshot Kit SNP Getting Started Guide 65
76 6 Settings Size Standard 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 66 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
77 A Advanced 54 Analysis Method Bin Set , 34, Analysis Method Editor Allele 53 General 53 Peak Detector 54 Peak Quality 54 Quality Flags 55 Analysis Method Editor Allele 53 Analysis Method Editor General 53 Analysis Method Editor Peak Detector 54 Analysis Method Editor Peak Quality 54 Analysis Method Editor Quality Flags 55 Applied Biosystems vii vii vii Auto Panel 45 B Bin Marker 29, 46 28, 45 30, , 19, 41 29, 47 Bin Set Analysis Method 53 19, , 46 21, 42 7, 19, 41 F Fill Down 12, 35, 56 G Genotype Quality GQ Genotypes Plot Genotypes 59 Genotypes 18, 40 GQ K Kit Primer Focus 3 Primer Focus Kit 43 SNaPshot Multiplex , 41 20, 42 7, 19, M Marker Bin 29, 46 Panel 30, 48 28, 45 24, 45 2, 7, 19, 41 5, 24, 25, 26, 27, 45, , 48 Min peak height ratio 54 MSDS P vii Panel 19, , 34, GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 67
78 19, 45 7, 19, Panel Manager 19, 41 Plot Setting 17, 39, 60, 66 Plot Genotypes Plot Samples Plot Primer Focus Kit 3 Primer Focus Kit Kit 43 5, 31 Primer Focus 34 R Report Settings 66 S Samples Plot , 39 18, 40 17, 39 Samples 34, 12, 52 Size Match Editor 15, 37 Size Quality (SQ) SQ Sizing 18, 40 SNaPshot Kit 2 SNaPshot Kit Marker SQ 16, 38 14, 36 15, 37 15, 37 T Table Settings 12, 13, 34, 35, 52, 56, 66 X X 17, 39, 61 18, 40, 61 Y Y 17, 39, 61 18, 40, 61 12, 34, 52 7, 12, 34, Genotypes Plot 64 Samples Plot Bin Set 19, 41 Panel 19, 41 Analysis Method 66 Bin Set 65 Genotypes Plot 65 Kit 65 Panel 65 Plot Settings 66 Report Settings 66 Samples Plot 65 Size Standard 66 Table Settings vi, vii SNaPshot Kit 49 Genotypes Plot 61 Samples Plot 17, 39 X 17, 39, 61 Y 17, 39, 61 17, 39, 61 vi 68 GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
79 18, 40, 61 18, 40, , 36 16, , 34, 56 16, 38 15, , 38 16, 38 16, Bin 30, 47 Marker 30, 48 16, 38 Analysis Method 12, 34, 52 Bin Set 21, 42 Bin 45 Bin 24 Kit 19, 41 Marker 24, 45 Panel 19, 45 10, , 39, 61 15, 37, 59 Primer Focus 34 15, 37, 59 17, 39, 61 16, 38 15, 37, , 32, 50 17, 39, 60 17, 39, 60 v 17, 39, 61 17, 39, 60 17, 39, 61 14, 36 SNaPshot Kit Marker Bin 29, 46 16, 38 10, 32, 50 Marker 5, 24, 25, 26, 27, 45, vii 54 v v! v v v v v vii v GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide 69
80 v Table Settings , 36 10, 32 10, 32, 50 13, 35, , 36 5, Bin 29, 47 Marker 30, 48 vi, vii 16, 38 Analysis Method 55 13, 35, 56 v Analysis Method v v vii ii ii Kit 21 Panel GeneMapper Software Version 4.0 SNaPshot Kit SNP Getting Started Guide
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NVivo 8 NVivo NVivo NVivo 8 ( ) Copyright 2008 QSR International Pty Ltd. ABN 47 006 357 213. All rights reserved. NVivo QSR ( ) QSR International Pty Ltd. Microsoft.NET SQL Server Windows XP Vista Windows