GeneMapper Software Version 3.7
Copyright 2004, Applied Biosystems. All rights reserved. Applied Biosystems Applied Biosystems Applera Corporation GeneMapper GeneMapper ABI PRISM Applied Biosystems GeneMapper GeneScan SNaPshot AB Design Applera GeneMapper GeneScan SNPlex ZipChute Applera Corporation / AFLP Keygene N.V AppleScript Macintosh Apple Computer, Inc. Apache Software Foundation http://www.apache.org/ Copyright 1999-2000 The Apache Software Foundation. All rights reserved. ExoLab Project http://www.exolab.org/ Copyright 2000 Intalio Inc. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., http://www.trustice.com Microsoft Windows NT Microsoft Excel Microsoft Corporation Oracle Oracle Corporation Applera Corporation Applera Corporation Applied Biosystems Celera Genomics 4359413 Rev. B 10/2004
....ix...x Applied Biosystems......x 1 GeneMapper...1-2 GeneMapper...1-3...1-4 Oracle....1-5 GeneMapper...1-6...1-7...1-9...1-12 GeneMapper...1-12 GeneMapperManager...1-13 Panel Manager...1-14 Cluster Plot Manager SNPlex...1-15 Cluster Plots...1-16 Report Manager...1-20 GeneMapper Software v3.7 v
2...2-2 Access Control...2-3 Administration...2-4...2-9...2-11...2-13 Audit...2-14 Audit Map Configuration...2-18 Audit History Viewer...2-22 3...3-2 Archiver...3-3...3-6...3-7 Archive Request...3-8...3-10...3-11...3-13 Archive Location...3-15 Archive Request Restoren Request...3-16 GeneMapper Software v3.7 vi
4...4-2...4-3...4-6 Peak Start Peak Ende Slope Threshold...4-10 Slope Threshold...4-12 - -...4-14 Classic Advanced...4-15...4-21 Component-Based Quality Values (PQV)...4-23 Process Quality Value...4-24 5...5-2 AFLP......5-3 LOH...5-6...5-9 OLA...5-11 SNaPshot...5-13 SNPlex TM...5-16 GeneMapper Software v3.7 vii
GeneMapper Software v3.7 viii
GeneMapper v3.7 Applied Biosystems 0 [Enter] [File] [Open] [Spot Set] [View Filter] [View All Runs] Applied Biosystems 2 GeneMapper GeneMapper Software v3.7 ix
GeneMapper [F1] [Help] [Contents and Index] GeneMapper GeneMapper Spftware v.3.7installation Guide P/N 4359289 Applied Biosystems Applied Biosystems 0120 477 120 http://www.appliedbiosystems.co.jp Customer Support Customer Support FAQ Applied Biosystems MSDS PDF http://www.appliedbiosystems.com Services and Support Applied Biosystems Applied Biosystems jptechsupport@appliedbiosystems.com GeneMapper Software v3.7 x
1 1. 2. 3. 4. 5. 6. 7. 8 Dye Set Data Collection GeneMapper / GeneMapper Software v3.7 xi
1 OS OS / MB MB MB OS OS GeneMapper Data Collection Applied Biosystems GeneMapper Software v3.7 xii
1 Applied Biosystems Analysis Method Bin Panel Size Standard.fsa GeneMapper_log.txt PanelImportLog.txt GeneMapper Software v3.7 xiii
1 GeneMapper...1-2 GeneMapper...1-3...1-4 Oracle...1-5 GeneMapper...1-6...1-7...1-9...1-12 GeneMapper...1-12 GeneMapperManager...1-13 Panel Manager...1-14 Cluster Plot Manager SNPlex... 1-15 Cluster Plots...1-16 Report Manager...1-20 GeneMapper Software v3.7 1-1
GeneMapper GeneMapper 3.7 LOH Amplified Fragment Length of Polymorphism AFLP Custom Plot Colors SNPlex on-the-fly Report Manager Samples Genotypes Samples Genotypes Report Manager Report Table Settings GeneMapper Software v3.7 1-2
GeneMapper GeneMapper Software v.3.7 Installarion Guide P/N4359289 * Intel Pentium IV 2.4GHz RAM 1GB 120GB 2 20/48 IDE CD-ROM 10/100 NIC RWU 1024 768 17 (OS) Microsoft Windows 2000 Professional Operating System Service Pack4 Microsoft Windows XP Professional Operating System Service Pack1 Intel Pentium 733MHz RAM 512MB 20/48 IDE CD-ROM 10/100 NIC RWU 800 600 17 Microsoft Windows 2000 Professional Operating Systems, Service Pack3 *Applied Biosystems GeneMapper Applied Biosystems GeneMapper Applied Biosystems Applied Biosystems 3730/3730xl DNA Analyzers Dell Precision 340 GeneMapper GeneMapper Intel Xeon TM GeneMapper 2 GeneMapper GeneMapper Software v3.7 1-3
1-1 GeneMapper v3.7 Applied Biosystems Windows Data Collection Genetic Analysis Applied Biosystems 3730/3730xl DNA Analyzer Applied Biosystems 3130/3130xl Genetic Analyzer ABI PRISM 3100 Genetic Analyzer ABI PRISM 3100-Avant Genetic Analyzer Applied PRISM 310 Genetic Analyzer Data Collection Data Collection v1.0 Windows2000, SP2 Data Collection v2.0 Windows2000, SP3 4 Data Collection v3.0 WindowsXP, SP1 Data Collection v3.0 WindowsXP, SP1 Data Collection v1.0/1.0.1/1.1 Windows NT, SP 5 Data Collection v2.0 Windows2000, SP3 Data Collection v1.0 Windows NT, SP 5 Data Collection v2.0 Windows2000, SP3 4 Data Collection v1.0/1.0.1/1.1/3.0 Windows NT 4.0, SP 3, 4, 5, 6a Data Collection v3.0 Windows2000, SP3 4 Data Collection v3.1 Windows XP, SP1 GeneMapper v3.7 GeneMapper Software v3.7 1-4
1-1 GeneMapper v3.7 Applied Biosystems Windows Data Collection Genetic Analysis ABI PRISM 377 DNA Sequencer ABI PRISM 3700 DNA Analyzer Data Collection Data Collection v3.0 Windows NT 4.0, SP 5 Data Collection v.1.0/1.0.1/1.1 Windows NT 4.0, SP 5 Data Collection v.2.0 Windows NT 4.0, SP 5 GeneMapper v3.7 Oracle GeneMapper Oracle GeneMapper Applied Biosystems GeneMapper Oracle GeneMapper v.3.7 Oracle TM 5 Named User 5 Named User GeneMapper Oracle Named User (Oracle ) Applied Biosystems Oracle TM GeneMapper Software v3.7 1-5
GeneMapper GeneMapper Software v3.7 1-6
GeneMapper Software v3.7 Installation Guide P/N 4359289 GeneMapper User Name GeneMapper GeneMapper 1. [Login to GeneMapper] a. User Namegm Passwordpassword b. [OK] 5 10 GeneMapper Software v3.7 1-7
2. [Password Change Required ] [OK] 3. [OK] [Change Password] 4. [OK] 5. 2 [Accept] GeneMapper GeneMapper Software v3.7 1-8
1. GeneMapper v3.7 [Start] [All Programs] [Applied Biosystems] [GeneMapper] [GeneMapper v.3.7] 2. [User Name] User Name User Name User Name User Name Password Password User Name Password 3. Applied Biosystems [expired] [OK] 4. [OK] Password Policy [invalid] [suspended] Password Policy [active] 2-3 Access Control GeneMapper Software v3.7 1-9
1. [Login to GeneMapper][New Host] 2. [New Host] [New Host] GeneMapper a. [Host Name] IP User Name You have entered an invalid host [OK] b. c. [OK] GeneMapper GeneMapper GeneMapper Software v3.7 1-10
GeneMapper 3 [File] [Logout] [File] [Exit] GeneMapper GeneMapper [File] [Logout] GeneMapper Yes No GeneMapper [Exit] GeneMapper Software v3.7 1-11
GeneMapper...1-12 GeneMapper Manager...1-13 Panel Manager...1-14 Cluster Plot Manager SNPlex...1-15 Report Manager...1-20 GeneMapper 1-1 GeneMapper New Project Open Project Display Cluster Plot Export Table Size Match Editor Panel Manager Analyze Low Quality to Top Table Setting Editor Find myscience Help Save Project Display Plots Current Setting Seletor Print Report Manager GeneMapper Manager Add Samples to Project Analysis Method Editor 1-2 GeneMapper GeneMapper Software v3.7 1-12
GeneMapperManager GeneMapperManager 1-3 [Save As] Project Analysis Method Table Settings Plot Settings Cluster Plot Settings Cluster Plot Matrices Size Standards SNPSet SNPlex TM Report Settings 1-3 GeneMapperManager GeneMapper Software v3.7 1-13
Panal Manager Panel Manager Panel Manager GeneMapper Project Panal Manager [Tools] [PanelManager] 1-4 Panel Manager Panal Manager Kit Panel Bin Set Marker Bin Reference Samples Clear Add Bin Edit Bin Bin Set Selector New Bin Set Add Reference Data Auto Bin Panel Reference Data New Kit/ New Panel/ New Marker Delete Bin Full View Show/Hide Project Alleles Auto Panel Show/Hide Dyes 1-5 Panel Manager GeneMapper Software v3.7 1-14
Cluster Plot Manager SNPlex Samples Genotypes Cluster Plot Cluster Plot Cluster Plot Manager Electropherogram Plot Cluster Plot Manager Cluster Plot Cluster Plot Scatter Plot SNP SNP Cluster Plot Genotypes Quality Value Cluster Plot Manager [Display Cluster Plots] SNP 1-6 Cluster Plot Manager Cluster Plot Manager Cluster Plot Manager Electropherogram Cluster Plot Setting Allele SNP / Cluster Plot / GeneMapper Software v3.7 1-15
Cluster Plots Cartesian Cluster Plot Cartesian Cluster Plots Allele1 x Allele2 y Cartesian Cluster Plots Polar Cluster Plot Allele1 Allele 2 NTC No-Template Control x y Lenear Intensity N/A Polar Cluster Plot Linear Cluster Plot x,y log r, r x Log10 2 x + y 2 Intensity x y- Polar Cluster Plot Allele1 Allele2 NTC No-Template Control x- Allele1 GeneMapper Software v3.7 1-16
SNP Cluster Plot Manager SNP SNP SNP Marker Run Name Panel Name Dye Allow Autocall SNPlex TM SNP SNP Set Panel.fsa Panel SNP ZipChute TM Cluster Plot Cluster Plot Genotypes SNP SNP Cluster Plot Manager Cluster Plot Genotypes Quality Value Sample File Sample Name Data Collection GeneMapper Software v3.7 1-17
A1 A1 Allele1 1 A2 Allele2 A2 A1 Allele1 A2 Allele2 1 Height 1 Allele1 Heigth 2 Allele2 CV CV GQ Genotype Quality Omit Hide Run Name Data Collection AE Allele Edit Allele OS Offscale PQV PQV PHR Peak Height Ratio PQV PQV LPH Low Peak Height PQV PQV SPU Spectral Pull-Up PQV PQV AN Allele Number PQV Allele PQV BD Broad Peak PQV PQV XTLK Crosstalk PQV PQV GeneMapper Software v3.7 1-18
Cluster Plot Manager Cluster Plot Cluster Plot SNP Genotypes 1. 2. Cluster Plot Cluster Plot Cluster Plot Cluster Plot Cluster Plot Cluster Plot 1. Cluster Plot [Graph Settings] 2. Cluster Plot [Cartesian][Polar] 3. x y [Auto Scale] x y [Auto Scale]Minimum Maximum 4. [OK] Cluster Plot Cluster Plot Zoom In Zoom Out GeneMapper Software v3.7 1-19
Report Manager Report Manager 1-7 1-7 Report Manager GeneMapper Software v3.7 1-20
2...2-2 Access Control...2-3 Administration...2-4... 2-9...2-11...2-13 Audit...2-14 Audit Map Configuration...2-18 Audit History Viewer...2-22 GeneMapper Software v3.7 2-1
GeneMapper 1. [Tool] [SecurityManager] Access Control 2-9 2-10 Password Policies 2-4 2-11 2. [Tools] [Audit Manager] [Settings] [Audit Map Configuration] GeneMapper 2-19 2-20 3. [Tools] [Audit Manager] [Report] [Audit History Viewrs] 2-23 GeneMapper Software v3.7 2-2
Access Control GeneMapper User Profile GeneMapper Software v3.7 2-3
Administration Administration Administration User Group 1 1 [User] [Applications] List of Users GeneMapper Software v3.7 2-4
[User Properties] Properties EULA End User License Agreement Control Security Group Administration [Security Group] User Profile [Properties] [Properties] GeneMapper Software v3.7 2-5
[List] [List] [List] 2-1 [List] Security Group GeneMapper Software v3.7 2-6
Tool tip Help 2-1 Save Administration Reload Administration [Files] [Exit] Yes No Cancel Duplicate [View] Password Policies GeneMapper Software v3.7 2-7
Change Password Administration [Change Password] GeneMapper Software v3.7 2-8
1. New User 2. [Create User] [Next] 3. [Configure][Next] Name Full Name Set Password Control Properties [Summary] [Finish] 4. Administration [Save] GeneMapper Software v3.7 2-9
Profile [User Properties][User Details] [User Details] [Status] [Inactive] GeneMapper Software v3.7 2-10
1. [New Profile] 2. [Create Profile] [Next] GeneMapper Software v3.7 2-11
3. [Configure] a. b. [OIR override inherited rights ] / [Execute] Execute: OIR: [OIR] 4. [Next] [Summary] 5. [Finish] User Profile Name GeneMapper Software v3.7 2-12
1. [Tools] [Security Manager] 2. [System Authentication] [OK] 3. [Access Control Administration][File] [Export Database] 4. <fn>.acc 5. a. [File] [Import Database] b. <fn>.acc GeneMapper Software v3.7 2-13
Audit Audit Trails GeneMapper Audit Analysis Mehtod Panel Audit 3 Analysis Method Panel Analysis Method Panel Audit Audit Audit Analysis Methods Panels Audit GQ Value Allele Analysis Method Analysis Method Panel Marker Bin Set Bin Kit Kit 1 Audit Kit Kit Panel Marker Bin Set Audit GeneMapper Software v3.7 2-14
Reasons For Change Audit [Reasons For Change ] Attribute Old Value New Value Reasons For Change [OK] Audit ON Audit 2-2 Reasons For Change GeneMapper Software v3.7 2-15
Audit Audit 1 Bin Reasons For Change 2-2 Bin 2-3 Reasons For Change Bin 2-2 Bin 2-3 Attribute PANEL.TestPanel.MARKER.TestMarker. BIN.235.modified [Panel]TestPanel TestMarker [Marker] BIN 235 Old Value [Right Offset] 32.46 [BINSET. Test BinSet] Right Offset 32.46 Bin [Bin Set]TestBinSet New Value [Right Offset] 76.8[BINSET.TestBinSet] Right Offset 76.8 Bin [Bin Set]TestBinSet GeneMapper Software v3.7 2-16
2 Allele 1. 2. Samples Plot 3. Allele [Reasons For Change] 2-3 Allele 2-4 Reasons For Change Allele 2-3 Allele 2-4 Attribute RUN.Microsatellite.SAMPLE.C00 Microsatellite 6_E019_Run_C006_2002-05-10_2 05_07.fsa.ALLELE.test.modified C006_E019_Run_C006_2002-05-10_205_07.fsa test Allele Old Value test [Kit.Microsatellite Tutorial Allele Microsatellite Tutorial PANEL.Tutorial Panel [Kit] [Panel]Tutorial Panel 9 9.MARKER.D6S264] [Marker]D6S264 test New Value newname[kit.microsatellite Tuto rial PANEL.Tutorial Panel 9.MA RKER.D6S264] Microsatellite Tutorial [Kit] [Panel]Tutorial Panel 9 [Marker]D6S264 Allele newname GeneMapper Software v3.7 2-17
Audit Map Configuration Audit Map Configuration Audit Map Configuration Audit Map Audit Map Audit Map Configuration Audit On Off Silent Audit Map Save Audit Map Configuration Application Security Security Application Application Audit Map GeneMapper Audit Map Configuration 1. GeneMapper [Tools] [Audit Manager] [Setting] 2. System Authentication Audit Map Configuration GeneMapper [OK] Audit Map Configuration GeneMapper Software v3.7 2-18
Audit Map Configuration Audit Map Audit Map Objects Enabled Audit StateAttributes State Audit State Audit State On OffSilent Audit Map [Enabled] 2-5 Audit Map Configuration GeneMapper Software v3.7 2-19
Audit Map Configuration 2-4 Audit Map Configuration File Visual Print Visual Print Preview Exit [Print] [Print Preview] Audit Map Configuration Auditing On Audit Map Configuration ON Audit Audit Map [Enabled] [State] Audit [A Reason For Change RFC ] RFC [OK] Map State Audit Record [Cancel] Map State Settings Silent Change Password Audit Map [Enabled] [State] Audit RFC Silent Audit Record Audit Map Configuration [Change Password] Help Audit Map Configuration Help About GeneMapper Software v3.7 2-20
Audit Map Audit Map Attributes ON [Audit Map Objects] ON 1 Audit Map Audit Map Kit Kit Audit Map Panel Panel PanelT Audit Map Panel Audit Map State 1. [Audit Map Objects] [Kit folder] 2. [Access to Audit map][panel Attribute] 3. [Panel Attribute] [State] 1 Off Panel Audit On/Silent Panel [Panel audit map] Audit [primitive] ON Audit Audit Map Object ON Audit Map Object Kit BINSET PANEL BinSetT PanelT BINSET PANEL Audit Audit Map Object BinSet Panel State Audit Map Object Kit Kit GeneMapper Software v3.7 2-21
Audit History Viewer Audit History Viewer Audit Audit Record Audit History Viewer Audit History Viewer Audit Record Audit Record Audit Audit Record 2-6 Audit History Viewer GeneMapper Software v3.7 2-22
Audit History Viewer 1. GeneMapper [Tools] [Audit Manager] [Report] 2. System Authentication Audit History Viewer GeneMapper [OK] Audit History Viewer 3. [Audit Object][Object] [Object] 4. [Object] 1 Detail Panel Audit Record Record GeneMapper Software v3.7 2-23
Filter Audit History Filter 1. Filer 2. [Filter Audit Records] Audit Record Name Date 2 User Name 3. [Query] GeneMapper Software v3.7 2-24
2-5 Audit History File Reload Report Audit Record View Settings Print Preview Page Setup Visual Print Preview Visual Print Exit Filter Details Panel Change Password [Print Preview] [Page Setup] [Object][Print Preview] [Object][Print] Audit History Viewer Filter Audit Record Audit Record Audit Record Audit History Viewer GeneMapper Software v3.7 2-25
3...3-2 Archiver...3-3...3-6...3-7 Archive Request...3-8...3-10...3-11...3-13 Archive Location...3-15 Archive Request Restore Request... 3-16 GeneMapper Software v3.7 3-1
GeneMapper [Archiver] GeneMapper OracleDatabase CD-ROM Audit Archiver Achiver GeneMapper [Tools] [Archiver] [File] [Exit] GeneMapper Software v3.7 3-2
Archiver Archiver Archiver Windows OS [Save]:Archiver [Cut]: [Copy] [Paste]: [File] [Save] [Edit] [Cut] [Ctrl]+[X] [Edit] [Copy] [Ctrl]+[C] [Edit] [Paste] [Ctrl]+[V] [Home]: [View Archive Requests] ID [View Archive Locations]: ID [Process Archive Request] [View] [Archive Requests] [View] [Archive Locations] [Process] [Process Requests] GeneMapper Software v3.7 3-3
Archiver [Object Archiver] [Object Archiver] 1. [Object Archiver] 2. [Clear All] [Object Archiver] [Object Archiver] [Expand All] [Object Archiver] [Collapse All] GeneMapper Software v3.7 3-4
Archiver 3-1 3-2 3-1 View Archive Requests Archive Requests Queue 3-2 View Archive Requests Archive Requests Queue GeneMapper Software v3.7 3-5
Archiver Archiver [date range] Archiver 1. [Tools] [Archiver] Archiver Client 2. 3. 4. [Process] [Process Requests].xml.xml GeneMapper Software v3.7 3-6
GeneMapper GeneMapper.xml.xml CD.xml.xml Destructive Archive GeneMapper GeneMapper Nondestructive Archive GeneMapper Nondestructive Archive GeneMapper Maker [Database Manager] GeneMapper.xml GeneMapper GeneMapper Destructive GeneMapper Restore with editing GeneMapper Restore with no editing GeneMapper GeneMapper GeneMapper Software v3.7 3-7
Archive Request [Tools] [Archiver] [Archiver Client] 1. [Shift] [Ctrl] 2. 1 [Add New Archive Request] Working Area Archive Request 3. Archive Request Name Description 4. Output Directory [Open] 5. Media Label Media Location Media Label Media Location Media Label 6. Nondestructive Archive GeneMapper GeneMapper Forced Restore Zipped Output xml zip Use Checksum Archiver GeneMapper Software v3.7 3-8
Structured Output XML Streamed Output Applied Biosystems 36 Archive Request [Streamed Output] Process Request Keep History Checksum Binaries BLOB BFILEs 7. [Remove from Request] 8. [File] [Save] 9. [Process] [Process Requests] GeneMapper Software v3.7 3-9
1. [Tools] [Archiver] [Archiver Client] 2. Destructive Archive Nondestructive Archive 3. a. Archive History [Restore All Objects] b. [Restore Archives][OK] 4. 1 a. [Archive History] [Edit Restore Objects] [Restore Request] Name Description b. [Restore Request Details] [R] 5. [File] [Save] 6..xml.xml 7. 8. [Process] [Process Requests].xml GeneMapper.xml GeneMapper Software v3.7 3-10
1. [Tools] [Archiver] [Archiver Client] 2. [Search For][Object] 3. [Type][Standard] [Advanced] [Standard] [Advanced] 4. [Standard] a. b. List c. [OK] [Advanced] a. [Column Name] b. [Condition] c. [Value1] [Value 2] List d. [OK] [Advanced][Condition] [LIKE] [Value][%] [_] 5. [Append] [Append] [Append] GeneMapper Software v3.7 3-11
6. [Find] 7. [Object Archiver] [Clear All] GeneMapper Software v3.7 3-12
1. [Tools] [Archiver] [Archiver Client] 2. [Search For][Archive History] 3. [Type][Standard] [Advanced] [Standard] [Advanced] 4. [Standard] a. b. List c. [OK] [Advanced] a. [Column Name] b. Condition c. [Value1] [Value2] List d. [OK] [Advanced][Condition] [LIKE] [Value] [%][_] GeneMapper Software v3.7 3-13
5. [Append] [Append] [Append] 6. [Find] 7. Destructive Archive Nondestructive Archive [Object Archive] [Clear All] GeneMapper Software v3.7 3-14
Archive Location Archive Location Archive Locations GeneMapper ID Archive Location [View] [Archive Locations] Archive Locations Archive Locatrions Archive Requests Queue Restor Request GeneMapper Software v3.7 3-15
Archive Request Restore Request Archive Resuest Restore Request Queue Archive Requests Archive Request Restore Request 1. [View] [Archive Requests] Archive Requests Queue Archive Request Restore Request 2. [ACTION] A Archive Request R Restore Request 3. STATUS REQUESTED Queue [File] [Save] COMPLETED Queue [Process] [Process Requests] ERROR Archive Request [Process Requests] Archive Request Archive Request Archive Requests Queue [Remove Request] Archive Request Archive Requests Queue GeneMapper Software v3.7 3-16
4...4-2...4-3...4-6 Peak Start Peak End Slope Threshold...4-10 Slope Threshold...4-12...4-14 Classic Advanced...4-15...4-21 Component-Based Quality Values PQV...4-23 Process Quality Values...4-24 GeneMapper Software v3.7 4-1
GeneMapper 5 Peak DetectionBasic Advanced Classic /Size-matching/calling Binning Allele-calling Process Quality value Quality Value 4-1 GeneMapper GeneMapper Applied Biosystems Applied Biosystems / / Caller1 Caller n Arbitrator Quality Value Quality Value 4-1 GeneMapper GeneMapper Software v3.7 4-2
Polynomial Degree Peak Window Size 2 Polynomial Degree Peak Window Size Polynomial Degree Peak Window Size Polynomial Degree Peak Window Size Polynomial Degree Peak Window Size Peak Window Size Polynomial Degree data points Polynomial Degree Peak Window Size Peak Window Size Peak Window Size Polynomial Degree Peak Window Size GeneMapper Software v3.7 4-3
Polynomial Degree Polynomial Degree Polynomial Degree 2 3 4 Peak Window Size Peak Window Size 1 2 GeneMapper [View] [Show Peak Positions] 4-2 Peak Window Size 15pts Polynomial Degree 23 4 Polynomial Degree 2 Polynomial Degree 2 Polynomial Degree4 Polynomial Degree3 Polynomial Degree2 4-2 3 Polynomial Degree GeneMapper Software v3.7 4-4
Peak Window Size 4-3 Polynomial Degree 3 Peak Window Size 15 31 Peak Window Size Peak Windows Size31 Peak Window Size15 4-3 4-2 Polynomial Degree 3 Peak Window Size GeneMapper Software v3.7 4-5
1 Peak Window Size 1 4-4 2 1 Polynomial Degree 3 Peak Window Size 19 4-4 2 4-4 Peak Window Size 4-5 Polynomial Degree 3 Peak Window Size 19 15 GeneMapper Software v3.7 4-6
4-5 Peak Window Size 2 2 2 Peak Window Size Polynomial Degree 2 4-6 Polynomial Degree 3 Peak Window Size 19 4-6 2 4 GeneMapper Software v3.7 4-7
Polynomial Degree Peak Window Size 4-7 Peak Window Size 11 Polynomial Degree 5 4-7 Peak Window Size Polynomial Degree 4 GeneMapper Software v3.7 4-8
3 4-8 Peak Window Size 11 Polynomial Degree 9 1 2 4-8 GeneMapper Software v3.7 4-9
Peak Start Peak End Slope Threshold Slope Threshold for Peak Start Slope Threshold for Peak End 0 (+) (-) 0 0 0 0 GeneMapper Software v3.7 4-10
Slope Threshold for Peak Start 0 Slope Threshold for Peak End GeneMapper Software v3.7 4-11
Slope Threshold Slope Threshold for Peak Start Slope Threshold for Peak End 0 4-9 4-9 GeneMapper Software v3.7 4-12
Slope Threshold for Peak End Slope Threshold for Peak End -35.0 4-10 Slope Threshold for Peak End GeneMapper Software v3.7 4-13
Quality Value 4-11 GeneScan 120 / 4-11 GeneMapper Software v3.7 4-14
Classic Advanced Least Square GeneMapper v.3.7 4 Least Square 2nd Order 2 3rd Order 3 Cubic Spline Interpolation 3 Local Southern Global Southern 2nd Order 3rd Order [Analysis Method] 2nd Order 3rd Order 2 3 4-12 4-13 DNA DNA GeneMapper Size Calling Method Best Fit 2nd OrderLeast Square Size Match Editer [Size Calling Curve] GeneScan v.3.7.1 GeneMapper v.3.7 GeneMapper Software v3.7 4-15
4-12 2nd Order Least Square 4-13 3rd Order Least Square GeneMapper Software v3.7 4-16
Cubic Spline Interpolation 3 Cubic Spline Interpolation 3 4-14 Cubic Spline Interpolation DNA 2 3 Cubic Spline Interpolation 3 Cubic Spline Interpolation GeneMapper Software v3.7 4-17
Local Southern Local Southern E.M.Sothern 1979 4-15 Local Southern Local Southern L=[c/(m-m0)]+L0 L0 GeneMapper Software v3.7 4-18
Local Southern Cubic Spline Interpolation 4 Local Southern a. 3 3 b. 3 2 1 c. 3 1 2 d. 2 GeneMapper Software v3.7 4-19
Global Southern Global Southern Least Squear 4-16 Global Southern Global Southern L=[c/(m-m0)]+L0 i{li-[c/(mi-m0)]+l0} 2 m L0 L0 m0 c Global Southern GeneMapper Software v3.7 4-20
envelope detection rule-based 4-22 4-17 16 3 i p Low Quality Value i Low Qualty Value i p GeneMapper Software v3.7 4-21
4-17 16 3 GeneMapper Software v3.7 4-22
Component-Based Quality Values PQV Process Quality Values PQV PQV Process Quality Values PQV PQV PQV 1. Quality Value PQV Process Component-Based Quality Values 2. PQV PQV [Analysis Method] GQ PQV GQ 0 3. Samples Genotypes SQ GQ PQV Pass Check Low Quality GeneMapper Low Quality PQV Analysis Method PQV GeneMapper Software v3.7 4-23
Process Quality Values PQV GeneMapper Quality Value PQV Samples Genotypes PQV Samples Genotypes 2 PQV Samples SFNF MNF SNF OS Pass Check 2 Sizing Quality SQ Pass Check Loq Quality Genotypes SHP AN AE OBA SPA Bin PHR LPH SPU BD SP OS CC OVL NB DP pass Check 2 Genotype Quality GQ Pass Check Low Quality Genotypes ADO AE PQV Samples SQ Quality Value Low Quality GQ Low Quality Analysis Method Editor Quality Flags SQ GQ GeneMapper Software v3.7 4-24
PQV 4-1 PQV PQV AFLP 2 OLA SNaPshot SNPlex TM ADO Allele Display Overflow AE Allele Edit AN Allele Number BD Broad Peak BIN Out of Bin Allele CC Control Concordance DP Double Peak GQ Genotype Quality HEMU HOMU Heterozygous Mutation Homozygous Mutation LPH Low Peak Height MA Missing Allele NB Narrow Bin OBA One Allele Basepair OS Off-Scale OVL PHR SQG Overlap Peak Ratio Height Sample Genotype Quality SHP Sharp Peak SP Split Peak SPA Single Artifact Peak SPU Spectral Pull-Up XTLK Cross Talk GeneMapper Software v3.7 4-25
PQV Samples Genotypes PQV Pass Check Low Quality Check PQV Samples SQ Genotypes GQ SQ GQ [Tools[Options] [Analysis] Quality Metrics Display Settings Symbol Number 0.75 1.0 0.25 0.75 Low Quality 0.0 0.25 GeneMapper Software v3.7 4-26
[Samples] PQV PQV Applied Biosystems Check Low Quality 4-2 [Sample] PQV PQV MNF OS SFNF SNF SQ Matrix Not Found Pass Check ABI PRISM 310 377 Offscale Pass Check Sample File Not Found Pass Check Size Standard Not Found Pass Check Sizing Quality Pass Check Low Quality Sizing Process Quality Sizing Quality - Classic SQ Check GeneMapper Fail Samples Low Quality GeneMapper Software v3.7 4-27
[Genotyps] PQV Genotype PQV Fail Applied Biosystems Check Low Quality 4-3 [Genotypes] PQV PQV ADO AE AN BD Allele Display Overflow Table Settings Editor 2 6 Allele Edit Plot View [Allele History Comment] Allele Number Pass Check [Analysis Method] GQ PQV 0 OLA SNPlex TM Broad Peak [Analysis Method] Pass Check 1.5 GeneMapper Software v3.7 4-28
4-3 [Genotypes] PQV PQV BIN CC DP Out of Bin allele Pass Check GQ PQV 20% 0.2 GeneMapperID v3.2 HID BIN PQV OL off-ladder alleles OLA SNPlex TM Control Concordance Pass Check Applied Biosystems 1 OLA SNaPshot SNPlex TM Double Peak 2 0.5 / Pass Check SNaPshot GeneMapper Software v3.7 4-29
4-3 [Genotypes] PQV PQV GQ Genotype Quality Low Quality Pass Check Low Quality [Analysis Method] GeneMapper AQ Allele Quality Genotype Quality Value AQ Sizing Quality Allele Calling Quality Bin Assignment Quality Bin Quality Quality Value SNPlex GeneMapper GQ GQ GeneMapper GQ GQ=MQ b PQV 1 PQV 2 PQV N MQ Maker Quality PQV GQ PQV 0 1 PQV 1 0 GQ 1-0 = 1 GQ 1 100%1-1 = 0GQ 0 GQ 0 0 1 GQ PQV GeneMapper Software v3.7 4-30
4-3 [Genotypes] PQV PQV HEMU HOMU LPH MA NB OBA Heterozygous Mutation Pass Chech Fail [Analysis Method] 0 1 2 4 OLA 0 Pass 1 Check 2 Fail 4 OLA Homozygous Mutation Pass Check Fail [Analysis Method] 0 1 2 4 OLA 0 Pass 1 Check 2 Fail 4 OLA Low Peak Height Pass Check Homozygous 200 Hetelozygous 100 [Analysis Method] [Peak Quality] GQ PQV 50% 0.5 OLA SnaPshot SNPlex TM Missing Allele Pass Check Fail [Analysis Method] 0 1 2 4 OLA 0 Pass 1 Check 2 Fail 4 OLA Narrow Bin 0.5 Pass Check SnaPshot One Basepair Allele 1 Pass Check 1 2 2 GeneMapper Software v3.7 4-31
4-3 [Genotypes] PQV PQV OS OVL PHR SGQ SHP Offscale Pass Check Overlap Panel Manager 2 Pass Check 2 GeneMapperID v3.2 HID Peak Height Ratio 2 Pass Check 3 PHR [Analysis Method] [Peak Quality] 50% LMS SNaPshot 2 2 OLA SNaPshot SNPlex TM Sample Genotype Quality Pass Check Fail [Analysis Method] 0 1 2 4 OLA 0 Pass 1 Check 2 Fail 4 OLA Sharp Peak Pass Check Check PQV SHP 50% 2 OLA GeneMapper Software v3.7 4-32
4-3 PQV PQV SP SPA SPU Split Peak GeneMapper Split Peak Pass Check Split Peak 2 0.25 2 Single Peak Artifact Pass Check 2 Stutter Peak 2 Spectral Pull-Up bleed-through Peak Pass Check 1 X% 10% GeneMapper Software v3.7 4-33
GeneMapper Software v3.7 4-34
5...5-2 AFLP......5-3 LOH...5-6...5-9 OLA...5-11 SNaPshot...5-13 SNPlex TM...5-16 GeneMapper Software v3.7 5-1
1. 2. 3. 4. GeneMapper v.3.7 2c 5 1. 2. GeneMapper [Samples] a. [Analysis Method][Microsatellite ] Allele Peak Detection Bin Set:[None] Peak Detection Algorithm Basic Advanced Classic Size Calling Method b. [Panel][None] c. [Size Standard] Classic Classic 3. Table Setting Plot Setting 4. [Analysis] [Analyze] 5. Sizing Quality 6. Samples Plot Sizing Table Samples Plot [View] [X-Axis] [Data Points] 7. GeneMapper Software v3.7 5-2
AFLP AFLP Panel GeneMapper GeneMapper AFLP Panel Panel Bin Panel Manager Auto Bin AFLP Bin AFLP Panel Bin AFLPAnalysis Method Panel AFLP amplified fragment length polymorphisms 1. 2. GeneMapper [Samples] a. [Analysis Method][AFLP]Analysis Method [Analysis Method] Allele Bin Set [Panel] [None] Panel Analyze Dyes Analysis Range bps Panel Panel [Generate panel using samples ] [Use specified panel ] Panel GeneMapper Bin Allele Calling [Name alleles using bin names Bin Name ] [Name alleles using labels] GeneMapper Software v3.7 5-3
Peak Detector Peak Quality Quality Flags Peak Detection Algorithm Basic Advanced Classic Classic Classic [Max Peak Width and Pull-Up Ratio] [Quality Flag Settings and PQV Thresholds] Analysis Method Panel Bin Set b. [Panel][None] Panel c. [Size Standard] 3. Table Setting Plot Setting Table Settings Editor [Genetype] Limit number of alleles shown to number of bins Bin Show only binned alleles in their respective bin positions 4. [Analysis] [Analyze] 5. GeneMapper [Sample] SQ 6. 3 AFLP 7. a. Size Match Editor Check GQ b. [Samples][Genotypes] PQV BD OS SPU c. GeneMapper Software v3.7 5-4
d. 8. 9. a. b. [Report Manager] 10. Panel a. Panel GeneMapper [File] [Export Project Panel] b. [Panel Manager] Panel Panel Manager [File [Import Panel][File] [Import BinSet] GeneMapper Software v3.7 5-5
LOH Sample Name GeneMapper LOH Plate Record Sample Sheet Sample Name GeneMapper Loss of Heterozygosity LOH Replication Error RER Panel Bin Set 1. Panel Bin Set a. [Tool] [Panel Manager] Panel Manager b. Marker Panel c. Bin Set d. Panel Manager 2. 3. GeneMapper [Samples] a. [Analysis Method] LOH Allele Peak Detector Bin Set 1c Bin Set Peak Detection Algorithm Basic Advanced Classic Classsic Classic b. [Panel] 1b Panel c. [Size Standard] 4. [Analysis] [Analyze] 5. Panel Bin Set Bin a. Panel Manager GeneMapper Software v3.7 5-6
b. 1b Panel c. [Bins] [Add Reference Samples] Panel [Ctrl] d. Bin Set e. [Bins] [Auto Bin] Bin Apply f. Marker Bin g. Panel Reference Samples [Bins] [Panel Reference Samples] Delete Panel Manager h. OK Panel Manager LOH 1. GeneMapper [Samples] a. [Sample Type] b. [Analysis Method] 5-6 3 c. [Panel] 5 d. [Size Standard] Analysis Method Panel Bin Set 2. 3. [Analysis] [Analyze] 4. [Samples] [Genotypes] 5. a. b. PQV BD BIN CC LPH OBA OS PHR SHP SP SPA SPU XTLK c. Sample Genotype 6. GeneMapper Software v3.7 5-7
7. a. Report Settings LOHDefault b. Report Manager GeneMapper Software v3.7 5-8
GeneMapper 2 7 DNA Panel Bin Set 1. Panel Bin Set a. Panel Manager b. Marker Panel c. Bin Set d. Panel Manager 2. 3. GeneMapper [Samples] a. [Analysis Method] Microsatellite Analysis Method Allele Peak Detector Bin Set 1c Peak Detection Algorithm Basic Advanced Classic Classic Peak Detection Algorithm Classic b. [Panel] 1b c. [Size Standard] 4. [Analysis] [Analyze] 5. Panel Bin Set Bin a. Panel Manager b. 1b Panel c. Panel Reference Sample Reference Sample [Ctrl] GeneMapper Software v3.7 5-9
d. Bin Set e. [Bins] [Auto Bin] Bin Apply f. Markar Bin g. Panel Reference Samples h. OK Panele Manager 1. GeneMapper [Samples] a. [Sample Type] b. [Analysis Method] 5-6 3 Analysis Method c. [Panel] 5a Panel d. [Size Standard] Analysis Method Panel Bin Set 2. Table Plot Settings 3. [Analysis] [Analyze] 4. a. b. PQV BD BIN CC LPH OBA OS PHR SHP SP SPA SPU XTLK c. Sample Genotype Plot 5. 6. a. Report Setting b. Report Manager Report Settings GeneMapper Software v3.7 5-10
OLA GeneMapper Oligo Nucleotide Ligation Assay OLA 1. 2. OLA Panel Bin Set a. Panel Manager b. [Panel Manager] c. OLA Panel d. [new panel holder] e. OLA Bin Set f. Panel Manager 3. OLAAnalysis Method Allele Peak Detector Bin Set 2e Bin Set Peak Detection Algorithm Basic Advanced Classic Classic Classic 4. Applied Biosystems GeneMapper Applied Biosystems 5. 6. GeneMapper [Samples] a. [Sample Type] b. [Analysis Method] 5-11 3 Analysis Method c. [Panel] 5-11 2c Panel d. [Size Standard] Analysis Method Panel Bin Set GeneMapper Software v3.7 5-11
7. Table Setting Plot Setting 8. [Analysis] [Analyze] 9. Sample Genotype a. Genotype Quality GQ b. c. Sample Genotype PQV BD BIN CC LPH OS PHR SHP SPU 10. a. b. c. 11. 12. a. Report Settings b. Report Manager Report Setting GeneMapper Software v3.7 5-12
SNaPshot GeneMapper SNP SNaPshot Primer Focus TM 1. SNaPshot Panel Bin 2. 5-14 1. 5-14 Primer Focus Panel Bin Auto Paneling Panel Bin 2. 5-14 SNaPshot Panel Bin 1. 2. GeneMapper [Samples] a. [Analysis Method] SNaPshot Analysis Method Allele Peak Detector Bin SetNone Peak Detection Algorithm Basic Advanced Classic Classic Classic b. [Panel][None] c. [Size Standard] 3. [Analysis] [Analyze] 4. SQ 5. Panel Bin a. Panel Manager GeneMapper Software v3.7 5-13
b. Kit SNP c. SNPKit Panel d. SNPKit Bin Set e. Reference Sample f. SNP Marker g. [Plot] SNP 6. 5-15 SNaPshot Primer Focus TM Panel Bin Primer Focus TM Auto Panel Panel Bin 1. Primer Focus 2. GeneMapper [Samples] a. [Sample Type][Primer Focus] b. [Anaylsis Method][SNaPshot ]Analysis Method c. [Panel][None] d. [Size Standard] GS120LIZ 3. [Analysis] [Analyze] GeneMapper 4. Panel Bin a. Panel Manager b. SNPKit c. SNP Kit SNPBin Set d. SNP Kit Primer Focus Reference Samples e. [Bins] [Auto Panel] Panel Apply f. Auto Panel Bin 5. SNaPshot GeneMapper Software v3.7 5-14
SNaPshot 1. 2. SNaPshot Analysis Method Allele Peak Detector Bin Set Bin Set Peak Detection Algorithm Basic Advanced Classic Classic Classic 3. GeneMapper [Samples] a. [Sample Type] b. [Anaylsis Method] 2 Analysis Method c. [Panel] Panel d. [Size Standard] Analysis Method Panel Bin Set Analysis Method 4. Table Plot Settings 5. [Analysis] [Analyze] 6. a. b. [Samples] [Genotypes] PQV AN BD CC DP LPH NB OS PHR SPU c. 7. 8. Report a. Report Settings b. Report Manager Report Settings GeneMapper Software v3.7 5-15
SNPlex TM GeneMapper Applied Biosystems SNPlex TM /PCR OLA/PCR SNP 1. SNPlex TM Panel Bin a. Panel Manager b. [Panel Manager] SNPlex_48plex_3730_Panels.txt c. SNPlex_48_plex SNPlex_48plex_3730_Bins.txt d. OK Panel Manager 2. SNP GeneMapper Manager SNPlex CD SNP Set 3. 4. GeneMapper [Samples] a. [Sample Type] b. [Anaylsis Method] SNPlex TM Analysis Method SNPlex_Model_3730 SNPlex_Rules_3730 c. [Panel] 1 [SNPlex_48_plex] d. [Size Standard] SNPlex_48plex_v1 e. [SNP Set] 2 SNP Set Analysis Method Panel Size Standard Analysis Method Panel Bin Set 5. Table Plot Settings SNPlex_v3 6. [Analysis] [Analyze] 7. a. b. Cluster Plot Polar_Plot_v3 Cartesian_Plot_v3 GeneMapper Software v3.7 5-16
c. Sample Genotype Plot 8. 9. a. Report Settings b. Report Manager Report Settings GeneMapper Software v3.7 5-17
ABB Automatic Bin Builder Acess Control List Admin Profile Admin Security Group Administrator User Admin User Group AE ADO All User Group Allele Allele-Calling Panel ABB Bin Bin Security Group admin 1 Admin Admin user group Admin security group Allele EditPQV 4-28 Allele Display OverflowPQV 4-28 -- Bin GeneMapper GeneMapper Software v3.7-1
AN Analysis Mehtod Allele Number PQV 4-28 Bin Set Association 2 Data Rights Audit Event Audit Map Audit Object Audit Record Autopanelizer BD BIN Bin Bin set Cache CC Challenge Control Security Group 1 1 Audit Primer Focus Reference Samples SNPMarker Bin Set Broad Peak PQV 4-28 Out of Bin Allele PQV 4-29 1 Bin Bin set Kit Admin Tool Admin Tool Admin API [save] Control Concordance PQV 4-29 User Authentication User User Group Security Group Profile Administrative GUI API GeneMapper Software v3.7-2
Data Access Control Data Group Deta Rights Database DP GQ Kit LMS LPH Marker Microsatellite MNF NB OBA OS OVL Panel PHR PQV Security Group Double Peak PQV 4-29 Genotype Quality PQV 4-30 Panel Linkage Mapping Set 2 Applied Biosystems Low Peak Height PQV 4-31 SNP Short Tandem Repeat 2-3- 4 Matrix Not Found 4-27 Narrow Bin PQV 4-31 One Basepair Allele PQV 4-31 Offscaoe PQV 4-32 Overlap PQV 4-32 1 Marker Bin Peak Height Ratio PQV 4-32 Process Component-Based Quality Values Profile Project GeneMapper Project Settings Rights GeneMapper Software v3.7-3
Security Group Security ID ID SFNF SHP Silent Auditing Size Match Editor SNaPshot System Multiplex Analysis SNF SNP SNPlex TM SP SPA SPU SQ ID Sample File Not Found 4-27 Sharp Peak PQV 4-32 Audit GeneMapper SNP Size Standard Not Found 4-27 Single-nucleotide Polymorphism SNaPshot SNPlex Split Peak PQV 4-33 Single Peak Artifact PQV 4-33 Spectral Pull-Up PQV 4-33 Sizing Quality GeneMapper Software v3.7-4