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  • GeneMapper v4.0

    Getting Started Guide

  • GeneMapper v4.0

    Getting Started Guide

  • ii GeneMapper Software Version 4.0 Getting Started Guide

    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 (http://www.apache.org/). Copyright 1999-2000

    The Apache Software Foundation. All rights reserved.

    This product includes software developed by the 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.

    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 worlds leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses.

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    GeneMapper v3.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

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    KitPanelMarker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

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    Table Settings . . . . . . . . . . . . . . . . . . . . . . . . . 14

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    Auto Bin Bin Set Bin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

    3 33Analysis Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

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    GeneMapper Software Version 4.0 Getting Started Guide iii

  • iv GeneMapper Software Version 4.0 Getting Started Guide

  • GeneMapper Software Version 4.0 Getting Started Guide Applied Biosystems Data Collection GeneMapper

    GeneMapper

    GeneMapper Software Version 4.0 Installation and Administration Guide(PN 4363080)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

  • Oracle ID

    1 96 1 Sample Entry

    GeneMapper Software v4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software v4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software 4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper Software v4.0 Installation and Administration Guide GeneMapper v4.0

    GeneMapper Software v4.0 Getting Started Guide GeneMapper 5 Applied Biosystems DataCollection LOHAFLP 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 Software v4.0 Documentation CD

    vii

    GeneMapper [F1] Help Contents and IndexGeneMapper 3

    vi GeneMapper Software Version 4.0 Getting Started Guide

  • Applied Biosystems

    jptechsupport@appliedbiosystems.com

    http://www.appliedbiosystems.co.jp Customer Support

    FAQ

    Applied Biosystems MSDSCertification of Analysis

    PDF

    Applied Biosystems

    GeneMapper Software Version 4.0 Getting Started Guide vii

    mailto:techpubs@appliedbiosystems.comhttp://www.appliedbiosystems.com

  • viii GeneMapper Software Version 4.0 Getting Started Guide

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    GeneMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

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    GeneMapper v3.7 . . . . . . . . . . . . . . . . . 5

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

    GeneMapper Software Version 4.0 Getting Started Guide 1

  • 1

    STR DNA 1 2 7 1

    PCR PCR GeneMapper

    Applied Biosystems PCR Applied Biosystems Web www.appliedbiosystems.co.jp

    Applied Biosystems GeneMapper Software Version 4.0 Quick Reference Guide(PN 4362816)

    2 GeneMapper Software Version 4.0 Getting Started Guide

  • 1

    3 .fsa

    :\AppliedBiosystems\GeneMapper\Example Data\Microsatellite

    GeneMapper D

    PCR GeneScan 500 LIZABI PRISM 3100

    17

    2 Panel Marker

    bp

    D6S264 Blue 108 130

    D6S1574 Blue 146 172

    D6S276 Blue 201 233

    D5S408 Blue 240 285

    D6S308 Blue 326 354

    D6S287 Green 104 138

    D6S292 Green 154 176

    D6S434 Green 201 245

    D5S426 Green 274 298

    D5S1981 Yellow 112 125

    D6S257 Yellow 167 195

    D6S446 Yellow 212 234

    D5S641 Yellow 299 339

    D5S433 Red 69 99

    D5S406 Red 168 196

    D5S400 Red 221 243

    D6S309 Red 307 333

    GeneMapper Software Version 4.0 Getting Started Guide 3

  • 1

    GeneMapper

    GeneMapper

    ( 4 )

    ( 2 )

    1. KitPanelMarker

    2.

    3. Table Settings

    4.

    5. Bin Set Bin Auto Bin

    ( 3 )

    1. Analysis Method Bin Set

    2.

    3.

    Analysis MethodSize StandardPanel GeneMapper

    Bin

    Marker bpBinMarker

    Bin Set

    Bin ) BinSet

    Marker

    bp

    Panel

    Marker GeneMapper Panel Bin SetMarker Bin

    Kit

    Panel

    4 GeneMapper Software Version 4.0 Getting Started Guide

  • 1

    GeneMapper

    1.StartAll ProgramApplied BiosystemsGeneMapperGeneMapper4.0

    2.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

  • 1

    GeneMapper

    GeneMapper 2 GeneMapper Data Collection GeneMapper Version 4.0 Installation and Administration Guide(PN 4363080)

    GeneMapper 2 GeneMapper GeneMapper Version 4.0 Installation and Administration Guide(PN 4363080)

    6 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    2

    4

    3

    1

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    KitPanelMarker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

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    Table Settings . . . . . . . . . . . . . . . 14

    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    Auto Bin Bin Set Bin . . . . . . . . . . . . . . . . . . . . . . . . . . 25

    GeneMapper Software Version 4.0 Getting Started Guide 7

  • 2

    KitPanelMarker

    Display Settings

    AutoBin Bin Set Bin

    GeneMapper GeneMapper Software Online Help

    Creating a New Kit Kit )

    Creating a Custom Panel )

    Creating MarkersMarker )

    Creating a Project )

    Adding Samples )

    Applying Analysis SettingsAnalysis Settings )

    Starting Analysis )

    Creating a New Bin SetBin Set )

    Using the Auto Bin FunctionAuto Bin )

    Help [F1]

    8 GeneMapper Software Version 4.0 Getting Started Guide

  • 2KitPanelMarker

    KitPanelMarker

    Panel Manager

    Kit Panel

    Panel Marker

    Marker bp

    Panel Marker Marker Panel AppliedBiosystems Linkage Mapping SetGeneMapper Panel Panel GeneMapper Software Online Help

    KitPanelMarker

    KitPanelMarker

    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

  • 2KitPanelMarker

    Microsatellite Kit

    4. Microsatellite Kit FileNew 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

  • 2KitPanelMarker

    8. 6 7 Marker

    9. Panel Manager OK

    12 .fsa

    Marker Dye Color Minimum Size (bp) Maximum Size (bp)

    Marker Repeat

    D6S1574 Blue 146 172 2

    D6S276 Blue 201 233 2

    D5S408 Blue 240 285 2

    D6S308 Blue 326 354 2

    D6S287 Green 104 138 2

    D6S292 Green 154 176 2

    D6S434 Green 201 245 2

    D5S426 Green 274 298 2

    D5S1981 Yellow 112 125 2

    D6S257 Yellow 167 195 2

    D6S446 Yellow 212 234 2

    D5S641 Yellow 299 339 2

    D5S433 Red 69 99 2

    D5S406 Red 168 196 2

    D5S400 Red 221 243 2

    D6S309 Red 307 333 2

    GeneMapper Software Version 4.0 Getting Started Guide 11

  • 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

    :\AppliedBiosystems\GeneMapper\Example Data

    GeneMapper D

    5. Microsatellite Add to ListAdd

    Microsatellite 3 2 [Ctrl] Add To List

    12 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    Microsatellite 3 Applied Biosystems Data Collection Samples

    14

    GeneMapper Software Version 4.0 Getting Started Guide 13

  • 2 Table Settings

    Table Settings

    GeneMapper

    Analysis MethodBin Set

    PanelMarker ) Size Standard

    GeneMapper

    Table Settings Plot Settings

    1.GeneMapperSamples

    2.Analysis Method NewAnalysis Method

    GeneMapper Manager Analysis Method

    3.New Analysis Method Analysis Type Microsatellite OK

    14 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 Table Settings

    4.Analysis Method Editor 5

    General NameMicrosatellite Analysis Method

    Allele Bin Set None

    GeneMapper Software Version 4.0 Getting Started Guide 15

  • 2 Table Settings

    Peak Detector Peak Detection Algorithm Basic

    Peak Quality Process Quality ValuesPQV (Pass) (Check)

    Homozygous min peak height 140.0

    Heterozygous min peak height 85.0

    Min peak height ratio 0.4

    16 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 Table Settings

    Quality Flags

    Process Quality Values (PQV) Genotype Quality (GQ) PQV 0 1 0 1

    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

  • 2 Table Settings

    6.Panel Select a Panel Microsatellite Kit Microsatellite Panel 9

    7.Size Standard GS500(-250)LIZ

    GeneMapper GeneScan 500 LIZ

    GS500LIZ GeneScan 500 LIZ

    GS500(-250)LIZ 250-bp GS500LIZ_3730 35-250-340-bp GS500LIZ_3130 35-250-340-bp

    1 35-bp 250-bp 340-bp GeneMapper Software Online Help

    8.Samples

    a. Analysis MethodPanelSize Standard 3

    b.Edit Fill Down[Ctrl] [D]

    Microsatellite Kit

    18 GeneMapper Software Version 4.0 Getting Started Guide

  • 2 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. File Save Project

    2.Save Project Microsatellite Project OK

    GeneMapper Microsatellite Project

    20

    GeneMapper Software Version 4.0 Getting Started Guide 19

  • 2

    Panel GeneMapper Analysis Method Bin Set GenotypeQuality (GQ)

    SQ PQV

    Raw Data

    Analysis Analyze

    GeneMapper GeneMapper

    SQ PQV Size Quality (SQ) Process Quality ValuePQV

    1.GeneMapper Analysis Completed

    2.SamplesSQ

    SQ (Pass) SQSFNFMNFSNFOS PQV

    SQ

    20 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    SQ

    SQ (Check) (Low Quality) PQVSFNFMNFSNFOS 21

    SQ Samples SQ

    1.Edit Select AllSamples

    2. Size Match Editor Analysis Size Match Editor

    2-1 Size Match Editor Size Matches

    3.Size Matches

    Size Quality (SQ)

    4. Sizing Quality 2-1 SQ (Pass) (Check) (LowQuality)

    Sizing Quality > 0.75 SQ (Pass)

    Sizing Quality SQ (Check)(Low Quality) 22 2-1

    5.

    2-1

    22 2-1

    Size Quality (SQ)

    GeneMapper Software Version 4.0 Getting Started Guide 21

  • 2

    6.Size Calling Curve

    7. Size Match Editor 3 6

    8.OKSize Match Editor

    GeneMapper SoftwareReference and Troubleshooting Guide

    Raw Data InfoRaw Data

    2-1

    Sizing Quality SQ (Check) (Low Quality)

    Size MatchesOverride SQSizing Quality 2-1Sizing Quality 1.0

    Size Matches Apply GeneMapper Software Online Help

    GeneMapper Software Online Help

    Raw Data

    22 GeneMapper Software Version 4.0 Getting Started Guide

  • 2

    1.View SamplesSamples

    2.Samples [Shift] [Ctrl] EditSelect All

    3. Analysis Display Plots

    Samples Plot

    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 ToOK

    Y

    Y Zoom ToApply to all electropherogramsOK

    X Y

    X Y Full View

    Plot Setting Microsatellite Default

    X -

    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 OnlineHelp

    Samples Plot

    25 Auto Bin Bin Set Bin

    2-2 Samples Plot

    Sizing

    Sizing

    Sizing

    [Ctrl] [Shift]

    : Sizing [Ctrl] [G] Sizing

    24 GeneMappe...

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